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Commit 792f5605 authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Change post stress PC cutoff to 80%

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r.scripts/sc-TissueMapper_RUN.D.R
+ 3
− 3
View file @ 792f5605
......@@ -91,11 +91,11 @@ option_list=list(
make_option("--ly",action="store",default=0.5,type='numeric',help="y low threshold for hvg selection"),
make_option("--cc",action="store",default=TRUE,type='logical',help="Scale cell cycle?"),
make_option("--pc",action="store",default=25,type='integer',help="Number of PCs to cacluate"),
make_option("--hpc",action="store",default=0.75,type='numeric',help="Max variance cutoff for PCs to use, pre-stress"),
make_option("--hpc",action="store",default=0.8,type='numeric',help="Max variance cutoff for PCs to use, pre-stