diff --git a/.gitignore b/.gitignore
index 74eacbfdda55345c05d3f29b0c55db02b45babc6..fa9ab1fcec34d2887fd38c4119bc31bfd3f714dc 100755
--- a/.gitignore
+++ b/.gitignore
@@ -10,3 +10,4 @@ WR/
*~
temp_png.png
Rplots.pdf
+stress/*
diff --git a/README.md b/README.md
index cfb0bb098f004ff6bb307f4e6d24454ab489540e..2612d2f655d5496786f6e09ae651ced4f13421ce 100755
--- a/README.md
+++ b/README.md
@@ -11,8 +11,8 @@ Determining cellular heterogeneity in the human prostate with single-cell RNA se
* <a href="https://orcid.org/0000-0002-0746-927X" target="orcid.widget" rel="noopener noreferrer" style="vertical-align:top;"><img src="https://orcid.org/sites/default/files/images/orcid_16x16.png" style="width:1em;margin-right:.5em;" alt="ORCID iD icon">orcid.org/0000-0002-0746-927X</a>
* PI Email: [douglas.strand@utsouthwestern.edu](mailto:douglas.strand@utsouthwestern.edu)
* **ANALYZED DATA FOR QUERYING AT: [StrandLab.net](http://strandlab.net/analysis.php)**
-* **Raw data at: [GEO (scRNA-Seq)](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117403) & [GEO (popRNA-Seq)](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117271) & [GenitoUrinary Development Molecular Anatomy Project (GUDMAP)]("https://doi.org/10.25548/W-R8CM")**
-* **Publication at: PENDING**
+* **Raw data at: [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE120716) & [GenitoUrinary Development Molecular Anatomy Project (GUDMAP)]("https://doi.org/10.25548/W-R8CM")**
+* **Publication at: [BioRxiv](https://www.biorxiv.org/content/early/2018/10/15/439935)**
Data Analysis
-------------
@@ -50,6 +50,10 @@ Data Analysis
* run bash script [sc\_TissueMapper\-D17\_FACS.sh](https://git.biohpc.swmed.edu/StrandLab/sc-TissueMapper_Pr/blob/master/bash.scripts/sc_TissueMapper-D17_FACS.sh)
* 3 Run on 2nd patient FACS samples
* run bash script [sc\_TissueMapper\-D27\_FACS.sh](https://git.biohpc.swmed.edu/StrandLab/sc-TissueMapper_Pr/blob/master/bash.scripts/sc_TissueMapper-D27_FACS.sh)
+ * 4 Run on several downsamples from 1 sample from 1st patient
+ * run bash script [sc\_TissueMapper\-DS\_D17.sh](https://git.biohpc.swmed.edu/StrandLab/sc-TissueMapper_Pr/blob/master/bash.scripts/sc_TissueMapper-DS_D17.sh)
+ * 5 Aggregate and compare several downsamples from #4
+ * run bash script [sc\_TissueMapper\_RUN.DS\_D17.aggr.R](https://git.biohpc.swmed.edu/StrandLab/sc-TissueMapper_Pr/blob/master/r.scripts/sc_TissueMapper_RUN.DS_D17.aggr.R)
* **Pipeline:**
* Link cellranger count/aggr output to analysis
* Create demultiplex file to add custom sample groups
@@ -118,4 +122,4 @@ Data Analysis
* "c2.all.v6.1.symbols.gmt" MSigDB C2 Curated Gene Sets [**MSigDB C2**](http://software.broadinstitute.org/gsea/msigdb/genesets.jsp?collection=C2)
* "c2.cp.kegg.v6.1.symbols" MSigDB C2 KEGG Gene Subsets [**KEGG**](http://software.broadinstitute.org/gsea/msigdb/genesets.jsp?collection=CP:KEGG)
* "c5.all.v6.1.symbols.gmt" MSigDB C5 Gene Ontology Gene Sets [**MSigDB C5**](http://software.broadinstitute.org/gsea/msigdb/genesets.jsp?collection=C5)
- * "c5.bp.v6.1.symbols.gmt" MSigDB C5 Gene Ontology Biological Processes Gene Subsets [**GO BP**](http://software.broadinstitute.org/gsea/msigdb/genesets.jsp?collection=BP)
\ No newline at end of file
+ * "c5.bp.v6.1.symbols.gmt" MSigDB C5 Gene Ontology Biological Processes Gene Subsets [**GO BP**](http://software.broadinstitute.org/gsea/msigdb/genesets.jsp?collection=BP)
diff --git a/bash.scripts/sc_TissueMapper-D17_FACS.sh b/bash.scripts/sc_TissueMapper-D17_FACS.sh
index a1b9e80f4b3ce0e426aa055443adfa3bf91f95cd..169f73d4397bafd30f8efab043255126f04ca0d4 100644
--- a/bash.scripts/sc_TissueMapper-D17_FACS.sh
+++ b/bash.scripts/sc_TissueMapper-D17_FACS.sh
@@ -1,5 +1,5 @@
#!/bin/bash
-#SBATCH --job-name R_FullAnalysis
+#SBATCH --job-name R_FullAnalysis.D17FACS
#SBATCH -p 256GB,256GBv1,384GB
#SBATCH -N 1
#SBATCH -t 7-0:0:0
@@ -8,6 +8,8 @@
#SBATCH --mail-type ALL
#SBATCH --mail-user gervaise.henry@utsouthwestern.edu
-module load R/3.4.1-gccmkl
+module load R/3.4.1-gccmkl_20181025
+
+sh ./sc_LinkData.sh D17_FACS
Rscript ../r.scripts/sc-TissueMapper_RUN.D17_FACS.R
diff --git a/bash.scripts/sc_TissueMapper-D27_FACS.sh b/bash.scripts/sc_TissueMapper-D27_FACS.sh
index 492d870914d32d72cbfe82f9a201fee8df210ae4..326afcab5959ce5aa0b5bcf33360484659bb55cc 100644
--- a/bash.scripts/sc_TissueMapper-D27_FACS.sh
+++ b/bash.scripts/sc_TissueMapper-D27_FACS.sh
@@ -1,5 +1,5 @@
#!/bin/bash
-#SBATCH --job-name R_FullAnalysis
+#SBATCH --job-name R_FullAnalysis.D27FACS
#SBATCH -p 256GB,256GBv1,384GB
#SBATCH -N 1
#SBATCH -t 7-0:0:0
@@ -8,6 +8,8 @@
#SBATCH --mail-type ALL
#SBATCH --mail-user gervaise.henry@utsouthwestern.edu
-module load R/3.4.1-gccmkl
+module load R/3.4.1-gccmkl_20181025
+
+sh ./sc_LinkData.sh D27_FACS
Rscript ../r.scripts/sc-TissueMapper_RUN.D27_FACS.R
diff --git a/bash.scripts/sc_TissueMapper-DS_D17.sh b/bash.scripts/sc_TissueMapper-DS_D17.sh
index 198685b1bb589757f0f23c097dea4d6f9d7f4a8b..b7ae6943ae8144209d7b4e98ab8d84957d917142 100644
--- a/bash.scripts/sc_TissueMapper-DS_D17.sh
+++ b/bash.scripts/sc_TissueMapper-DS_D17.sh
@@ -1,6 +1,6 @@
#!/bin/bash
-#SBATCH --job-name R_FullAnalysis
-#SBATCH -p 256GB,256GBv1
+#SBATCH --job-name R_FullAnalysis.DS
+#SBATCH -p 256GB,256GBv1,384GB
#SBATCH -N 1
#SBATCH -t 7-0:0:0
#SBATCH -o job_%j.out
@@ -8,6 +8,6 @@
#SBATCH --mail-type ALL
#SBATCH --mail-user gervaise.henry@utsouthwestern.edu
-module load R/3.4.1-gccmkl
+module load R/3.4.1-gccmkl_20181025
Rscript ../r.scripts/sc-TissueMapper_RUN.DS_D17.R
diff --git a/bash.scripts/sc_TissueMapper-Pd.sh b/bash.scripts/sc_TissueMapper-Pd.sh
index c75360c8ed4efff44f2eb37a5bee3eb9f152e5b5..ba634e4d1d16a18814001c81718de640c0db6f56 100644
--- a/bash.scripts/sc_TissueMapper-Pd.sh
+++ b/bash.scripts/sc_TissueMapper-Pd.sh
@@ -1,5 +1,5 @@
#!/bin/bash
-#SBATCH --job-name R_FullAnalysis
+#SBATCH --job-name R_FullAnalysis.Pd
#SBATCH -p 256GB,256GBv1,384GB
#SBATCH -N 1
#SBATCH -t 7-0:0:0
@@ -8,6 +8,9 @@
#SBATCH --mail-type ALL
#SBATCH --mail-user gervaise.henry@utsouthwestern.edu
-module load R/3.4.1-gccmkl
+module load R/3.4.1-gccmkl_20181025
-Rscript ../r.scripts/sc-TissueMapper_RUN.Pd.R
\ No newline at end of file
+sh ./sc_LinkData.sh Pd
+
+Rscript ../r.scripts/sc-TissueMapper_RUN.Pd.R
+Rscript ../r.scripts/sc-TissueMapper_RUN.Pd.StressCompare.R
diff --git a/genesets/genes.deg.Epi.csv b/genesets/genes.deg.Epi.csv
index 56b5c01aa34c17f4dcb75276f990a88da8e96708..162ed1ac91c06654d4bc0f6c7655f6a22fa6930c 100644
--- a/genesets/genes.deg.Epi.csv
+++ b/genesets/genes.deg.Epi.csv
@@ -1,46 +1,26 @@
"","p_val","avg_logFC","pct.1","pct.2","p_val_adj"
-"KRT17",0,2.64673644764602,0.91,0.38,0
"TACSTD2",0,2.58231159715341,0.981,0.282,0
"KRT19",0,2.45083620114524,0.872,0.185,0
-"CLDN4",0,2.33798655274461,0.83,0.229,0
-"S100A2",0,2.14736694057859,0.824,0.336,0
"SFN",0,2.14188708633312,0.849,0.126,0
-"KRT15",0,2.13730992361203,0.705,0.122,0
"KRT8",0,1.98122977079159,0.878,0.156,0
-"SLPI",0,1.97212133924044,0.609,0.126,0
"KRT23",0,1.9475241025607,0.647,0.109,0
"KRT7",0,1.85832624877284,0.762,0.135,0
-"WFDC2",0,1.82603184536208,0.706,0.142,0
-"AQP3",0,1.75707702047555,0.714,0.138,0
"KLF5",0,1.72630607453798,0.808,0.128,0
"KRT18",0,1.65532949882324,0.889,0.214,0
-"FXYD3",0,1.61927290958347,0.793,0.123,0
-"DST",0,1.61622963903937,0.608,0.203,0
-"KRT5",0,1.61473814532591,0.661,0.08,0
-"AZGP1",0,1.59595095398688,0.423,0.063,0
"ERRFI1",0,1.5002166398309,0.671,0.207,0
"PERP",0,1.43991512228113,0.913,0.305,0
-"ELF3",0,1.39422648108229,0.616,0.113,0
"SPINT2",0,1.39239631839613,0.792,0.11,0
-"AREG",0,1.3786787337354,0.444,0.097,0
"ACTG1",0,1.37293440601088,0.992,0.839,0
-"DEFB1",0,1.34503533365797,0.431,0.055,0
"ANXA1",0,1.30604259801877,0.86,0.505,0
-"F3",0,1.30192501208712,0.549,0.139,0
"S100A14",0,1.29343286078518,0.589,0.071,0
-"FHL2",0,1.26558560397518,0.705,0.222,0
-"CLDN7",0,1.23141144972301,0.523,0.056,0
-"CXCL17",0,1.21533791862415,0.375,0.051,0
"PHLDA2",0,1.19530647532187,0.808,0.394,0
"GADD45A",0,1.18964097065961,0.83,0.473,0
"EZR",0,1.15296351442262,0.754,0.253,0
"CLDN1",0,1.11410745865298,0.457,0.064,0
-"EDN1",0,1.10942157265544,0.394,0.057,0
"EHF",0,1.08296266097339,0.531,0.042,0
"SERPINB5",0,1.08108443063903,0.462,0.034,0
"S100A16",0,1.0769615457348,0.858,0.416,0
"LAMB3",0,1.07163577834265,0.532,0.055,0
-"HBEGF",0,1.06681378224294,0.522,0.201,0
"LIMA1",0,1.0513260826661,0.647,0.19,0
"ACTB",0,1.05079544839747,0.992,0.9,0
"VAMP8",0,1.02255596752927,0.607,0.073,0
@@ -50,22 +30,17 @@
"ANXA2",0,1.0000025381118,0.987,0.867,0
"MPZL2",0,0.994372861783234,0.644,0.149,0
"CEACAM1",0,0.98928633223492,0.501,0.086,0
-"ZG16B",0,0.979605923698475,0.429,0.036,0
"CD9",0,0.939348912075797,0.955,0.613,0
-"STK17A",0,0.937434104556968,0.612,0.222,0
"SLC14A1",0,0.921059272534142,0.443,0.052,0
"HMGA1",0,0.882636420446482,0.838,0.494,0
-"ALDH1A3",0,0.876037021829772,0.475,0.13,0
"EPCAM",0,0.870929113732984,0.478,0.045,0
"GSTP1",0,0.869236837206919,0.935,0.801,0
"IRF6",0,0.857811859218995,0.471,0.038,0
"PRSS22",0,0.855291125992551,0.367,0.028,0
"MAST4",0,0.847336115298592,0.678,0.235,0
-"TSPAN1",0,0.832731564261921,0.392,0.04,0
"PRDX5",0,0.822551687733958,0.789,0.438,0
"TNFRSF12A",0,0.808337370482687,0.892,0.483,0
"PHLDA3",0,0.795531021308692,0.494,0.111,0
-"S100A6",0,0.784779708737913,0.981,0.977,0
"JUP",0,0.784069000314477,0.488,0.074,0
"IRF2BP2",0,0.769645482116694,0.557,0.19,0
"ITGA2",0,0.76350554541392,0.595,0.199,0
@@ -73,29 +48,780 @@
"LAMC2",0,0.762354398240465,0.432,0.097,0
"ANXA11",0,0.756371185335363,0.605,0.21,0
"SDC4",0,0.753410062764128,0.503,0.146,0
-"MAL2",0,0.75247074578316,0.355,0.044,0
-"HEBP2",0,0.743409923773958,0.673,0.332,0
-"SDC1",0,0.718054645280138,0.351,0.04,0
"CD47",0,0.71273810568372,0.599,0.22,0
"CXCL16",0,0.704014318224997,0.426,0.071,0
"KLK11",0,0.702290293393313,0.352,0.037,0
-"PPDPF",0,0.70023197306758,0.851,0.544,0
+"CXADR",0,0.682728184104463,0.36,0.024,0
+"CDH1",0,0.674154937581008,0.378,0.037,0
+"TPM4",0,0.665390527459183,0.882,0.642,0
+"CTSH",0,0.651038534005104,0.452,0.119,0
+"DSP",0,0.649945510556723,0.412,0.077,0
+"SH3YL1",0,0.649862517154306,0.424,0.068,0
+"CHCHD10",0,0.647290706620096,0.548,0.203,0
+"GALNT3",0,0.646752520268792,0.362,0.038,0
+"BLVRB",0,0.640846930500552,0.571,0.212,0
+"RPL34",0,0.623261226516861,1,0.996,0
+"MT-CO2",0,0.623178038590082,0.998,0.988,0
+"CAPG",0,0.610318540905005,0.385,0.06,0
+"MYL12B",0,0.603290199865749,0.883,0.596,0
+"MT-ND3",0,0.590398991312797,0.983,0.892,0
+"MT-CO3",0,0.573559780540274,0.998,0.991,0
+"RPS28",0,0.553690081504897,0.998,0.968,0
+"EEF1B2",0,0.509069527860713,0.936,0.809,0
+"RPS6",0,0.49104352394156,1,1,0
+"RPL10A",0,0.487048695095379,0.998,0.988,0
+"HINT1",0,0.477149313891008,0.964,0.847,0
+"RPS18",0,0.47497715864807,1,0.999,0
+"RPLP1",0,0.473331793692911,1,1,0
+"RPL35",0,0.455180716949743,0.998,0.978,0
+"RPL41",0,0.45381688224465,0.999,0.98,0
+"RPS21",0,0.447207020446747,0.97,0.838,0
+"RPL7",0,0.446806615913834,1,0.999,0
+"RPL14",0,0.441762196679012,0.999,0.99,0
+"COX4I1",0,0.43708583647804,0.935,0.803,0
+"RPS24",0,0.431325215570685,0.999,0.983,0
+"MT-ND4",0,0.429547974916627,0.999,0.996,0
+"RPL31",0,0.425848412916239,0.996,0.968,0
+"RPL27A",0,0.423930015540595,0.999,0.995,0
+"MT-ND2",0,0.422132195130864,0.998,0.994,0
+"RPL13",0,0.41723283848094,1,1,0
+"RPS14",0,0.413666863457065,1,0.997,0
+"RPL37",0,0.411052707605669,0.991,0.933,0
+"RPS8",0,0.404835082914067,0.999,0.996,0
+"RPS17",0,0.398507424092199,0.999,0.992,0
+"RPS3A",0,0.398498604064203,1,0.997,0
+"RPL11",0,0.397901474885931,1,0.998,0
+"RPL8",0,0.397707736939974,0.999,0.995,0
+"RPS19",0,0.389848599735937,1,0.998,0
+"RPL39",0,0.38398522125877,0.999,0.985,0
+"RPLP0",0,0.379250257631086,0.998,0.986,0
+"MT-ATP6",0,0.376223402291977,0.998,0.992,0
+"RPL12",0,0.3738286169652,0.999,0.983,0
+"RPS4X",0,0.373374952178908,0.999,0.997,0
+"RPL29",0,0.372323860330485,0.999,0.987,0
+"RPS15",0,0.363280078644564,1,0.995,0
+"RPL4",0,0.361371982378262,0.986,0.948,0
+"RPL36",0,0.35854388636846,0.996,0.959,0
+"RPL37A",0,0.356203264205121,0.997,0.972,0
+"MT-CYB",0,0.354364068846342,0.998,0.995,0
+"RPS5",0,0.337426804651343,0.998,0.989,0
+"RPS27A",0,0.334029879554744,1,0.997,0
+"RPLP2",0,0.324328124139672,1,0.996,0
+"RPL18",0,0.3230909284071,0.999,0.993,0
+"RPS20",0,0.321522378944988,0.997,0.985,0
+"RPS27",0,0.316801780814128,1,0.996,0
+"RPL30",0,0.309661436743183,0.998,0.988,0
+"RPL21",0,0.304160337300494,0.998,0.996,0
+"RPS3",0,0.30364065750145,0.999,0.995,0
+"RPL35A",0,0.295149166095953,0.999,0.992,0
+"RPL13A",0,0.284664979241853,1,1,0
+"RPS15A",0,0.268999309227566,0.999,0.994,0
+"GNA15",5.26760094598966e-308,0.602940781889119,0.324,0.022,1.2247172199426e-303
+"TSPO",5.08694702458726e-305,0.587539934840981,0.683,0.369,1.18271518321654e-300
+"ARF6",1.16937551640765e-302,0.596519023619793,0.743,0.458,2.7187980756478e-298
"FAM110C",4.68811670147243e-302,0.81952198692582,0.321,0.023,1.08998713309234e-297
-"LMO7",3.54562564288941e-287,0.776064729336601,0.34,0.045,8.24357961971787e-283
-"LCN2",1.29929397078246e-279,1.98321221152763,0.43,0.13,3.02085848206921e-275
-"GPX2",1.75911908897727e-269,0.849509542409469,0.325,0.043,4.08995188187215e-265
-"RAB11FIP1",3.69529627971261e-269,0.720818871919051,0.341,0.055,8.59156385033181e-265
+"KRTCAP3",3.44447625850914e-299,0.553352327681038,0.331,0.032,8.00840730103375e-295
+"DENND2C",1.11363748436042e-297,0.639192529088025,0.338,0.037,2.58920715113797e-293
+"RAB25",5.41584805917774e-294,0.544363817724539,0.318,0.025,1.25918467375883e-289
+"RPL23A",7.33703939620977e-289,0.245978471114441,0.999,0.997,1.70586165961877e-284
+"RPS11",3.39881460478599e-281,0.302931826128929,0.99,0.957,7.90224395612742e-277
+"CNN2",4.05012721109887e-281,0.631165148344992,0.411,0.1,9.41654576580487e-277
+"SLC20A2",2.47775309439284e-280,0.650069265799129,0.41,0.103,5.76077594446336e-276
+"TMEM30B",1.2751809133078e-277,0.562214342051172,0.313,0.03,2.96479562344063e-273
+"GPR87",3.23883564913689e-271,0.598634871325721,0.291,0.019,7.53029288424326e-267
+"ITGA6",4.41007745518142e-267,0.604843304589125,0.451,0.141,1.02534300832968e-262
"HSPB1",7.16440246438237e-267,0.785961433480702,0.893,0.779,1.6657235729689e-262
+"HMGN1",1.34796793849197e-265,0.463694247179976,0.792,0.513,3.13402545699382e-261
+"SPINT1",2.88846189278283e-263,0.528953785459025,0.314,0.038,6.71567390072008e-259
+"ITGB6",1.36889930953494e-260,0.584888411571596,0.289,0.023,3.18269089466874e-256
+"S100A10",4.07189190482733e-260,0.551306009472249,0.875,0.626,9.46714867872354e-256
+"RPS25",2.24360880668673e-259,0.244555687815167,0.998,0.991,5.21639047554665e-255
"HIST1H1C",1.61000939082964e-254,0.719287302119213,0.48,0.184,3.74327183367892e-250
-"AGR2",2.68285137014948e-231,1.0612067064208,0.295,0.044,6.23762943559755e-227
-"KRT14",1.00746316626082e-212,1.65359002160063,0.295,0.056,2.3423518615564e-208
-"MMP7",9.3259028722788e-212,1.30588565024517,0.278,0.042,2.16827241780482e-207
-"KRT13",2.33641834478255e-210,1.63851273006006,0.292,0.056,5.43217265161943e-206
+"RTN4",5.85120704723716e-253,0.470355135448811,0.924,0.786,1.36040563848264e-248
+"C6orf132",7.61618522468219e-253,0.54254917070424,0.302,0.036,1.77076306473861e-248
+"RP11-532F12.5",4.07867680069211e-252,0.50407328120471,0.285,0.024,9.48292356160917e-248
+"RPL3",5.37741629516777e-252,0.249271937443157,0.999,1,1.25024928862651e-247
+"RAP2B",3.10083321810542e-248,0.579656552021967,0.329,0.056,7.2094372320951e-244
+"PLPP2",1.48440376748235e-245,0.503125334558343,0.322,0.053,3.45123875939646e-241
+"RPS29",2.32073360342752e-245,0.364304220098967,0.922,0.773,5.39570562796898e-241
+"RBM47",3.89837871103605e-242,0.539013877244408,0.294,0.035,9.06373050315883e-238
+"LAD1",6.08562983450572e-242,0.51304162746677,0.278,0.025,1.41490893652258e-237
+"IFNGR2",2.39553712700618e-241,0.602396399527995,0.559,0.274,5.56962382028937e-237
+"PDLIM5",5.03157420212395e-241,0.588365644059605,0.589,0.297,1.16984100199382e-236
+"NEDD4L",1.56234389270558e-239,0.548498698092763,0.331,0.062,3.63244955054047e-235
+"RPL6",1.93906065133033e-238,0.254984122580807,0.996,0.988,4.50831601434301e-234
+"FOXA1",3.23663877853851e-238,0.50285733855307,0.27,0.021,7.52518516010203e-234
+"OCIAD2",2.74341998396604e-236,0.482401716154301,0.392,0.109,6.37845146272104e-232
+"DMKN",2.18421169420211e-235,0.521028669535862,0.3,0.043,5.0782921890199e-231
+"F11R",7.70703888804721e-235,0.517216287451599,0.353,0.083,1.79188654147098e-230
+"NDFIP2",1.4845049728853e-233,0.495761727890993,0.344,0.076,3.45147406195832e-229
+"DSG2",9.41514651241712e-233,0.486799727899804,0.284,0.033,2.18902156413698e-228
+"AES",1.4865959900676e-228,0.497781857383302,0.492,0.202,3.45633567690717e-224
+"RPSA",2.24633190933223e-228,0.310524293627684,0.981,0.942,5.22272168919744e-224
+"RPL9",3.04478914002676e-226,0.214506651478197,0.999,0.996,7.07913475056222e-222
+"RPS12",1.71736283435373e-225,0.247649256596657,1,0.997,3.99286858987243e-221
+"RPL22",1.87127999170076e-225,0.28705022666241,0.984,0.934,4.35072598070427e-221
+"NDUFV2",3.39825235922115e-225,0.533205910720629,0.651,0.377,7.90093673518917e-221
+"PRRG4",4.96373310707572e-224,0.478504996257865,0.302,0.049,1.15406794739511e-219
+"ABCC3",2.66847014500624e-223,0.518216421304029,0.288,0.041,6.2041930871395e-219
+"RPL26",9.88318062158244e-221,0.267013463699691,0.997,0.972,2.29783949451792e-216
+"TRIM29",1.07603372486319e-219,0.447477110262707,0.262,0.025,2.50177841030693e-215
+"PTP4A2",4.24631048140261e-219,0.456175227909694,0.776,0.547,9.87267186926108e-215
+"ARG2",6.18640839473579e-219,0.560137422323085,0.326,0.071,1.43833995177607e-214
+"TES",3.38350025293914e-218,0.530468418215126,0.36,0.098,7.86663808808351e-214
+"FAM49B",1.60225555181122e-217,0.485063850027875,0.326,0.07,3.72524415796108e-213
+"MT-CO1",2.68911269952034e-213,0.308512331936758,0.999,0.994,6.25218702638479e-209
+"SH2D3A",3.77607298411325e-213,0.46773966908827,0.257,0.025,8.7793696880633e-209
+"UQCRH",1.49205791474022e-211,0.391477974067325,0.825,0.639,3.469034651771e-207
+"ACTN4",3.19052594333442e-210,0.461552298049195,0.558,0.268,7.41797281825253e-206
+"SRI",1.27862996079441e-208,0.469501021859283,0.669,0.408,2.97281465884701e-204
+"RPL23",8.82892922279512e-207,0.266448671237046,0.986,0.954,2.05272604429987e-202
+"RPL5",5.30770829524112e-206,0.231414218258166,0.997,0.992,1.23404217864356e-201
+"CRNDE",2.92375953341899e-204,0.456512601951435,0.34,0.089,6.79774091519914e-200
+"RPL28",1.76632225013347e-203,0.245834043663787,0.998,0.989,4.10669923156031e-199
"KRT16",1.07784000202821e-200,1.19125071652985,0.258,0.034,2.50597800471559e-196
-"S100P",8.37182577735041e-198,1.57588848571193,0.35,0.117,1.94644949323397e-193
-"ZFP36L2",2.94915164836327e-188,0.715517638044633,0.652,0.404,6.85677758244461e-184
+"ID1",2.11548622399879e-198,0.676051137523618,0.487,0.22,4.9185054707972e-194
+"SH3BGRL3",1.06194935873988e-197,0.405802349223273,0.876,0.671,2.46903225907021e-193
+"PITX1",1.06465909477702e-195,0.54284135936575,0.261,0.038,2.47533239535657e-191
+"ITGB8",2.7622408600621e-195,0.487572099116258,0.299,0.063,6.42220999964437e-191
+"TRAF4",6.47526611361727e-194,0.480027013084331,0.444,0.182,1.50549937141601e-189
+"SGMS2",1.10248472750907e-186,0.453384328808711,0.345,0.099,2.56327699145859e-182
+"LRRC8A",2.35780420270211e-186,0.498423471563895,0.432,0.178,5.48189477128241e-182
+"ARPC2",4.99936951740681e-185,0.403593566050493,0.813,0.635,1.16235341279708e-180
+"TALDO1",1.99114640209053e-184,0.447140087375825,0.517,0.252,4.62941538486048e-180
+"MEAF6",7.6691749125722e-184,0.477211636474946,0.43,0.177,1.78308316717304e-179
+"DUSP14",1.66927697345636e-181,0.544559710007191,0.336,0.101,3.88106896328603e-177
+"CAPN1",2.89962771935499e-181,0.404009474283014,0.304,0.075,6.74163444750034e-177
+"VMP1",4.49765488662403e-180,0.575647418195846,0.732,0.524,1.04570476114009e-175
+"RPS9",9.87176404470425e-178,0.19055178234231,0.999,0.997,2.29518514039374e-173
+"HOOK2",5.62428509160119e-177,0.419171163559046,0.278,0.06,1.30764628379728e-172
+"HIGD2A",4.52496004924197e-176,0.415053351621007,0.616,0.362,1.05205321144876e-171
+"EPHA2",2.86735753701359e-175,0.417918030313374,0.252,0.043,6.66660627355659e-171
+"BAIAP2L1",4.15625259355435e-175,0.399786985082088,0.254,0.044,9.66328728001387e-171
+"COX5B",5.85045808170635e-175,0.362258724468622,0.764,0.548,1.36023150399673e-170
+"LSR",1.3057453967587e-174,0.411699650240522,0.325,0.093,3.03585804746397e-170
+"MAP3K13",1.56407292934521e-174,0.457136485408175,0.507,0.252,3.63646956072762e-170
+"GNB2L1",1.73627416827959e-173,0.229529292073493,0.994,0.982,4.03683744125004e-169
+"MT-ND1",1.92109455519519e-173,0.250835450776723,0.993,0.978,4.46654484082881e-169
+"CHPT1",1.3332018811348e-172,0.503124829893086,0.492,0.245,3.0996943736384e-168
+"RARRES3",2.52025726004647e-171,0.521400081976809,0.315,0.092,5.85959812960805e-167
+"NTN4",2.3534241910671e-169,0.442231340038293,0.274,0.062,5.47171124423101e-165
+"RPL32",5.28784632595041e-168,0.18270281179361,1,0.998,1.22942427078347e-163
+"TMA7",9.89711211917181e-168,0.371010518504703,0.777,0.565,2.30107856770745e-163
+"SYNGR2",1.79385395728725e-167,0.420216860283629,0.434,0.19,4.17071045069285e-163
"MTRNR2L1",4.92681915776347e-166,0.796880879549293,0.498,0.282,1.14548545418001e-161
-"CD24",5.22646762822138e-146,0.921382790745211,0.331,0.131,1.21515372356147e-141
-"DKK1",8.30819005061725e-110,0.756949927526965,0.291,0.115,1.93165418676851e-105
-"GDF15",5.94555679467146e-81,1.18807270039704,0.276,0.139,1.38234195476112e-76
-"MSMB",6.76126653486279e-16,2.27369721884818,0.289,0.234,1.5719944693556e-11
+"ATP5J2",1.96577225124387e-165,0.398262488796922,0.51,0.257,4.570420484142e-161
+"ATP5G3",7.20701466863767e-165,0.40622379407963,0.663,0.441,1.67563091045826e-160
+"C3orf52",2.49148342286825e-164,0.41477613880512,0.309,0.091,5.79269895816868e-160
+"EIF6",1.19731360820309e-159,0.456880811411808,0.524,0.287,2.78375413907219e-155
+"RGS12",2.95805635203648e-159,0.415330902059318,0.287,0.077,6.87748101848481e-155
+"TXNDC17",3.42684205055683e-159,0.409667124341012,0.412,0.178,7.96740776754463e-155
+"TOB1",4.54399855710395e-159,0.463109187572677,0.36,0.134,1.05647966452667e-154
+"ATP5G2",6.06861659537551e-159,0.338797990222394,0.787,0.59,1.41095335842481e-154
+"TGIF1",1.13171715988051e-158,0.549763851261012,0.668,0.471,2.63124239672218e-154
+"SMIM15",1.80572517436357e-157,0.380633686128841,0.328,0.108,4.19831103039529e-153
+"HN1",6.52794965216971e-153,0.415749552126773,0.349,0.129,1.51774829412946e-148
+"FAM60A",3.73241848842515e-152,0.386069609748637,0.462,0.223,8.67787298558847e-148
+"GIPC1",5.34106822598907e-152,0.367104478992179,0.285,0.08,1.24179836254246e-147
+"RPS10",6.21713972985776e-152,0.339479481124691,0.798,0.6,1.44548498719193e-147
+"TMEM141",1.6657863307148e-151,0.389766121914455,0.315,0.104,3.87295321891192e-147
+"FAM3C",7.00867683007591e-151,0.442008012272973,0.553,0.326,1.62951736299265e-146
+"RPS7",1.599265000382e-149,0.194222428932417,0.998,0.992,3.71829112588814e-145
+"BCL10",1.10451724358642e-146,0.434851211505752,0.346,0.132,2.56800259133842e-142
+"TECR",1.71875069330341e-146,0.377637578679288,0.41,0.178,3.99609536193044e-142
+"SMS",3.24459504464504e-146,0.363941641665485,0.467,0.223,7.54368347879973e-142
+"LGALS3",7.4972234004011e-146,0.352718579824611,0.785,0.59,1.74310444059326e-141
+"DYNLT1",1.17014038205351e-144,0.364918667306895,0.568,0.331,2.72057638827442e-140
+"MAOA",9.63317937683047e-144,0.382115638399355,0.304,0.099,2.23971420511308e-139
+"HIST1H2AC",1.34122980884889e-143,0.488193850808706,0.276,0.081,3.11835930557368e-139
+"DCXR",1.6684950362894e-141,0.395897474579449,0.414,0.187,3.87925095937285e-137
+"TMED3",9.62672625923751e-141,0.355854051523304,0.343,0.131,2.23821385527272e-136
+"BCAR3",1.09518378227656e-140,0.40642462596457,0.275,0.082,2.54630229379299e-136
+"BLCAP",7.41099783760847e-139,0.349026135041072,0.265,0.074,1.72305699724397e-134
+"TUBB4B",5.15634164484043e-138,0.414539829672054,0.762,0.591,1.1988494324254e-133
+"YWHAZ",1.59518332907314e-136,0.351977718216669,0.716,0.525,3.70880124009505e-132
+"MYL12A",1.889396459916e-136,0.309487145053639,0.875,0.683,4.39284676930471e-132
+"RPL19",3.32790145549648e-136,0.163465877266454,0.999,0.996,7.73737088402931e-132
+"LY6E",1.0037914646864e-135,0.379084933687634,0.592,0.374,2.33381515539587e-131
+"TMEM134",8.5484812963304e-135,0.338513365375185,0.292,0.097,1.98752190139682e-130
+"FRMD6",1.06232466011986e-133,0.379284721750602,0.298,0.102,2.46990483477868e-129
+"MYO6",3.31731482640661e-132,0.373010634685932,0.324,0.124,7.71275697139536e-128
+"RPL27",3.51564580743922e-132,0.196631581166927,0.986,0.961,8.1738765022962e-128
+"MMP24-AS1",1.09752426148001e-128,0.35292011741581,0.402,0.189,2.55174390794103e-124
+"COMMD6",2.20589117649809e-128,0.312059277882635,0.758,0.553,5.12869698535807e-124
+"PLP2",4.5486065414767e-128,0.365740481360173,0.517,0.295,1.05755102089333e-123
+"MET",1.02079289785644e-127,0.37762346602226,0.253,0.076,2.37334348751622e-123
+"PEBP1",5.92356630131334e-127,0.302790162256414,0.715,0.497,1.37722916505535e-122
+"WEE1",8.38047411204371e-127,0.403025746993669,0.273,0.09,1.94846023105016e-122
+"TMEM54",1.65725851997687e-126,0.335783740493203,0.314,0.118,3.85312605894623e-122
+"RPL15",1.80639630625053e-126,0.150002790864036,0.999,0.999,4.19987141203248e-122
+"RPL7A",6.59337224394591e-126,0.182629751129857,0.997,0.989,1.53295904671743e-121
+"KCNK1",7.26581853229152e-126,0.294930440353739,0.407,0.184,1.68930280875778e-121
+"NET1",2.50812640167693e-125,0.380380597849183,0.265,0.083,5.83139388389887e-121
+"MTRNR2L8",1.32002932612697e-124,0.307714694741331,0.842,0.705,3.06906818324521e-120
+"NABP1",1.97866200293888e-124,0.365523565399095,0.276,0.09,4.6003891568329e-120
+"TMEM123",6.41842970021521e-122,0.338796903890607,0.56,0.342,1.49228490530004e-117
+"CXCL8",1.73210068605393e-121,0.156451020572729,0.815,0.659,4.02713409507538e-117
+"CHMP2B",1.76666934100439e-121,0.340876975048407,0.539,0.317,4.10750621783522e-117
+"COX7C",1.13525633032693e-120,0.257672393645114,0.893,0.795,2.63947096801011e-116
+"COMT",1.27775780492231e-120,0.342945919625846,0.42,0.213,2.97078689644438e-116
+"MDK",2.65311036341344e-119,0.381800075651582,0.388,0.187,6.16848159493626e-115
+"TUBA4A",3.257480799712e-118,0.426333759126907,0.28,0.103,7.57364285933041e-114
+"BAG1",5.95550370788314e-118,0.357501064010449,0.618,0.414,1.38465461208283e-113
+"UQCR10",7.74017222620858e-118,0.349414551851849,0.508,0.298,1.79959004259349e-113
+"LPAR6",9.28069458294608e-118,0.381682158306573,0.359,0.165,2.15776149053496e-113
+"RAB4A",2.35755888489702e-117,0.320001101174492,0.374,0.175,5.48132440738557e-113
+"PKM",1.39471729220566e-116,0.345697119795159,0.737,0.558,3.24271770437816e-112
+"CSNK1A1",1.48005317255432e-116,0.359193395878952,0.731,0.559,3.4411236261888e-112
+"RNASET2",2.49502955489579e-115,0.295458764023311,0.26,0.085,5.80094371513271e-111
+"UCHL3",1.5882948833999e-114,0.313261170229774,0.264,0.091,3.69278560390477e-110
+"PMAIP1",4.89937838351897e-114,0.372379835258696,0.469,0.264,1.13910547416816e-109
+"APRT",7.6555217762058e-114,0.333416402527447,0.624,0.421,1.77990881296785e-109
+"ATP5G1",1.56317806688919e-113,0.332198649031319,0.508,0.298,3.63438900551737e-109
+"MARCKS",2.14049818322465e-113,0.264083220128875,0.669,0.433,4.97665827599731e-109
+"ATP1B1",3.99672562437639e-112,0.307350117441649,0.312,0.122,9.2923870766751e-108
+"PABPC1",3.0411979409655e-109,0.261282752222223,0.879,0.782,7.07078521274478e-105
+"ZNF593",1.48755107298095e-108,0.331848477912137,0.428,0.232,3.4585562446807e-104
+"COX6B1",1.19018494720631e-106,0.291372779820569,0.718,0.547,2.76718000225468e-102
+"SPATS2L",1.59048547753624e-106,0.291936741774722,0.507,0.295,3.69787873527176e-102
+"DNPH1",1.62725173455176e-106,0.287273492688659,0.262,0.093,3.78336028283285e-102
+"CTSD",9.79087292246719e-106,0.307949475147561,0.408,0.208,2.27637795447362e-101
+"SERP1",1.07988788673552e-105,0.232408501587586,0.849,0.7,2.51073933666007e-101
+"ALDH3A2",4.84450979481506e-104,0.315596518583193,0.269,0.101,1.1263485272945e-99
+"ABI1",5.33310939130336e-104,0.320362600671615,0.349,0.167,1.23994793347803e-99
+"UQCRC1",1.58504515782739e-102,0.28676538641187,0.332,0.15,3.68522999194869e-98
+"FBXO32",4.6699986662884e-102,0.437785419698237,0.288,0.12,1.08577468991205e-97
+"NBEAL1",1.28630257897205e-101,0.34359685809828,0.623,0.434,2.99065349611001e-97
+"ATP5L",2.70566491193865e-101,0.258057154471095,0.772,0.617,6.29067092025736e-97
+"CUTA",3.00301709962729e-101,0.286625572643452,0.556,0.348,6.98201475663346e-97
+"EHD4",4.87063653900562e-101,0.295243334481115,0.351,0.17,1.13242299531881e-96
+"CHMP2A",5.02368168230528e-100,0.283313476739799,0.57,0.367,1.16800599113598e-95
+"RPS13",4.33133347075484e-99,0.141101236108645,0.998,0.993,1.0070350319505e-94
+"ATPIF1",8.11494017513069e-98,0.290857352556878,0.418,0.227,1.88672359071789e-93
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+"ATP5O",3.52368128368984e-87,0.256083162526555,0.596,0.408,8.19255898457888e-83
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+"CAPZB",1.20297665615783e-07,0.0193897985444251,0.553,0.471,0.00279692072556695
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+"TMEM14C",1.60690305158682e-07,0.0262965787352799,0.343,0.282,0.00373604959493936
+"PA2G4",1.74502340473694e-07,0.0860313340132515,0.51,0.451,0.00405717941601339
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+"COPS6",5.25624307640985e-07,0.014822422226283,0.292,0.237,0.0122207651526529
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+"LAMP1",6.40478065996675e-07,0.0113269439345274,0.33,0.272,0.0148911150344227
+"RSL1D1",8.465070441439e-07,0.0364935537168709,0.564,0.489,0.0196812887763457
+"NDUFS6",1.05874047222643e-06,0.0218614323793078,0.398,0.333,0.0246157159792645
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+"RNF7",1.11165410021713e-06,0.0225395132606878,0.383,0.321,0.0258459578300482
+"CD164",1.62099475349513e-06,0.0367353354793787,0.483,0.416,0.0376881280187617
+"WASF2",1.67668019860183e-06,0.046170466642491,0.521,0.45,0.0389828146174925
+"HAX1",2.02214271064714e-06,0.0190244440207531,0.284,0.233,0.047014818022546
+"SRSF9",2.07122003446332e-06,0.0292088485128308,0.598,0.515,0.0481558658012722
+"PUF60",2.08967736090938e-06,0.0417383761027246,0.263,0.219,0.0485849986411431
diff --git a/genesets/genes.deg.LE.csv b/genesets/genes.deg.LE.csv
index da2020b38bba0b4d14c255766b80f6f9d9dc3dc0..a5c286f623e5c2418f62c4b7aac8d99673924d73 100644
--- a/genesets/genes.deg.LE.csv
+++ b/genesets/genes.deg.LE.csv
@@ -1,80 +1,72 @@
"","p_val","avg_logFC","pct.1","pct.2","p_val_adj"
-"MSMB",0,4.37447239718553,0.686,0.25,0
-"KLK3",0,3.78840323642459,0.672,0.08,0
-"ACPP",0,3.13382648140614,0.596,0.031,0
-"PLA2G2A",0,2.81892272901388,0.444,0.02,0
-"KLK2",0,2.49353927858673,0.594,0.025,0
-"TFF1",0,2.15334059243419,0.329,0.041,0
-"AZGP1",0,2.0049490413152,0.897,0.345,0
-"MT1G",0,1.98581083516144,0.254,0.053,0
-"TSPAN8",0,1.82868329126073,0.741,0.077,0
-"CLDN3",0,1.81872600017444,0.678,0.078,0
-"NEAT1",0,1.66342555320245,0.992,0.932,0
-"SEC11C",0,1.50139213870143,0.616,0.159,0
-"RDH11",0,1.43938695807039,0.54,0.1,0
-"CPE",0,1.42726881338742,0.609,0.195,0
-"AGR2",0,1.38739010258592,0.569,0.185,0
-"ADIRF",0,1.20378597343587,0.662,0.266,0
-"TMPRSS2",0,1.17657374095478,0.598,0.1,0
-"CD24",0,1.169691225058,0.679,0.256,0
-"NPDC1",0,1.09945973647627,0.691,0.197,0
-"ZG16B",0,1.09632759033173,0.705,0.381,0
-"DHRS7",0,1.0780600230455,0.538,0.175,0
-"SLC12A2",0,1.05453438337529,0.48,0.056,0
-"ALDH1A3",0,1.00938272421439,0.708,0.409,0
-"SORD",0,1.00762400392571,0.38,0.101,0
-"KLK4",0,1.00075010108915,0.383,0.007,0
-"SMIM14",0,0.990064601095013,0.664,0.201,0
-"LMO7",0,0.981449368568302,0.611,0.256,0
-"TMC5",0,0.944131304887237,0.446,0.062,0
-"HMGCS1",0,0.928927221396835,0.375,0.112,0
-"TPD52",0,0.921812891053796,0.65,0.253,0
-"PPP3CA",0,0.918524421978158,0.497,0.095,0
-"RASEF",0,0.918474385055297,0.443,0.041,0
-"SLC44A4",0,0.915536056294867,0.565,0.098,0
-"CIB1",0,0.910802697071163,0.822,0.534,0
-"DSC2",0,0.908460413879168,0.476,0.123,0
-"ELF3",0,0.90825329652683,0.83,0.543,0
-"PART1",0,0.897849167503269,0.422,0.041,0
-"PSCA",0,0.883834790597298,0.406,0.073,0
-"INSIG1",0,0.879088049701038,0.435,0.138,0
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-"FXYD3",0,0.795341516329355,0.919,0.751,0
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-"LINC00844",0,0.755952806149427,0.266,0.024,0
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-"MT1F",0,0.735175225812285,0.275,0.06,0
-"BACE2",0,0.734623852847882,0.652,0.299,0
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-"RNF144B",1.55475455202509e-306,0.760182455666201,0.38,0.119,3.61480433345833e-302
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-"MARCKSL1",3.87076430258232e-298,0.770455303625736,0.608,0.273,8.99952700350389e-294
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-"H2AFJ",1.02086674628759e-266,0.715945859194024,0.799,0.556,2.37351518511864e-262
-"NDRG1",1.60403620345049e-258,0.831848305281009,0.566,0.291,3.72938417302238e-254
-"PLPP1",3.7845405697958e-257,0.852158040389265,0.364,0.126,8.79905682477522e-253
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-"NKX3-1",4.7758881227118e-173,0.714910742253142,0.291,0.107,1.11039398853049e-168
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-"MT1E",1.64237321428792e-145,1.85089781749558,0.454,0.266,3.81851772321941e-141
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-"FDPS",4.05857338821562e-111,0.779405255968596,0.412,0.229,9.43618312760133e-107
-"GADD45B",2.47436197380962e-62,0.957716958200775,0.512,0.375,5.75289158910737e-58
-"MT2A",4.48785503840556e-60,1.21424445779221,0.712,0.623,1.04342629642929e-55
-"JUN",6.73977419884717e-60,0.807603248779742,0.684,0.58,1.56699750123197e-55
+"MSMB",0,4.41464597666458,0.686,0.239,0
+"KLK3",0,3.79927069647092,0.672,0.077,0
+"ACPP",0,3.1386912452006,0.596,0.031,0
+"PLA2G2A",0,2.82011634326759,0.444,0.02,0
+"KLK2",0,2.49685405203231,0.594,0.024,0
+"TFF1",0,2.14654338516735,0.329,0.049,0
+"AZGP1",0,2.01859676603558,0.897,0.363,0
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+"TSPAN8",0,1.84829135427538,0.741,0.07,0
+"CLDN3",0,1.52902244520835,0.678,0.129,0
+"NEAT1",0,1.51900228702682,0.992,0.94,0
+"SEC11C",0,1.50870296196156,0.616,0.162,0
+"CPE",0,1.46883854734414,0.609,0.176,0
+"RDH11",0,1.43791145325306,0.54,0.106,0
+"AGR2",0,1.20104069415542,0.569,0.26,0
+"TMPRSS2",0,1.11615430581965,0.598,0.134,0
+"ZG16B",0,1.1068824310419,0.705,0.394,0
+"NPDC1",0,1.10185293373806,0.691,0.205,0
+"DHRS7",0,1.09703119088929,0.538,0.17,0
+"SLC12A2",0,1.06008931420528,0.48,0.057,0
+"CD24",0,1.0023510757434,0.679,0.287,0
+"KLK4",0,1.0021842053216,0.383,0.007,0
+"SMIM14",0,0.984221962278597,0.664,0.215,0
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+"HMGCS1",3.42461756531418e-303,0.921004561752512,0.375,0.123,7.96223583935546e-299
+"LMO7",2.71147973468059e-301,0.864726032278975,0.611,0.306,6.30419038313236e-297
+"SORD",8.31601295337064e-295,0.953794980653706,0.38,0.13,1.93347301165867e-290
+"FXYD3",1.82555434125871e-291,0.72276053621229,0.919,0.777,4.24441384342649e-287
+"ALDH1A3",2.81626138046117e-290,0.96151656515069,0.708,0.445,6.54780770957222e-286
+"IL6ST",1.76482583457318e-279,0.720964598078865,0.532,0.248,4.10322006538265e-275
+"TSC22D1",2.00482551149997e-278,0.973848388488826,0.72,0.451,4.66121931423742e-274
+"DBI",4.58584954232928e-275,0.83482691237847,0.708,0.472,1.06621001859156e-270
+"PLPP1",4.11040262169908e-270,0.863079043578098,0.364,0.126,9.55668609545036e-266
+"H2AFJ",1.13241110585981e-266,0.716349174750414,0.799,0.574,2.63285582112405e-262
+"ELF3",5.4285571136693e-254,0.750384596642815,0.83,0.589,1.26213952892811e-249
+"SPINK1",4.00680293998379e-247,0.76488254323365,0.288,0.081,9.31581683546232e-243
+"NDRG1",5.11762466241304e-211,0.773387403674286,0.566,0.327,1.18984773401103e-206
+"RPS27L",2.73209808270906e-210,0.820414918744851,0.675,0.447,6.35212804229856e-206
+"SAT1",4.68375548904372e-209,0.782698466152202,0.988,0.972,1.08897315120266e-204
+"NKX3-1",1.05503565393114e-206,0.73914604464308,0.291,0.098,2.4529578953899e-202
+"TXNIP",4.11598983981011e-200,0.81506575663786,0.559,0.317,9.56967637755851e-196
+"MT1E",1.27120095406914e-171,1.90413450179974,0.454,0.251,2.95554221821074e-167
+"FDPS",9.5545509588763e-102,0.772645903487662,0.412,0.241,2.22143309793874e-97
+"MT2A",6.29978747466877e-90,1.3228614857529,0.712,0.597,1.46470058786049e-85
+"JUN",1.13685849258666e-64,0.829884133857674,0.684,0.586,2.64319599526398e-60
+"GADD45B",1.11647864383533e-59,0.960832459862578,0.512,0.387,2.59581284691715e-55
diff --git a/genesets/genes.deg.St.csv b/genesets/genes.deg.St.csv
index 015986317ed1c70b827af9f5132112cc0b36f0b9..f403a300c0cec3b4550decf488839b1b95ba8bf7 100644
--- a/genesets/genes.deg.St.csv
+++ b/genesets/genes.deg.St.csv
@@ -1,159 +1,465 @@
"","p_val","avg_logFC","pct.1","pct.2","p_val_adj"
-"C11orf96",0,3.35657963778659,0.708,0.036,0
"IGFBP7",0,3.15209871939752,0.951,0.191,0
-"APOD",0,3.14186916624101,0.321,0.038,0
-"IL6",0,3.06378549509199,0.398,0.015,0
-"PTGDS",0,2.984059301983,0.313,0.016,0
"VIM",0,2.90884774131888,0.944,0.054,0
"SPARCL1",0,2.51839371967671,0.914,0.215,0
-"IGFBP5",0,2.46788937022088,0.496,0.019,0
-"HMOX1",0,2.42981899011226,0.429,0.077,0
-"MGP",0,2.35886107426051,0.707,0.178,0
-"IGFBP6",0,2.32348070236816,0.515,0.105,0
-"DCN",0,2.31379725539251,0.38,0.007,0
-"IFI27",0,2.20757404198392,0.424,0.033,0
-"MT1A",0,2.20743898939655,0.336,0.031,0
-"TIMP1",0,2.17577995338573,0.864,0.693,0
-"CSF3",0,2.12390991586269,0.348,0.016,0
"LGALS1",0,2.07717174859661,0.818,0.194,0
-"CXCL2",0,2.05804809463236,0.377,0.14,0
-"TPM2",0,2.04592836769388,0.475,0.183,0
-"STC1",0,1.88561607702683,0.26,0.005,0
-"ADAMTS4",0,1.81500599991667,0.564,0.007,0
-"AKAP12",0,1.80327333175128,0.599,0.051,0
-"GEM",0,1.79996977665522,0.475,0.094,0
-"PLPP3",0,1.69957895148618,0.613,0.05,0
-"LUM",0,1.66670206288439,0.271,0.005,0
-"SRGN",0,1.64344531928405,0.483,0.016,0
-"CREM",0,1.60448971960675,0.593,0.155,0
"SERPINE1",0,1.53907665601399,0.397,0.043,0
-"MT2A",0,1.4799735243476,0.807,0.61,0
"SPARC",0,1.47829443640837,0.616,0.045,0
-"HLA-DRB1",0,1.47634274469489,0.394,0.069,0
"A2M",0,1.45799667776449,0.495,0.004,0
"PMP22",0,1.44794368173077,0.553,0.014,0
-"ADAMTS9",0,1.44495270614977,0.574,0.164,0
-"CLDN5",0,1.44050806195018,0.303,0.004,0
-"CRISPLD2",0,1.43726540805598,0.406,0.022,0
-"PTN",0,1.42623318419868,0.298,0.012,0
-"TFPI",0,1.42503244810105,0.522,0.016,0
-"COL6A2",0,1.39466732816361,0.471,0.017,0
-"C1S",0,1.38628102492775,0.403,0.036,0
-"C1R",0,1.3692177726174,0.431,0.093,0
-"SPRY1",0,1.3639582174392,0.328,0.035,0
"IGFBP4",0,1.35101177234523,0.665,0.217,0
-"SOCS3",0,1.30902910056725,0.418,0.181,0
-"GSN",0,1.30506520995541,0.703,0.387,0
-"SERPING1",0,1.28834521910818,0.557,0.133,0
-"S100A4",0,1.27948497386243,0.353,0.061,0
-"GNG11",0,1.25187116035782,0.47,0.027,0
-"ICAM1",0,1.25103868390613,0.446,0.039,0
-"HLA-DRA",0,1.2259993006124,0.349,0.084,0
"SLC2A3",0,1.21183184009103,0.427,0.007,0
-"TCF4",0,1.20734785319568,0.454,0.079,0
-"ADAMTS1",0,1.19384763998005,0.395,0.051,0
"GYPC",0,1.1673645902117,0.432,0.012,0
"COL4A1",0,1.13947001893179,0.471,0.018,0
-"MFAP4",0,1.13829254663562,0.276,0.002,0
-"CD93",0,1.12773696486979,0.311,0.004,0
-"GPX3",0,1.12278424381216,0.486,0.168,0
-"MFGE8",0,1.11186494379527,0.4,0.066,0
"FTL",0,1.10570201052532,0.998,0.996,0
"IFITM2",0,1.09622088605487,0.76,0.361,0
-"SOD3",0,1.09468773550915,0.434,0.141,0
"PKIG",0,1.07015872616231,0.478,0.037,0
-"MYLK",0,1.06946804501044,0.302,0.036,0
-"BNIP3L",0,1.06788042106125,0.433,0.19,0
-"BGN",0,1.06276175727964,0.313,0.003,0
-"TSC22D1",0,1.05168004930845,0.686,0.481,0
-"MMP2",0,1.03460951598224,0.281,0.03,0
"SELM",0,1.02476214699384,0.757,0.449,0
-"MAP1B",0,1.01356950057548,0.446,0.092,0
-"CD200",0,1.00409776872784,0.307,0.037,0
-"RCAN1",0,1.00170028016025,0.304,0.057,0
-"THBD",0,0.980596462419037,0.257,0.033,0
"IFITM3",0,0.974068058325107,0.926,0.681,0
"INSIG1",0,0.960355420020766,0.503,0.186,0
-"PLVAP",0,0.952720084540191,0.257,0.002,0
-"PCAT19",0,0.952181434680814,0.312,0.006,0
"EDNRB",0,0.931344504753404,0.282,0.003,0
-"CALCRL",0,0.930942471056838,0.282,0.004,0
-"CST3",0,0.929672005124908,0.88,0.765,0
"BST2",0,0.913124402829383,0.385,0.049,0
"NNMT",0,0.908560912811799,0.285,0.025,0
"CDKN1A",0,0.906912920184886,0.741,0.508,0
-"HLA-E",0,0.894902609452439,0.847,0.677,0
"ARID5A",0,0.894653770761093,0.432,0.106,0
"TMSB4X",0,0.890780468436511,0.994,0.933,0
-"PNP",0,0.871669283948557,0.438,0.16,0
-"HLA-DPA1",0,0.868784894532554,0.277,0.033,0
-"HLA-DRB5",0,0.856338051000458,0.293,0.032,0
"CSRP2",0,0.856307944468502,0.462,0.187,0
-"PRRX1",0,0.850329911778928,0.267,0.002,0
-"EPAS1",0,0.846723163830484,0.452,0.184,0
"CTSL",0,0.831629591236177,0.426,0.168,0
-"MSN",0,0.825510160656912,0.508,0.187,0
"CLIC4",0,0.823840293995555,0.542,0.185,0
"LDHA",0,0.820439830453995,0.854,0.658,0
"LMCD1",0,0.816340194922396,0.278,0.054,0
-"HLA-B",0,0.815462136912527,0.897,0.851,0
"NR4A2",0,0.811533094858348,0.29,0.072,0
"ISG15",0,0.806543148248116,0.318,0.104,0
"PTMA",0,0.806243172762274,0.999,0.995,0
"SOD2",0,0.802390117820088,0.867,0.727,0
-"ADGRL4",0,0.790049027802065,0.27,0.001,0
"HLA-A",0,0.787853857294099,0.942,0.881,0
-"AEBP1",0,0.785610185559771,0.296,0.026,0
-"KLF9",0,0.778492702325455,0.42,0.13,0
"TUBB6",0,0.772256008730784,0.452,0.133,0
"B2M",0,0.769814019730839,0.999,0.993,0
-"COL6A1",0,0.763727402726993,0.303,0.025,0
"TAGLN2",0,0.763119639179336,0.782,0.596,0
"TIMP2",0,0.75568361353686,0.323,0.026,0
-"LMO4",0,0.742279783424695,0.342,0.115,0
"ANKRD28",0,0.735829733099667,0.331,0.074,0
-"HLA-DPB1",0,0.729023816843719,0.316,0.085,0
-"UPP1",0,0.725307402202424,0.289,0.062,0
"MGLL",0,0.721964801625337,0.296,0.034,0
-"ITM2A",0,0.721630260940231,0.271,0.032,0
"PNRC1",0,0.717757180341393,0.871,0.744,0
"LIMS1",0,0.713087383931869,0.433,0.191,0
-"ZEB1",0,0.705878855482179,0.298,0.009,0
-"PDLIM3",0,0.705015400914034,0.263,0.025,0
-"RDX",0,0.702942722577951,0.404,0.158,0
"SLC4A7",0,0.700038612371655,0.423,0.152,0
"NR2F2",0,0.693158207033491,0.275,0.058,0
+"SH3BP5",0,0.688065730477343,0.284,0.021,0
+"UBB",0,0.686674527484554,0.906,0.624,0
+"LHFP",0,0.669287685992829,0.292,0.022,0
+"TGM2",0,0.65691496027195,0.311,0.069,0
+"FNIP2",0,0.655447897062214,0.329,0.1,0
+"NEAT1",0,0.653717094486885,0.995,0.946,0
+"HLA-C",0,0.648904225681005,0.919,0.86,0
+"SASH1",0,0.63380074349733,0.261,0.018,0
+"COL4A2",0,0.628627061373869,0.292,0.025,0
+"YBX3",0,0.608326943436122,0.967,0.919,0
+"ASAP1",0,0.587117571916316,0.337,0.079,0
+"ST3GAL1",0,0.516271518858347,0.256,0.055,0
+"GAPDH",0,0.487178307500678,0.98,0.958,0
"SDCBP",2.46573538682373e-303,0.725006527999333,0.769,0.618,5.73283477436517e-299
-"RHOQ",1.26201125468556e-297,0.74817983114089,0.301,0.101,2.93417616714393e-293
-"RHOB",1.04471468902897e-288,1.10062146709578,0.37,0.149,2.42896165199236e-284
-"ADIRF",1.98505986794133e-285,0.969182689910121,0.615,0.361,4.6152641929636e-281
-"CFD",2.38155931175815e-265,2.39969795139114,0.33,0.14,5.53712539983769e-261
-"PTGS2",4.62549512629227e-263,1.7060512398562,0.304,0.113,1.07542761686295e-258
-"DNAJB9",6.80794908033878e-263,0.88797779440846,0.488,0.264,1.58284816117877e-258
-"EMP1",1.48913957056734e-237,0.763723324457966,0.708,0.506,3.46224950156906e-233
-"NR4A1",1.22718049755861e-229,0.837831820630746,0.383,0.18,2.85319465682378e-225
+"NFKBIZ",1.89622756624629e-292,0.599722159918504,0.339,0.123,4.40872909152262e-288
+"BTG1",1.73474965818222e-259,0.633298401983891,0.895,0.794,4.03329295527366e-255
+"MAFG",9.33651225827838e-250,0.603625847806162,0.506,0.29,2.17073910004972e-245
+"ANKRD10",1.40028866471761e-244,0.502510765914624,0.336,0.136,3.25567114546845e-240
+"WBP5",1.25280358712486e-243,0.546616914271543,0.653,0.435,2.9127683400653e-239
+"JAG1",6.02209495235991e-243,0.603920002331138,0.305,0.116,1.40013707642368e-238
+"STAT3",1.50654094705807e-236,0.546819358035265,0.499,0.278,3.50270770191e-232
+"CD63",1.24685598985996e-235,0.397103210187786,0.972,0.949,2.89894017642441e-231
+"POMP",7.74481438394833e-226,0.590064874061715,0.782,0.679,1.80066934426799e-221
+"SCML1",1.71785690110916e-225,0.438026057963635,0.271,0.097,3.9940172950788e-221
+"EIF1",4.79020536025929e-223,0.288222772224892,0.999,0.998,1.11372274626028e-218
+"ABL2",2.92890485948378e-222,0.54626051221211,0.287,0.109,6.80970379829978e-218
+"CALU",4.9492559536271e-221,0.571467915840369,0.44,0.233,1.1507020092183e-216
+"RAB21",3.8965586298439e-220,0.509034692386,0.449,0.242,9.05949881438707e-216
+"TUBA1B",9.09289143515462e-214,0.525741369130039,0.798,0.679,2.11409725867345e-209
"NFKBIA",4.82553449692386e-210,0.914208640247266,0.824,0.74,1.1219367705348e-205
-"CALD1",1.72500904923064e-204,1.14154292862704,0.617,0.442,4.01064603946125e-200
-"CD74",3.88565437377328e-179,1.20813744245922,0.453,0.288,9.03414641902287e-175
-"CEBPB",1.36300247365197e-172,0.956025111624211,0.617,0.501,3.16898075124083e-168
-"GADD45B",1.00971788613334e-170,1.48685101121296,0.545,0.401,2.34759408526002e-166
-"ID2",2.87216712605345e-170,0.775127853168569,0.335,0.162,6.67778856807426e-166
-"FBLN1",9.23575305864446e-163,2.05188484165657,0.358,0.218,2.14731258613484e-158
-"PDK4",1.00167849804243e-161,1.53851073742064,0.434,0.272,2.32890250794865e-157
-"JUNB",7.54008368734433e-160,0.901090221151883,0.757,0.649,1.75306945730756e-155
-"RHOBTB3",6.82827318365995e-155,0.860102156319912,0.323,0.171,1.58757351520094e-150
-"THBS1",3.25534197878508e-127,0.764440348204278,0.329,0.182,7.56867010067531e-123
-"NDRG1",4.20625936420683e-126,0.745475396464599,0.486,0.354,9.77955302178088e-122
+"TACC1",6.57267175873055e-208,0.541144066622703,0.34,0.151,1.52814618390485e-203
+"SEPT11",1.69617429643778e-203,0.408613156381485,0.26,0.096,3.94360523921784e-199
+"VAMP5",3.74637115677164e-202,0.534685806145891,0.311,0.132,8.71031293949407e-198
+"ATP1B3",6.40118361854786e-202,0.640201702225988,0.77,0.644,1.48827519131238e-197
+"IL1R1",2.24937090638381e-198,0.480743952583964,0.298,0.121,5.22978735734236e-194
+"UBC",3.2860341027097e-193,0.618419556845085,0.955,0.933,7.64002928880006e-189
+"AHCYL1",1.00110153306981e-192,0.583254804174385,0.47,0.282,2.32756106438731e-188
+"C5orf24",7.89439001548115e-190,0.420224386441307,0.267,0.104,1.83544567859937e-185
+"YBX1",7.27344223451133e-187,0.319057025719002,0.96,0.927,1.69107531952388e-182
+"ETS1",3.01959933574263e-185,0.424440169636642,0.27,0.108,7.0205684556016e-181
+"SNHG7",9.18267020675672e-185,0.572998547006911,0.484,0.297,2.13497082307094e-180
+"ATP13A3",5.07980202841579e-182,0.485473304706304,0.366,0.184,1.18105397160667e-177
+"MALAT1",2.72555129731651e-171,0.233647432556594,1,0.999,6.33690676626089e-167
+"SNX3",3.61010229777176e-171,0.461637822611208,0.702,0.569,8.39348784231935e-167
+"LGMN",2.4967080079583e-166,0.38149673909688,0.276,0.119,5.80484611850305e-162
+"PTPN1",2.99982664655654e-165,0.56664505316636,0.309,0.147,6.97459695324394e-161
+"C6orf48",2.14132192310224e-163,0.48517477875532,0.486,0.307,4.97857347121272e-159
+"MAP1LC3B",5.42279165363747e-163,0.477991654178041,0.622,0.469,1.26079905947071e-158
+"RHOA",2.72890330630721e-162,0.432470999837567,0.704,0.578,6.34470018716427e-158
+"FOSL2",2.27432031225097e-161,0.487232520682271,0.407,0.231,5.28779472598351e-157
+"DDX3Y",3.86838753916138e-161,0.447052110900714,0.408,0.23,8.9940010285502e-157
+"PNPLA8",3.94857219580205e-158,0.497225308020493,0.467,0.292,9.18043035523976e-154
+"DEGS1",4.36943178878854e-157,0.374533357307321,0.267,0.114,1.01589289089334e-152
+"KMT2E",5.36704566004942e-157,0.509481334133135,0.476,0.307,1.24783811596149e-152
+"FTH1",4.50912383022232e-156,0.626923578230653,0.999,1,1.04837129052669e-151
+"TNPO1",5.09253810033499e-155,0.435880662241157,0.305,0.148,1.18401510832788e-150
+"CHD1",7.75722883485145e-153,0.530714995608857,0.411,0.242,1.80355570410296e-148
+"NAP1L1",1.10141268118087e-150,0.392397591156987,0.831,0.779,2.56078448374553e-146
+"NAMPT",8.57994602521873e-150,0.508786437203101,0.657,0.506,1.99483745086335e-145
+"SOX4",8.20755584852875e-149,0.555248706690433,0.394,0.218,1.90825673478294e-144
+"SPTBN1",1.2615701786563e-145,0.409110953086121,0.338,0.175,2.9331506653759e-141
+"TMEM70",7.16840024292282e-145,0.521116238318356,0.261,0.118,1.66665305647955e-140
+"GOLT1B",4.43754431674793e-144,0.366739905683276,0.255,0.112,1.03172905364389e-139
+"PITPNC1",2.00515890256442e-143,0.402974824015735,0.302,0.148,4.66199444846228e-139
+"CCL2",3.03503819124968e-140,0.465717620234039,0.385,0.206,7.0564637946555e-136
+"PRKAR1A",2.5464822222587e-138,0.502199045981151,0.425,0.269,5.92057116675149e-134
+"WSB1",3.65949330940396e-137,0.530147384180215,0.531,0.376,8.5083219443642e-133
+"PSMA7",2.60451086376812e-133,0.352615348296111,0.772,0.68,6.05548775826089e-129
+"HIF1A",1.63036772827789e-131,0.435533309829802,0.403,0.245,3.79060496824609e-127
+"CD99",2.69620744992001e-131,0.3998169599813,0.659,0.536,6.26868232106401e-127
+"PNISR",2.72445890964046e-130,0.385915491859681,0.72,0.618,6.33436696491406e-126
+"AKAP13",3.92747966698242e-130,0.487998146066768,0.427,0.275,9.13139022573414e-126
+"EID1",6.38852168475194e-128,0.464756249755948,0.421,0.269,1.48533129170483e-123
+"GNAI2",5.9916881607895e-127,0.43212701657048,0.304,0.162,1.39306749738356e-122
+"JAK1",8.21114569128424e-127,0.407726330554881,0.547,0.399,1.90909137322359e-122
+"CLEC2B",8.1707558113974e-125,0.570460696064279,0.296,0.154,1.8997007261499e-120
+"SERPINH1",5.31875844843117e-124,0.260670364448104,0.443,0.254,1.23661133926025e-119
+"CCNH",1.84429124712561e-120,0.503806607493783,0.284,0.148,4.28797714956704e-116
+"ATF4",9.73283349458394e-117,0.372246285814425,0.696,0.593,2.26288378749077e-112
+"EIF5",4.35330862466819e-116,0.466261186735176,0.633,0.528,1.01214425523535e-111
+"ENY2",4.65837535218193e-112,0.392166226655439,0.585,0.474,1.0830722693823e-107
+"IL6ST",6.63024862489116e-112,0.364173629076251,0.431,0.28,1.54153280528719e-107
+"SRP14",7.31177982175626e-112,0.310478639256837,0.92,0.893,1.69998880855833e-107
"JUN",2.70455477103472e-109,0.721844399479531,0.693,0.597,6.28808984265572e-105
-"CRYAB",9.73661536133703e-68,0.778831474614523,0.491,0.391,2.26376307151086e-63
-"MEG3",1.29729904607994e-67,0.934605755066499,0.449,0.378,3.01622028213587e-63
-"IER3",2.0785905969469e-65,1.36964112412111,0.635,0.627,4.83272313790153e-61
-"TAGLN",7.14527016840783e-56,1.7655497331943,0.375,0.296,1.66127531415482e-51
+"MTPN",1.51836956321737e-108,0.378507069026809,0.353,0.216,3.53020923448038e-104
+"MGAT1",2.54622035203211e-108,0.344571072310937,0.309,0.171,5.91996231847465e-104
+"HIPK2",3.82058344742851e-108,0.383900315230618,0.281,0.149,8.88285651527129e-104
+"CAMLG",1.46130271169959e-107,0.375546778236845,0.441,0.3,3.39752880470156e-103
+"MRFAP1",3.9365234980287e-107,0.35458290659968,0.638,0.535,9.15241713291673e-103
+"RYBP",5.05379569753432e-107,0.37129535695224,0.314,0.177,1.17500749967673e-102
+"GABARAPL1",7.03446285537416e-105,0.499284450206643,0.511,0.381,1.63551261387449e-100
+"MBNL1",1.13680701146987e-104,0.340550798813536,0.279,0.149,2.64307630166745e-100
+"RABAC1",2.10738731147684e-104,0.368455720845379,0.55,0.42,4.89967549918365e-100
+"ARF1",3.58983502900407e-103,0.312878040154295,0.705,0.609,8.34636644243447e-99
+"TCEB1",1.18100813218968e-101,0.444431652661764,0.62,0.521,2.745843907341e-97
+"CLK1",4.22338695352365e-101,0.41081517948202,0.505,0.368,9.81937466694248e-97
+"HNRNPA2B1",5.95916062146011e-99,0.294541898223241,0.86,0.825,1.38550484448947e-94
+"FCGRT",3.40436834148966e-97,0.405082747373246,0.438,0.312,7.91515639396346e-93
+"CCNI",1.85950537347767e-95,0.291516962488098,0.852,0.824,4.32334999333557e-91
+"COPS8",1.16265454206234e-94,0.333303826548017,0.267,0.146,2.70317181029493e-90
+"H2AFZ",7.83227526614915e-94,0.306658533745728,0.8,0.73,1.82100399937968e-89
+"AXL",9.81971798428135e-93,0.534890230807542,0.331,0.205,2.28308443134541e-88
+"G3BP1",3.66989682476421e-92,0.361335989978338,0.433,0.302,8.5325101175768e-88
+"VAPA",1.11479886844319e-90,0.288296258924686,0.731,0.66,2.59190736913042e-86
+"SEPT7",4.78591356390731e-90,0.401484496767952,0.497,0.378,1.11272490360845e-85
+"KDM6B",6.24882052086779e-90,0.371021369177918,0.386,0.256,1.45285077110176e-85
+"SPAG9",1.8462833226919e-89,0.379746086696423,0.49,0.371,4.29260872525866e-85
+"ATP2B1",9.01475271668743e-88,0.424570776915681,0.311,0.192,2.09593000662983e-83
+"SERINC1",1.04238150711612e-86,0.333545788353267,0.359,0.233,2.42353700404498e-82
+"ELL2",1.69772295468259e-86,0.36145455806199,0.436,0.305,3.94720586963703e-82
+"DDX21",2.63588860060255e-86,0.320020234238965,0.705,0.61,6.12844099640094e-82
+"RCN1",1.11419503562541e-85,0.332416548861517,0.425,0.295,2.59050345782907e-81
+"STOM",1.13600694628373e-85,0.339035936548011,0.521,0.393,2.64121615010968e-81
+"ATP6V0E1",1.3811945573235e-85,0.317735840076637,0.713,0.658,3.21127734577713e-81
+"SEC61B",1.78798154947821e-84,0.341728096197297,0.726,0.679,4.15705710253683e-80
+"FUNDC2",2.51558409534181e-83,0.385219955412666,0.428,0.308,5.84873302166972e-79
+"SEC11A",3.56985646779275e-82,0.331095214817943,0.538,0.437,8.29991628761813e-78
+"SPHK1",4.74971802042853e-82,0.287297616843187,0.274,0.155,1.10430943974963e-77
+"LEPROT",9.86893703616125e-82,0.332353739619182,0.361,0.24,2.29452786090749e-77
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+"PSMB3",4.47923765325153e-22,0.193024401389302,0.502,0.47,1.04142275438098e-17
+"DUSP1",1.0545117926935e-21,0.616469162841139,0.589,0.57,2.45173991801239e-17
+"PSMB5",1.1968138632843e-21,0.189599534851709,0.475,0.438,2.78259223213599e-17
+"SRRM2",1.28689861034437e-21,0.156724374152438,0.678,0.67,2.99203926905067e-17
+"TRAM1",1.77372280859372e-21,0.197594337179036,0.367,0.315,4.1239055299804e-17
+"IVNS1ABP",4.67233132109414e-21,0.321091767687215,0.276,0.227,1.08631703215439e-16
+"NTMT1",5.52172142939561e-21,0.193438224402165,0.306,0.252,1.28380023233448e-16
+"HNRNPC",6.05673036568317e-21,0.146290758834734,0.776,0.79,1.40818981002134e-16
+"NONO",6.79613534663399e-21,0.174503322237002,0.315,0.262,1.5801014680924e-16
+"SLC25A5",8.64936369617551e-21,0.141752323552117,0.744,0.714,2.01097705936081e-16
+"SEC62",8.66876362133204e-21,0.185818237332262,0.532,0.505,2.0154875419597e-16
+"SUB1",8.89565511581372e-21,0.13554930825782,0.803,0.815,2.06823981442669e-16
+"SURF4",3.25103635311528e-20,0.201644510742295,0.283,0.232,7.55865952099302e-16
+"SEC61G",4.57634668467058e-20,0.182604868782854,0.635,0.632,1.06400060418591e-15
+"EPB41L4A-AS1",4.92608794458392e-20,0.192588305430775,0.374,0.326,1.14531544711576e-15
+"SH3GLB1",5.45223961028132e-20,0.189896248733538,0.372,0.328,1.26764570939041e-15
+"RAB7A",6.83769855445797e-20,0.178594102145196,0.623,0.617,1.58976491391148e-15
+"MRPL32",7.97976817604886e-20,0.210939335893008,0.306,0.258,1.85529610093136e-15
+"SERINC3",8.04486811406235e-20,0.193033097493243,0.262,0.213,1.8704318365195e-15
+"PPIB",8.63037443417883e-20,0.189096776288716,0.695,0.697,2.00656205594658e-15
+"YWHAQ",2.37371261312656e-19,0.166214809005987,0.663,0.654,5.51888182551925e-15
+"HSP90AB1",3.28832015072687e-19,0.118673478504918,0.979,0.958,7.64534435043996e-15
+"COPRS",5.21412886960186e-19,0.152587550884827,0.27,0.214,1.21228496218243e-14
+"IDI1",8.58676177109494e-19,0.191755710393838,0.28,0.226,1.99642211177957e-14
+"GDI2",1.08624743779596e-18,0.173463419092291,0.372,0.325,2.52552529287561e-14
+"PPIA",2.69594733132857e-18,0.121222851808059,0.861,0.87,6.26807754533893e-14
+"AP2S1",3.34804613532737e-18,0.211523296528581,0.351,0.309,7.78420726463614e-14
+"NFIC",3.76798209205226e-18,0.181504310391888,0.39,0.347,8.76055836402151e-14
+"VCP",4.97469105185519e-18,0.168600740396353,0.371,0.326,1.15661566955633e-13
+"POLE4",5.53017850100523e-18,0.173448280845972,0.317,0.267,1.28576650148372e-13
+"NFAT5",5.76734633666351e-18,0.180796296511249,0.293,0.245,1.34090802327427e-13
+"SSR2",9.41717498161458e-18,0.188833585379651,0.505,0.485,2.18949318322539e-13
+"ZC3H15",9.75690468152541e-18,0.168293733658722,0.452,0.411,2.26848033845466e-13
+"RAB5C",1.81916938487136e-17,0.184198078940707,0.331,0.288,4.22956881982591e-13
+"PSMD11",2.08666167753417e-17,0.177460989860143,0.352,0.309,4.85148840026694e-13
+"SNX9",3.3776857037778e-17,0.173835533426622,0.354,0.311,7.85311926128338e-13
+"C14orf166",3.75461439874655e-17,0.185589093814739,0.504,0.483,8.72947847708574e-13
+"PGRMC1",1.03907783731827e-16,0.255611834793004,0.366,0.335,2.41585597176497e-12
+"DYNC1LI2",2.36906841871515e-16,0.158195764272255,0.257,0.211,5.50808407351273e-12
+"BRK1",7.65887138629363e-16,0.153782374410678,0.62,0.621,1.78068759731327e-11
+"ZFP36",1.70100016048471e-15,0.672815560184769,0.633,0.658,3.95482537312696e-11
+"SPTSSA",2.36085126434503e-15,0.18794192776202,0.386,0.351,5.48897918960221e-11
+"C19orf43",3.0052273319971e-15,0.143481990871846,0.589,0.583,6.98715354689326e-11
+"LSM14A",3.01493675954422e-15,0.145094770422276,0.278,0.231,7.0097279659403e-11
+"PGAM1",3.12336382761507e-15,0.148842303205975,0.447,0.407,7.26182089920504e-11
+"SNU13",4.32096529137753e-15,0.114842999609438,0.701,0.709,1.00462443024528e-10
+"SREK1",4.8767171162906e-15,0.15743580437609,0.273,0.229,1.13383672953756e-10
+"RELB",5.20426608141212e-15,0.172791548477643,0.35,0.309,1.20999186392832e-10
+"PSMC4",6.58634020088868e-15,0.169650385307214,0.27,0.227,1.53132409670662e-10
+"ASH1L",7.14343779113941e-15,0.159731519169217,0.319,0.277,1.66084928643991e-10
+"SDF2L1",1.3196796207511e-14,0.0814070238427956,0.244,0.323,3.06825511824631e-10
+"TRIM56",2.86307261656644e-14,0.157907872649452,0.256,0.211,6.65664383351696e-10
+"SEC63",7.25882868389703e-14,0.164141231734924,0.254,0.215,1.68767766900606e-09
+"SNRPB",7.42794993817487e-14,0.126964946047602,0.652,0.646,1.72699836062566e-09
+"PAIP2",8.93312116320846e-14,0.150153728765604,0.468,0.443,2.07695067044597e-09
+"CHORDC1",9.72039789375516e-14,0.180851458098453,0.327,0.285,2.25999251029807e-09
+"SPCS3",1.04340316326049e-13,0.148097499927882,0.328,0.287,2.42591235458063e-09
+"NCKAP1",1.70956733056235e-13,0.135864310806497,0.288,0.247,3.97474404355747e-09
+"XRN2",1.76640619406838e-13,0.166135862775321,0.295,0.255,4.10689440120898e-09
+"RNF114",2.05163157168216e-13,0.152114846499061,0.365,0.329,4.77004340416102e-09
+"PCBP2",2.15033722907804e-13,0.135325564767427,0.586,0.582,4.99953405760644e-09
+"SEPT2",2.36004010002269e-13,0.151964524135604,0.338,0.302,5.48709323255275e-09
+"H3F3B",2.96200147760013e-13,0.0871383090412468,0.976,0.976,6.8866534354203e-09
+"LINC00657",3.06622809327778e-13,0.171064130323383,0.378,0.351,7.12898031687085e-09
+"C1orf43",3.39006324289627e-13,0.155662517277586,0.404,0.374,7.88189703973382e-09
+"VDAC1",5.12742910804778e-13,0.131715134026357,0.57,0.558,1.19212726762111e-08
+"EEF1A1",8.9643071993014e-13,0.0384043159659599,1,0.999,2.08420142383758e-08
+"HNRNPA0",1.35900429312688e-12,0.11851543540661,0.684,0.687,3.15968498151999e-08
+"ZC3H11A",1.71671871292367e-12,0.151884229709763,0.261,0.223,3.99137100754753e-08
+"COX14",2.05581360852217e-12,0.163720061297597,0.308,0.272,4.77976663981404e-08
+"SRSF11",2.20499845109425e-12,0.15157714540848,0.573,0.577,5.12662139879413e-08
+"DAD1",2.85565218448073e-12,0.173105498729281,0.444,0.428,6.6393913289177e-08
+"TIPARP",3.04703572315877e-12,0.234522716132027,0.297,0.264,7.08435805634414e-08
+"AP3S1",3.9820429684558e-12,0.152261103941253,0.323,0.289,9.25824990165973e-08
+"PITPNB",4.09076956491537e-12,0.155240022516283,0.35,0.318,9.51103923842824e-08
+"MTCH1",4.31507077895441e-12,0.15485066909222,0.473,0.46,1.0032539561069e-07
+"RWDD1",5.47069521062486e-12,0.154157500449604,0.442,0.42,1.27193663647028e-07
+"NUDT4",5.9025991940368e-12,0.27540904281977,0.332,0.306,1.37235431261356e-07
+"PTTG1IP",7.68676806860741e-12,0.166362595884141,0.306,0.274,1.78717357595122e-07
+"SLC25A3",1.37647919596465e-11,0.0927265117717864,0.787,0.789,3.20031413061781e-07
+"GRPEL1",3.17171322686889e-11,0.127611462548028,0.355,0.318,7.37423325247018e-07
+"CTNNAL1",3.19022873792705e-11,0.106215599470571,0.283,0.235,7.41728181568039e-07
+"ELOVL5",3.29512727079113e-11,0.0983720642790686,0.306,0.262,7.66117090458938e-07
+"SAP18",3.3201042431841e-11,0.152038667212092,0.633,0.64,7.71924236540304e-07
+"ACTN1",5.21234358249846e-11,0.12297023900324,0.348,0.311,1.21186988293089e-06
+"AGO2",6.02599420699535e-11,0.132079734236759,0.283,0.248,1.40104365312642e-06
+"SYF2",1.60865380098747e-10,0.135363058496907,0.333,0.302,3.74012008729586e-06
+"HNRNPA1",2.23933759080515e-10,0.0842144812609265,0.853,0.857,5.20645989862197e-06
+"PPP1CB",2.5015335170786e-10,0.161863515360669,0.514,0.493,5.81606542720774e-06
+"BUD31",2.91644265510721e-10,0.139137743907362,0.392,0.368,6.78072917312427e-06
+"METTL9",3.24923797979058e-10,0.118126155337662,0.331,0.301,7.55447830301309e-06
+"RSF1",3.68763764116019e-10,0.133668117719449,0.254,0.222,8.57375751569743e-06
+"TNFAIP3",4.28513033270627e-10,0.191106740933678,0.258,0.222,9.96292802354207e-06
+"RAD21",4.75340079162922e-10,0.121585521249221,0.27,0.236,1.10516568405379e-05
+"ATOX1",6.5753110262884e-10,0.172389971681587,0.298,0.271,1.52875981361205e-05
+"GGNBP2",6.82815886329949e-10,0.149905673117453,0.281,0.251,1.58754693571713e-05
+"NFKB1",8.30275223343848e-10,0.15131731510882,0.261,0.229,1.93038989427445e-05
+"ATRX",1.02248149943361e-09,0.134916260141714,0.324,0.296,2.37726948618315e-05
+"TFG",1.31050514611397e-09,0.147822536090574,0.336,0.311,3.04692446471499e-05
+"POLR2H",1.4451929071247e-09,0.12022510151616,0.286,0.253,3.36007350906492e-05
+"EIF4H",1.63746721707218e-09,0.155847494428246,0.394,0.375,3.80711127969282e-05
+"RBPJ",2.47856108875458e-09,0.122594091661899,0.282,0.25,5.76265453135439e-05
+"CELF1",2.5572948481091e-09,0.133571258718893,0.275,0.245,5.94571052185366e-05
+"EGR1",2.95654952382533e-09,0.102054430022086,0.26,0.324,6.87397764289389e-05
+"MESDC1",4.15709294990005e-09,0.185211482451773,0.277,0.251,9.66524110851762e-05
+"DHX36",7.3633448473267e-09,0.137661426856076,0.373,0.35,0.000171197767700346
+"ARL2",7.4780522607043e-09,0.152170612021531,0.268,0.242,0.000173864715061375
+"ERH",8.29753062886531e-09,0.124505910774092,0.518,0.509,0.000192917587121118
+"GADD45GIP1",1.07484333296966e-08,0.115796083326485,0.473,0.458,0.000249901074915445
+"BRD2",1.14801283832855e-08,0.151322129657428,0.441,0.433,0.000266912984911387
+"LAMP2",1.48596036269538e-08,0.14660727375067,0.278,0.25,0.000345485784326676
+"HNRNPDL",1.5442804961263e-08,0.0880852273284691,0.76,0.782,0.000359045215349364
+"RBMX",2.0826244432e-08,0.12971116716652,0.417,0.399,0.000484210183044
+"ANP32B",2.12267168386074e-08,0.137020351833188,0.477,0.474,0.000493521166497621
+"RBM39",2.8077544642908e-08,0.0893944813350251,0.728,0.745,0.000652802912947612
+"PSMB1",2.85796244846037e-08,0.0938846195864582,0.632,0.637,0.000664476269267036
+"JUND",3.56196788044591e-08,0.131827369060936,0.509,0.498,0.000828157532203673
+"UBE2A",3.63356502533689e-08,0.120358991339324,0.299,0.273,0.000844803868390827
+"CCT3",4.40199695076247e-08,0.107691522507793,0.471,0.46,0.00102346429105228
+"CBX3",5.37294491479705e-08,0.127170890701478,0.312,0.285,0.00124920969269031
+"MED28",5.49906657703358e-08,0.124534351488342,0.331,0.309,0.00127853297916031
+"BCAP29",6.29769303055208e-08,0.088218595488714,0.275,0.242,0.00146421362960336
+"TNFRSF1A",7.46999640774154e-08,0.142163927542725,0.355,0.334,0.00173677416479991
+"KIF5B",1.75873739388657e-07,0.125921028480209,0.467,0.466,0.00408906444078627
+"KLF4",1.860052868372e-07,0.130495970808193,0.342,0.421,0.0043246229189649
+"GPBP1",1.97237687873327e-07,0.117125631095422,0.526,0.528,0.00458577624305485
+"OSTC",2.08518493025043e-07,0.134321074078736,0.363,0.347,0.00484805496283225
+"NDUFS5",3.35225537888107e-07,0.109738576365973,0.671,0.691,0.00779399375589848
+"BRD4",3.72759815484934e-07,0.114968125842253,0.343,0.322,0.00866666571002473
+"PPP4R2",3.95107082896164e-07,0.124439059055814,0.322,0.303,0.0091862396773358
+"PAK2",6.78032751790217e-07,0.100195921279197,0.323,0.297,0.0157642614791225
+"AK2",8.21531648859067e-07,0.143513132593735,0.302,0.286,0.0191006108359733
+"COX17",1.60502651904422e-06,0.148769280821938,0.397,0.388,0.0373168665677782
+"IPO7",1.73759982672915e-06,0.118106191255484,0.331,0.312,0.0403991959714527
+"VAMP2",1.89220469424302e-06,0.119571698012654,0.381,0.365,0.0439937591411503
+"ATP6AP2",1.95769563461957e-06,0.146212141763961,0.332,0.32,0.0455164235049049
+"GNG12",1.979806782854e-06,0.113794770169401,0.285,0.264,0.0460305077013555
diff --git a/r.scripts/sc-TissueMapper.R b/r.scripts/sc-TissueMapper.R
index 5d140421d36cb0d62711788a8edf0923384207d1..23c05d11db319d030dd883965457a781f4f5b029 100644
--- a/r.scripts/sc-TissueMapper.R
+++ b/r.scripts/sc-TissueMapper.R
@@ -103,17 +103,14 @@ scCellCycle <- function(sc10x,sub=FALSE){
sc10x <- ScaleData(object=sc10x,display.progress=FALSE,do.par=TRUE,num.cores=45)
sc10x <- CellCycleScoring(object=sc10x,s.genes=genes.s,g2m.genes=genes.g2m,set.ident=TRUE)
- tryCatch({
- postscript(paste0(folder,"Ridge_cc.Raw.eps"))
- plot <- RidgePlot(object=sc10x,features.plot=c("PCNA","TOP2A","MCM6","MKI67"),y.log=TRUE,nCol=2,do.return=TRUE)
- plot(plot)
- dev.off()
- postscript(paste0(folder,"Violin_cc.Raw.eps"))
- plot <- VlnPlot(object=sc10x,features.plot=c("PCNA","TOP2A","MCM6","MKI67"),nCol=2,point.size.use=1,size.title.use=20,x.lab.rot=TRUE)
- plot(plot)
- dev.off()
- },error=function(e){cat("ERROR : ",conditionMessage(e),"/\n")})
-
+ postscript(paste0(folder,"Ridge_cc.Raw.eps"))
+ plot <- RidgePlot(object=sc10x,features.plot=c("PCNA","TOP2A","MCM6","MKI67"),y.log=TRUE,nCol=2,do.return=TRUE)
+ plot(plot)
+ dev.off()
+ postscript(paste0(folder,"Violin_cc.Raw.eps"))
+ plot <- VlnPlot(object=sc10x,features.plot=c("PCNA","TOP2A","MCM6","MKI67"),nCol=2,point.size.use=1,size.title.use=20,x.lab.rot=TRUE)
+ plot(plot)
+ dev.off()
sc10x <- RunPCA(object=sc10x,pc.genes=c(genes.s,genes.g2m),do.print=FALSE,pcs.store=2)
postscript(paste0(folder,"PCA_cc.Raw.eps"))
plot <- PCAPlot(object=sc10x,do.return=TRUE)
@@ -349,6 +346,8 @@ scStress <- function(sc10x,stg="go",res.use=1,pc.use=10,cut=0.95){
sc10x.Stress <- t(sc10x.Stress)
sc10x.Stress <- sc10x.Stress[,apply(sc10x.Stress,2,var)!=0]
sc10x.Stress.pca <- prcomp(sc10x.Stress,center=TRUE,scale.=TRUE)
+ sc10x.Stress.pca.pc1var <- round((sc10x.Stress.pca$sdev[1]^2)/sum(sc10x.Stress.pca$sdev^2)*100,0)
+ sc10x.Stress.pca.pc2var <- round((sc10x.Stress.pca$sdev[2]^2)/sum(sc10x.Stress.pca$sdev^2)*100,0)
sc10x.Stress.pca <- sc10x.Stress.pca$x[,1:2]
colnames(x=sc10x.Stress.pca) <- paste0("Stress",1:2)
if (skewness(sc10x.Stress.pca[,1])<0){
@@ -366,6 +365,8 @@ scStress <- function(sc10x,stg="go",res.use=1,pc.use=10,cut=0.95){
plot <- plot+geom_density2d(color="black",bins=25,alpha=0.5)
plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20))
plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
+ plot <- plot+xlab(paste0("Stress PC1 (",sc10x.Stress.pca.pc1var,"%)"))
+ plot <- plot+ylab(paste0("Stress PC2 (",sc10x.Stress.pca.pc2var,"%)"))
plot(plot)
dev.off()
@@ -400,11 +401,13 @@ scStress <- function(sc10x,stg="go",res.use=1,pc.use=10,cut=0.95){
plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20))
plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
plot <- plot+geom_vline(xintercept=cut.x,color="red",lwd=2.5)
+ plot <- plot+xlab(paste0("Stress PC1 (",sc10x.Stress.pca.pc1var,"%)"))
+ plot <- plot+ylab(paste0("Stress PC2 (",sc10x.Stress.pca.pc2var,"%)"))
plot(plot)
dev.off()
#Subsample all cells (+Stress) to better visualize their clustering
- if (ncol(sc10x@data)>2500){
+ if (ncol(sc10x@data)<2500){
rnd <- sample(1:ncol(sc10x@data),2500)
} else {
rnd <- 1:ncol(sc10x@data)
@@ -848,6 +851,8 @@ scNE <- function(sc10x,neg="EurUro",cut=0.95){
sc10x.NE <- t(sc10x.NE)
sc10x.NE <- sc10x.NE[,apply(sc10x.NE,2,var)!=0]
sc10x.NE.pca <- prcomp(sc10x.NE,center=TRUE,scale.=TRUE)
+ sc10x.NE.pca.pc1var <- round((sc10x.NE.pca$sdev[1]^2)/sum(sc10x.NE.pca$sdev^2)*100,0)
+ sc10x.NE.pca.pc2var <- round((sc10x.NE.pca$sdev[2]^2)/sum(sc10x.NE.pca$sdev^2)*100,0)
sc10x.NE.pca <- sc10x.NE.pca$x[,1:2]
colnames(x=sc10x.NE.pca) <- paste0("NE",1:2)
if (skewness(sc10x.NE.pca[,1])<0){
@@ -864,6 +869,8 @@ scNE <- function(sc10x,neg="EurUro",cut=0.95){
plot <- DimPlot(object=sc10x,reduction.use="NE",pt.size=2.5,do.return=TRUE,vector.friendly=FALSE)
plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20))
plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
+ plot <- plot+xlab(paste0("NE PC1 (",sc10x.NE.pca.pc1var,"%)"))
+ plot <- plot+ylab(paste0("NE PC2 (",sc10x.NE.pca.pc2var,"%)"))
plot(plot)
dev.off()
@@ -897,11 +904,13 @@ scNE <- function(sc10x,neg="EurUro",cut=0.95){
plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20))
plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
plot <- plot+geom_vline(xintercept=cut.x,color="red",lwd=2.5)
+ plot <- plot+xlab(paste0("NE PC1 (",sc10x.NE.pca.pc1var,"%)"))
+ plot <- plot+ylab(paste0("NE PC2 (",sc10x.NE.pca.pc2var,"%)"))
plot(plot)
dev.off()
#Subsample all cells (+NE) to better visualize their clustering
- if (ncol(sc10x@data)>2500){
+ if (ncol(sc10x@data)<2500){
rnd <- sample(1:ncol(sc10x@data),2500)
} else {
rnd <- 1:ncol(sc10x@data)
diff --git a/r.scripts/sc-TissueMapper_RUN.D17_FACS.R b/r.scripts/sc-TissueMapper_RUN.D17_FACS.R
index 7812cd1180f5bd6ac6604f8cd4d15fd8bdae8992..fb8f5a8865a16879e52db962097f7055d68099f4 100644
--- a/r.scripts/sc-TissueMapper_RUN.D17_FACS.R
+++ b/r.scripts/sc-TissueMapper_RUN.D17_FACS.R
@@ -167,13 +167,12 @@ if (opt$st==TRUE){
sc10x <- scCluster(sc10x,pc.use=pc.use.poststress,res.use=0.5,folder="post.stress",red="pca")
}
-gene.set1 <- read_delim("./genesets/genes.deg.Epi.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
-gene.set1 <- gene.set1[1]
+
+gene.set1 <- read_delim("./genesets/DEG_Epi_5FC.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
gene.set1 <- as.list(gene.set1)
names(gene.set1) <- "Epi"
gene.set <- c(gene.set1)
-gene.set1 <- read_delim("./genesets/genes.deg.St.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
-gene.set1 <- gene.set1[1]
+gene.set1 <- read_delim("./genesets/DEG_FMSt_5FC.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
gene.set1 <- as.list(gene.set1)
names(gene.set1) <- "St"
gene.set <- c(gene.set,gene.set1)
diff --git a/r.scripts/sc-TissueMapper_RUN.D27_FACS.R b/r.scripts/sc-TissueMapper_RUN.D27_FACS.R
index 61cadc9c0da54b927d49f81fb35f9f76986d82e8..0337bd6bbd42914eed17258f52e65991e66273e0 100644
--- a/r.scripts/sc-TissueMapper_RUN.D27_FACS.R
+++ b/r.scripts/sc-TissueMapper_RUN.D27_FACS.R
@@ -167,13 +167,12 @@ if (opt$st==TRUE){
sc10x <- scCluster(sc10x,pc.use=pc.use.poststress,res.use=0.5,folder="post.stress",red="pca")
}
-gene.set1 <- read_delim("./genesets/genes.deg.Epi.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
-gene.set1 <- gene.set1[1]
+
+gene.set1 <- read_delim("./genesets/DEG_Epi_5FC.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
gene.set1 <- as.list(gene.set1)
names(gene.set1) <- "Epi"
gene.set <- c(gene.set1)
-gene.set1 <- read_delim("./genesets/genes.deg.St.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
-gene.set1 <- gene.set1[1]
+gene.set1 <- read_delim("./genesets/DEG_FMSt_5FC.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
gene.set1 <- as.list(gene.set1)
names(gene.set1) <- "St"
gene.set <- c(gene.set,gene.set1)
diff --git a/r.scripts/sc-TissueMapper_RUN.DS_D17.R b/r.scripts/sc-TissueMapper_RUN.DS_D17.R
index b1766dc054b9bec797537e88a4d194604f7aa1d7..efec340dbda666de55b016f037b22f4ee3e04c78 100644
--- a/r.scripts/sc-TissueMapper_RUN.DS_D17.R
+++ b/r.scripts/sc-TissueMapper_RUN.DS_D17.R
@@ -13,6 +13,8 @@ library(viridis)
library(reshape2)
library(NMI)
+options(bitmapType="cairo")
+
source("../r.scripts/sc-TissueMapper.R")
#Create folder structure
@@ -101,7 +103,7 @@ option_list=list(
make_option("--lx",action="store",default=0.2,type='numeric',help="x low threshold for hvg selection"),
make_option("--hx",action="store",default=5,type='numeric',help="x high threshold for hvg selection"),
make_option("--ly",action="store",default=1,type='numeric',help="y low threshold for hvg selection"),
- make_option("--cc",action="store",default=TRUE,type='logical',help="Scale cell cycle?"),
+ make_option("--cc",action="store",default=FALSE,type='logical',help="Scale cell cycle?"),
make_option("--cca",action="store",default=50,type='integer',help="Number of CCAs to cacluate"),
make_option("--acca",action="store",default=30,type='integer',help="Number of CCAs to align"),
make_option("--pc",action="store",default=50,type='integer',help="Number of PCs to cacluate"),
@@ -178,13 +180,11 @@ if (opt$st==TRUE){
sc10x <- scCluster(sc10x,pc.use=pc.use.poststress,res.use=opt$res.poststress,folder="post.stress",red="pca")
}
-gene.set1 <- read_delim("./genesets/genes.deg.Epi.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
-gene.set1 <- gene.set1[1]
+gene.set1 <- read_delim("./genesets/DEG_Epi_5FC.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
gene.set1 <- as.list(gene.set1)
names(gene.set1) <- "Epi"
gene.set <- c(gene.set1)
-gene.set1 <- read_delim("./genesets/genes.deg.St.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
-gene.set1 <- gene.set1[1]
+gene.set1 <- read_delim("./genesets/DEG_FMSt_5FC.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
gene.set1 <- as.list(gene.set1)
names(gene.set1) <- "St"
gene.set <- c(gene.set,gene.set1)
@@ -305,6 +305,11 @@ rm(gene.set)
sc10x.Epi.NE <- scNE(sc10x.Epi,neg="dws",cut=opt$cut.ne)
sc10x <- scMerge(sc10x,sc10x.Epi,sc10x.St,i.1="Epi.dws.sc",i.2="St.dws.sc",nm="Merge_Epi.dws.sc_St.dws.sc")
+cells.ne <- names(sc10x.Epi.NE@ident[sc10x.Epi.NE@ident=="NE"])
+sc10x <- SetAllIdent(object=sc10x,id="Merge_Epi.dws.sc_St.dws.sc")
+sc10x <- SetIdent(object=sc10x,cells.use=cells.ne,ident.use="NE")
+sc10x <- StashIdent(object=sc10x,save.name="Merge_Epi.dws.sc_St.dws.sc_NE")
+rm(cells.ne)
sc10x <- SetAllIdent(object=sc10x,id="Merge_Epi.dws.sc_St.dws.sc")
sc10x <- SetAllIdent(object=sc10x,id="Merge_Epi.dws.sc_St.dws.sc")
@@ -316,7 +321,7 @@ plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
plot(plot)
dev.off()
-scTables(sc10x,i.1="samples",i.2="Merge_Epi.dws.sc_St.dws.sc")
+scTables(sc10x,i.1="samples",i.2="Merge_Epi.dws.sc_St.dws.sc_NE")
sctSNECustCol(sc10x,i="Lin",bl="Epi",rd="St",file="D17")
sctSNECustCol(sc10x,i="Merge_Epi.dws.sc_St.dws.sc",bl=c("BE","LE","OE_SCGB","OE_KRT13"),rd=c("Fib","SM","Endo","Leu"),file="D17")
@@ -344,6 +349,41 @@ for (g in c("Fib","SM","Endo","Leu")){
rm(i)
rm(g)
+try(genes.deg.Stress <- scDEG(sc10x.Stress,i="Stress",g.1="Stress",g.2="ALL",pct=0.5,t=5))
+
+try(genes.deg.Epi <- scDEG(sc10x,i="Lin",g.1="Epi",g.2="St",t=2))
+try(genes.deg.St <- scDEG(sc10x,i="Lin",g.1="St",g.2="Epi",t=2))
+
+try(genes.deg.BE <- scDEG(sc10x,i="Merge_Epi.dws.sc_St.dws.sc_NE",g.1="BE",g.2=c("LE","OE_SCGB","OE_KRT13"),pct=0.25,t=2))
+try(genes.deg.LE <- scDEG(sc10x,i="Merge_Epi.dws.sc_St.dws.sc_NE",g.1="LE",g.2=c("BE","OE_SCGB","OE_KRT13"),pct=0.25,t=2))
+try(genes.deg.OE1 <- scDEG(sc10x,i="Merge_Epi.dws.sc_St.dws.sc_NE",g.1="OE_SCGB",g.2=c("BE","LE","OE_KRT13"),pct=0.25,t=2))
+try(genes.deg.OE2 <- scDEG(sc10x,i="Merge_Epi.dws.sc_St.dws.sc_NE",g.1="OE_KRT13",g.2=c("BE","LE","OE_SCGB"),pct=0.25,t=2))
+
+try(genes.deg.NE <- scDEG(sc10x,i="Merge_Epi.dws.sc_St.dws.sc_NE",g.1="NE",g.2=c("BE","LE","OE_SCGB","OE_KRT13"),pct=0.01,t=1))
+
+try(genes.deg.Fib <- scDEG(sc10x.St,i="Merge_Epi.dws.sc_St.dws.sc",g.1="Fib",g.2=c("SM","Endo","Leu"),pct=0.25,t=2))
+try(genes.deg.SM <- scDEG(sc10x.St,i="Merge_Epi.dws.sc_St.dws.sc",g.1="SM",g.2=c("Fib","Endo","Leu"),pct=0.25,t=2))
+try(genes.deg.Endo <- scDEG(sc10x.St,i="Merge_Epi.dws.sc_St.dws.sc",g.1="Endo",g.2=c("Fib","SM","Leu"),pct=0.25,t=2))
+try(genes.deg.Leu <- scDEG(sc10x.St,i="St.dws.sc",g.1="Leu",g.2=c("Fib","SM","Endo"),pct=0.25,t=2))
+
+try(genes.deg.BE.unique <- setdiff(rownames(genes.deg.BE),Reduce(union,list(rownames(genes.deg.LE),rownames(genes.deg.OE1),rownames(genes.deg.OE2),rownames(genes.deg.NE),rownames(genes.deg.Fib),rownames(genes.deg.SM),rownames(genes.deg.Endo),rownames(genes.deg.Leu)))))
+try(genes.deg.LE.unique <- setdiff(rownames(genes.deg.LE),Reduce(union,list(rownames(genes.deg.BE),rownames(genes.deg.OE1),rownames(genes.deg.OE2),rownames(genes.deg.NE),rownames(genes.deg.Fib),rownames(genes.deg.SM),rownames(genes.deg.Endo),rownames(genes.deg.Leu)))))
+try(genes.deg.OE1.unique <- setdiff(rownames(genes.deg.OE1),Reduce(union,list(rownames(genes.deg.BE),rownames(genes.deg.LE),rownames(genes.deg.OE2),rownames(genes.deg.NE),rownames(genes.deg.Fib),rownames(genes.deg.SM),rownames(genes.deg.Endo),rownames(genes.deg.Leu)))))
+try(genes.deg.OE2.unique <- setdiff(rownames(genes.deg.OE2),Reduce(union,list(rownames(genes.deg.BE),rownames(genes.deg.LE),rownames(genes.deg.OE1),rownames(genes.deg.NE),rownames(genes.deg.Fib),rownames(genes.deg.SM),rownames(genes.deg.Endo),rownames(genes.deg.Leu)))))
+try(genes.deg.NE.unique <- setdiff(rownames(genes.deg.NE),Reduce(union,list(rownames(genes.deg.BE),rownames(genes.deg.LE),rownames(genes.deg.OE1),rownames(genes.deg.OE2),rownames(genes.deg.Fib),rownames(genes.deg.SM),rownames(genes.deg.Endo),rownames(genes.deg.Leu)))))
+try(genes.deg.Fib.unique <- setdiff(rownames(genes.deg.Fib),Reduce(union,list(rownames(genes.deg.BE),rownames(genes.deg.LE),rownames(genes.deg.OE1),rownames(genes.deg.OE2),rownames(genes.deg.NE),rownames(genes.deg.SM),rownames(genes.deg.Endo),rownames(genes.deg.Leu)))))
+try(genes.deg.SM.unique <- setdiff(rownames(genes.deg.SM),Reduce(union,list(rownames(genes.deg.BE),rownames(genes.deg.LE),rownames(genes.deg.OE1),rownames(genes.deg.OE2),rownames(genes.deg.NE),rownames(genes.deg.Fib),rownames(genes.deg.Endo),rownames(genes.deg.Leu)))))
+try(genes.deg.Endo.unique <- setdiff(rownames(genes.deg.Endo),Reduce(union,list(rownames(genes.deg.BE),rownames(genes.deg.LE),rownames(genes.deg.OE1),rownames(genes.deg.OE2),rownames(genes.deg.NE),rownames(genes.deg.Fib),rownames(genes.deg.SM),rownames(genes.deg.Leu)))))
+try(genes.deg.Leu.unique <- setdiff(rownames(genes.deg.Leu),Reduce(union,list(rownames(genes.deg.BE),rownames(genes.deg.LE),rownames(genes.deg.OE1),rownames(genes.deg.OE2),rownames(genes.deg.NE),rownames(genes.deg.Fib),rownames(genes.deg.SM),rownames(genes.deg.Endo)))))
+
+try(genes.deg.5 <- c(genes.deg.BE.unique[1:5],genes.deg.LE.unique[1:5],genes.deg.OE1.unique[1:5],genes.deg.OE2.unique[1:5],genes.deg.NE.unique[1:5],genes.deg.Fib.unique[1:5],genes.deg.SM.unique[1:5],genes.deg.Endo.unique[1:5],genes.deg.Leu.unique[1:5]))
+try(genes.deg.5 <- rev(genes.deg.5))
+try(genes.deg.10 <- c(genes.deg.BE.unique[1:10],genes.deg.LE.unique[1:10],genes.deg.OE1.unique[1:10],genes.deg.OE2.unique[1:10],genes.deg.NE.unique[1:10],genes.deg.Fib.unique[1:10],genes.deg.SM.unique[1:10],genes.deg.Endo.unique[1:10],genes.deg.Leu.unique[1:10]))
+try(genes.deg.10 <- rev(genes.deg.10))
+
+for (i in ls(pattern="^genes.deg")){
+ try(write.table(get(i),file=paste0("./analysis/deg/",i,".csv"),row.names=TRUE,col.names=NA,append=FALSE,sep=","))
+}
save(list=ls(pattern="sc10x.Stress"),file="./analysis/sc10x.Stress.Rda")
rm(list=ls(pattern="sc10x.Stress"))
diff --git a/r.scripts/sc-TissueMapper_RUN.DS_D17.aggr.R b/r.scripts/sc-TissueMapper_RUN.DS_D17.aggr.R
index cac02a21cb42514e98900e8a21a90ffc2f57dadb..91ae977c98f84b5dfcb9943b4293cccbb35f5625 100755
--- a/r.scripts/sc-TissueMapper_RUN.DS_D17.aggr.R
+++ b/r.scripts/sc-TissueMapper_RUN.DS_D17.aggr.R
@@ -13,6 +13,8 @@ library(viridis)
library(reshape2)
library(NMI)
+options(bitmapType="cairo")
+
source("../r.scripts/sc-TissueMapper.R")
setwd("../")
diff --git a/r.scripts/sc-TissueMapper_RUN.Pd.R b/r.scripts/sc-TissueMapper_RUN.Pd.R
index 7772609db250c04cfb7c6511a9d7f3b344563a11..f55a0bd1024ad202beeb9611e854639aeae5389e 100644
--- a/r.scripts/sc-TissueMapper_RUN.Pd.R
+++ b/r.scripts/sc-TissueMapper_RUN.Pd.R
@@ -11,6 +11,8 @@ library(monocle)
library(dplyr)
library(viridis)
+options(bitmapType="cairo")
+
source("../r.scripts/sc-TissueMapper.R")
#Create folder structure
@@ -407,14 +409,16 @@ scTables(sc10x,i.1="Merge_Epi.dws_St.go_NE",i.2="Merge_Epi.dws_St.go")
genes.deg.Stress <- scDEG(sc10x.Stress,i="Stress",g.1="Stress",g.2="ALL",pct=0.5,t=5)
-genes.deg.Epi <- scDEG(sc10x,i="Lin",g.1="Epi",g.2="St",t=2)
-genes.deg.St <- scDEG(sc10x,i="Lin",g.1="St",g.2="Epi",t=2)
+genes.deg.Epi <- scDEG(sc10x,i="Lin",g.1="Epi",g.2="St",t=0)
+genes.deg.St <- scDEG(sc10x,i="Lin",g.1="St",g.2="Epi",t=0)
genes.deg.BE <- scDEG(sc10x.Epi.NE,i="Epi.dws.sub",g.1="BE",g.2=c("LE","OE1","OE2"),pct=0.25,t=2)
-genes.deg.LE <- scDEG(sc10x.Epi.NE,i="Epi.dws.sub",g.1="LE",g.2=c("BE","LE","OE1"),pct=0.25,t=2)
+genes.deg.LE <- scDEG(sc10x.Epi.NE,i="Epi.dws.sub",g.1="LE",g.2=c("BE","OE1","OE2"),pct=0.25,t=2)
genes.deg.OE1 <- scDEG(sc10x.Epi.NE,i="Epi.dws.sub",g.1="OE1",g.2=c("BE","LE","OE2"),pct=0.25,t=2)
genes.deg.OE2 <- scDEG(sc10x.Epi.NE,i="Epi.dws.sub",g.1="OE2",g.2=c("BE","LE","OE1"),pct=0.25,t=2)
+genes.deg.Epi <- genes.deg.Epi[rownames(genes.deg.Epi) %in% setdiff(rownames(genes.deg.Epi),union(union(union(rownames(genes.deg.BE),rownames(genes.deg.LE)),rownames(genes.deg.OE1)),rownames(genes.deg.OE2))),]
+
genes.deg.NE <- scDEG(sc10x.Epi.NE,i="NE",g.1="NE",g.2="ALL",pct=0.01,t=1)
genes.deg.Fib <- scDEG(sc10x.St,i="Merge_Epi.dws_St.go_NE",g.1="Fib",g.2=c("SM","Endo","Leu"),pct=0.25,t=2)
@@ -422,6 +426,8 @@ genes.deg.SM <- scDEG(sc10x.St,i="Merge_Epi.dws_St.go_NE",g.1="SM",g.2=c("Fib","
genes.deg.Endo <- scDEG(sc10x.St,i="Merge_Epi.dws_St.go_NE",g.1="Endo",g.2=c("Fib","SM","Leu"),pct=0.25,t=2)
genes.deg.Leu <- scDEG(sc10x.St,i="St.go",g.1="Leu",g.2=c("Fib","SM","Endo"),pct=0.25,t=2)
+genes.deg.St <- genes.deg.St[rownames(genes.deg.St) %in% setdiff(rownames(genes.deg.St),union(union(union(rownames(genes.deg.Fib),rownames(genes.deg.SM)),rownames(genes.deg.Endo)),rownames(genes.deg.Leu))),]
+
genes.deg.BE.unique <- setdiff(rownames(genes.deg.BE),Reduce(union,list(rownames(genes.deg.LE),rownames(genes.deg.OE1),rownames(genes.deg.OE2),rownames(genes.deg.NE),rownames(genes.deg.Fib),rownames(genes.deg.SM),rownames(genes.deg.Endo),rownames(genes.deg.Leu))))
genes.deg.LE.unique <- setdiff(rownames(genes.deg.LE),Reduce(union,list(rownames(genes.deg.BE),rownames(genes.deg.OE1),rownames(genes.deg.OE2),rownames(genes.deg.NE),rownames(genes.deg.Fib),rownames(genes.deg.SM),rownames(genes.deg.Endo),rownames(genes.deg.Leu))))
genes.deg.OE1.unique <- setdiff(rownames(genes.deg.OE1),Reduce(union,list(rownames(genes.deg.BE),rownames(genes.deg.LE),rownames(genes.deg.OE2),rownames(genes.deg.NE),rownames(genes.deg.Fib),rownames(genes.deg.SM),rownames(genes.deg.Endo),rownames(genes.deg.Leu))))
diff --git a/r.scripts/sc-TissueMapper_RUN.Pd.StressCompare.R b/r.scripts/sc-TissueMapper_RUN.Pd.StressCompare.R
new file mode 100755
index 0000000000000000000000000000000000000000..fc23ed8ce0e316175feeb4840d48c6b99a85b61e
--- /dev/null
+++ b/r.scripts/sc-TissueMapper_RUN.Pd.StressCompare.R
@@ -0,0 +1,135 @@
+library(methods)
+library(optparse)
+library(Seurat)
+library(readr)
+library(fBasics)
+library(pastecs)
+library(qusage)
+library(RColorBrewer)
+library(VennDiagram)
+library(Cairo)
+
+options(bitmapType="cairo")
+
+if (!dir.exists("../analysis/stress")){
+ dir.create("../analysis/stress")
+}
+
+load("../analysis/sc10x.Stress.Rda")
+sc10x.Stress <- SetAllIdent(object=sc10x.Stress,id="ALL")
+gene.exp <- as.data.frame(as.matrix(sc10x.Stress@raw.data[,colnames(sc10x.Stress@data)]))
+
+genes.stress.go <- read_csv("../genesets/DEG_C2.CGP.M10970.txt")
+genes.stress.go <- genes.stress.go[2:nrow(genes.stress.go),]
+genes.stress.go <- as.list(genes.stress.go)
+
+genes.stress.dws <- read_delim("../genesets/genes.deg.Stress.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
+genes.stress.dws <- genes.stress.dws[1]
+colnames(genes.stress.dws) <- "scDWS.Stress"
+genes.stress.dws <- as.list(genes.stress.dws)
+
+#genes.stress.vdb <- read_delim("./vanderBrink.Stress.mus.tsv","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
+#colnames(genes.stress.vdb) <- "vdBrink.Stress"
+
+genes.stress.vdb <- c("Actg1__chr11","Ankrd1__chr19","Arid5a__chr1","Atf3__chr1","Atf4__chr15","Bag3__chr7","Bhlhe40__chr6","Brd2__chr17","Btg1__chr10","Btg2__chr1","Ccnl1__chr3","Ccrn4l__chr3","Cebpb__chr2","Cebpd__chr16","Cebpg__chr7","Csrnp1__chr9","Cxcl1__chr5","Cyr61__chr3","Dcn__chr10","Ddx3x__chrX","Ddx5__chr11","Des__chr1","Dnaja1__chr4","Dnajb1__chr8","Dnajb4__chr3","Dusp1__chr17","Dusp8__chr7","Egr1__chr18","Egr2__chr10","Eif1__chr11","Eif5__chr12","Erf__chr7","Errfi1__chr4","Fam132b__chr1","Fos__chr12","Fosb__chr7","Fosl2__chr5","Gadd45a__chr6","Gcc1__chr6","Gem__chr4","H3f3b__chr11","Hipk3__chr2","Hsp90aa1__chr12","Hsp90ab1__chr17","Hspa1a__chr17","Hspa1b__chr17","Hspa5__chr2","Hspa8__chr9","Hspb1__chr5","Hsph1__chr5","Id3__chr4","Idi1__chr13","Ier2__chr8","Ier3__chr17","Ifrd1__chr12","Il6__chr5","Irf1__chr11","Irf8__chr8","Itpkc__chr7","Jun__chr4","Junb__chr8","Jund__chr8","Klf2__chr8","Klf4__chr4","Klf6__chr13","Klf9__chr19","Litaf__chr16","Lmna__chr3","Maff__chr15","Mafk__chr5","Mcl1__chr3","Midn__chr10","Mir22hg__chr11","Mt1__chr8","Mt2__chr8","Myadm__chr7","Myc__chr15","Myd88__chr9","Nckap5l__chr15","Ncoa7__chr10","Nfkbia__chr12","Nfkbiz__chr16","Nop58__chr1","Nppc__chr1","Nr4a1__chr15","Odc1__chr12","Osgin1__chr8","Oxnad1__chr14","Pcf11__chr7","Pde4b__chr4","Per1__chr11","Phlda1__chr10","Pnp__chr14","Pnrc1__chr4","Ppp1cc__chr5","Ppp1r15a__chr7","Pxdc1__chr13","Rap1b__chr10","Rassf1__chr9","Rhob__chr12","Rhoh__chr5","Ripk1__chr13","Sat1__chrX","Sbno2__chr10","Sdc4__chr2","Serpine1__chr5","Skil__chr3","Slc10a6__chr5","Slc38a2__chr15","Slc41a1__chr1","Socs3__chr11","Sqstm1__chr11","Srf__chr17","Srsf5__chr12","Srsf7__chr17","Stat3__chr11","Tagln2__chr1","Tiparp__chr3","Tnfaip3__chr10","Tnfaip6__chr2","Tpm3__chr3","Tppp3__chr8","Tra2a__chr6","Tra2b__chr16","Trib1__chr15","Tubb4b__chr2","Tubb6__chr18","Ubc__chr5","Usp2__chr9","Wac__chr18","Zc3h12a__chr4","Zfand5__chr19","Zfp36__chr7","Zfp36l1__chr12","Zfp36l2__chr17","Zyx__chr6","Gadd45g__chr13","Hspe1__chr1","Ier5__chr1","Kcne4__chr1")
+genes.stress.vdb <- gsub("\\__.*","",genes.stress.vdb)
+genes.stress.vdb <- data.frame(vdBrink.Stress=genes.stress.vdb)
+genes.homolog <- read_delim("../genesets/Ensemble.mus-hum.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
+genes.stress.vdb <- list("vdBrink.Stress"=merge(genes.stress.vdb,genes.homolog[,c(2,4)],by.x="vdBrink.Stress",by.y="Gene name")[,2])
+
+venn.diagram(list(go=unlist(genes.stress.go),dws=unlist(genes.stress.dws),vdb=unlist(genes.stress.vdb)),"../analysis/stress/Venn.tiff")
+
+
+for (i in c("go","dws","vdb")){
+ genes.stress=get(paste0("genes.stress.",i))
+
+ gene.stress.pct <- apply(gene.exp,2,function(x) sum(x[rownames(gene.exp) %in% unlist(genes.stress)])/sum(x))
+
+ #histo <- hist(gene.stress.pct,breaks=100,prob=TRUE,plot=TRUE,main="Distribution of Stress Gene Expression in Transcriptome",xlab="% of transcriptome associated to stress genes")
+ #abline(v=.0575,col="red")
+
+ sc10x.Stress <- SetAllIdent(object=sc10x.Stress,id="ALL+Stress")
+ cell.index.stress <- names(sc10x.Stress@ident[sc10x.Stress@ident=="Stress"])
+ cell.index.stress <- which(colnames(gene.exp) %in% cell.index.stress)
+ cell.index.ntstress <- names(sc10x.Stress@ident[sc10x.Stress@ident=="ALL"])
+ cell.index.ntstress <- which(colnames(gene.exp) %in% cell.index.ntstress)
+
+ histo.stress <- hist(gene.stress.pct[cell.index.stress],breaks=seq(0,ceiling(max(gene.stress.pct)*100)/100,0.005),main="Distribution of Stress Gene Expression in Transcriptome",xlab="% of transcriptome associated to stress genes",plot=FALSE)
+ #abline(v=.0575,col="red")
+ histo.ntstress <- hist(gene.stress.pct[cell.index.ntstress],breaks=seq(0,ceiling(max(gene.stress.pct)*100)/100,0.005),main="Distribution of Stress Gene Expression in Transcriptome",xlab="% of transcriptome associated to stress genes",plot=FALSE)
+ #abline(v=.0575,col="red")
+
+ Cairo(paste0("../analysis/stress/Hist.Stress.",i,".png"),width=1000,height=500,bg="white")
+ plot(histo.ntstress$mids,histo.ntstress$density,col=rgb(0,1,0,1/5),xlim=c(0,ceiling(max(gene.stress.pct)*100)/100),ylim=c(0,ceiling(max(histo.stress$density,histo.ntstress$density)/10)*10),type="h",lend="square",lwd=10,xlab="Fraction of transcriptome associated to stress genes",ylab="Density")
+ par(new=TRUE)
+ plot(histo.stress$mids,histo.stress$density,col=rgb(1,0,0,1/5),xlim=c(0,ceiling(max(gene.stress.pct)*100)/100),ylim=c(0,ceiling(max(histo.stress$density,histo.ntstress$density)/10)*10),type="h",lend="square",lwd=10,axes=FALSE,xlab="",ylab="")
+ abline(v=0.0575,col="red")
+ text(0.0575+0.01,(ceiling(max(histo.stress$density,histo.ntstress$density)/10)*10)/4*3+2.5,paste0(round(sum(histo.ntstress$counts[histo.ntstress$breaks>0.035][!is.na(histo.ntstress$counts[histo.ntstress$breaks>0.035])])/sum(histo.ntstress$counts[!is.na(histo.ntstress$counts)])*100),"%"),col="green")
+ text(0.0575-0.01,(ceiling(max(histo.stress$density,histo.ntstress$density)/10)*10)/4*3+2.5,paste0(round(sum(histo.ntstress$counts[histo.ntstress$breaks<=0.035][!is.na(histo.ntstress$counts[histo.ntstress$breaks<=0.035])])/sum(histo.ntstress$counts[!is.na(histo.ntstress$counts)])*100),"%"),col="green")
+ text(0.0575+0.01,(ceiling(max(histo.stress$density,histo.ntstress$density)/10)*10)/4*3-2.5,paste0(round(sum(histo.stress$counts[histo.stress$breaks>0.035][!is.na(histo.stress$counts[histo.stress$breaks>0.035])])/sum(histo.stress$counts[!is.na(histo.stress$counts)])*100),"%"),col="red")
+ text(0.0575-0.01,(ceiling(max(histo.stress$density,histo.ntstress$density)/10)*10)/4*3-2.5,paste0(round(sum(histo.stress$counts[histo.stress$breaks<=0.035][!is.na(histo.stress$counts[histo.stress$breaks<=0.035])])/sum(histo.stress$counts[!is.na(histo.stress$counts)])*100),"%"),col="red")
+ text(0.0575+0.05,(ceiling(max(histo.stress$density,histo.ntstress$density)/10)*10)/4*3+2.5,"Not Stressed",col="green")
+ text(0.0575+0.05,(ceiling(max(histo.stress$density,histo.ntstress$density)/10)*10)/4*3-2.5,"Stressed",col="red")
+ dev.off()
+}
+rm(i)
+rm(genes.stress)
+rm(gene.stress.pct)
+rm(cell.index.stress)
+rm(cell.index.ntstress)
+rm(histo.stress)
+rm(histo.ntstress)
+
+for (cut in c(0.9,0.95)){
+ for (i in c("go","dws","vdb")){
+ genes.stress=get(paste0("genes.stress.",i))
+ sc10x.Stress <- SetAllIdent(object=sc10x.Stress,id="ALL")
+ sc10x.Stress.dta <- as.data.frame(as.matrix(sc10x.Stress@data[rownames(sc10x.Stress@scale.data) %in% unlist(genes.stress),]))
+
+ #Run PCA of subsetted stress genes
+ sc10x.Stress.dta <- t(sc10x.Stress.dta)
+ sc10x.Stress.dta <- sc10x.Stress.dta[,apply(sc10x.Stress.dta,2,var)!=0]
+ sc10x.Stress.dta.pca <- prcomp(sc10x.Stress.dta,center=TRUE,scale.=TRUE)
+ sc10x.Stress.dta.pca <- sc10x.Stress.dta.pca$x[,1:2]
+ colnames(x=sc10x.Stress.dta.pca) <- paste0("Stress",1:2)
+ if (skewness(sc10x.Stress.dta.pca[,1])<0){
+ sc10x.Stress.dta.pca[,1] <- (-sc10x.Stress.dta.pca[,1])
+ }
+ if (skewness(sc10x.Stress.dta.pca[,2])<0){
+ sc10x.Stress.dta.pca[,2] <- (-sc10x.Stress.dta.pca[,2])
+ }
+ sc10x.dta <- sc10x.Stress
+ sc10x.dta <- SetDimReduction(object=sc10x.dta,reduction.type="Stress",slot="cell.embeddings",new.data=sc10x.Stress.dta.pca)
+ sc10x.dta <- SetDimReduction(object=sc10x.dta,reduction.type="Stress",slot="key",new.data="Stress")
+
+ #CDS
+ cdf <- ecdf(GetCellEmbeddings(object=sc10x.dta,reduction.type="Stress",dims.use=1))
+ cut.x <- quantile(cdf,probs=cut)
+
+ assign(i,GetCellEmbeddings(object=sc10x.dta,reduction.type="Stress",dims.use=1))
+ assign(paste0("cut.",i,".",cut),cut.x)
+}}
+rm(cut)
+rm(i)
+rm(genes.stress)
+rm(sc10x.Stress.dta)
+rm(sc10x.Stress.dta.pca)
+rm(sc10x.dta)
+rm(cdf)
+rm(cut.x)
+
+comp <- cbind(vdb,go[match(rownames(vdb),rownames(go))],dws[match(rownames(vdb),rownames(dws))])
+colnames(comp) <- c("vdb","go","dws")
+comp <- data.frame(comp)
+
+Cairo(paste0("../analysis/stress/Stress.vdb.vs.go.png"),width=1000,height=500,bg="white")
+ggplot(comp,aes(x=vdb,y=go))+geom_point(size=0.01)+geom_vline(xintercept=cut.vdb.0.95)+geom_hline(yintercept=cut.go.0.95)+annotate("text",x=max(comp$vdb)/4*3,y=max(comp$go)/4*3,col="red",size=10,fontface=2,label=paste0(round(nrow(comp[comp$vdb>cut.vdb.0.95,][comp[comp$vdb>cut.vdb.0.95,"go"]>cut.go.0.95,])/nrow(comp[comp$vdb>cut.vdb.0.95,])*100,1),"%"))+annotate("text",x=max(comp$vdb)/100,y=max(comp$go)/100,col="green",size=10,fontface=2,label=paste0(round(nrow(comp[comp$vdb<=cut.vdb.0.95,][comp[comp$vdb<=cut.vdb.0.95,"go"]<=cut.go.0.95,])/nrow(comp[comp$vdb<=cut.vdb.0.95,])*100,1),"%"))
+dev.off()
+Cairo(paste0("../analysis/stress/Stress.vdb.vs.dws.png"),width=1000,height=500,bg="white")
+ggplot(comp,aes(x=vdb,y=dws))+geom_point(size=0.01)+geom_vline(xintercept=cut.vdb.0.95)+geom_hline(yintercept=cut.dws.0.95)+annotate("text",x=max(comp$vdb)/4*3,y=max(comp$dws)/4*3,col="red",size=10,fontface=2,label=paste0(round(nrow(comp[comp$vdb>cut.vdb.0.95,][comp[comp$vdb>cut.vdb.0.95,"dws"]>cut.dws.0.95,])/nrow(comp[comp$vdb>cut.vdb.0.95,])*100,1),"%"))+annotate("text",x=max(comp$vdb)/100,y=max(comp$dws)/100,col="green",size=10,fontface=2,label=paste0(round(nrow(comp[comp$vdb<=cut.vdb.0.95,][comp[comp$vdb<=cut.vdb.0.95,"dws"]<=cut.dws.0.95,])/nrow(comp[comp$vdb<=cut.vdb.0.95,])*100,1),"%"))
+dev.off()
+Cairo(paste0("../analysis/stress/Stress.go.vs.dws.png"),width=1000,height=500,bg="white")
+ggplot(comp,aes(x=go,y=dws))+geom_point(size=0.01)+geom_vline(xintercept=cut.go.0.95)+geom_hline(yintercept=cut.dws.0.95)+annotate("text",x=max(comp$go)/4*3,y=max(comp$dws)/4*3,col="red",size=10,fontface=2,label=paste0(round(nrow(comp[comp$go>cut.go.0.95,][comp[comp$go>cut.go.0.95,"dws"]>cut.dws.0.95,])/nrow(comp[comp$go>cut.go.0.95,])*100,1),"%"))+annotate("text",x=max(comp$go)/100,y=max(comp$dws)/100,col="green",size=10,fontface=2,label=paste0(round(nrow(comp[comp$go<=cut.go.0.95,][comp[comp$go<=cut.go.0.95,"dws"]<=cut.dws.0.95,])/nrow(comp[comp$go<=cut.go.0.95,])*100,1),"%"))
+dev.off()
+
+rm(comp)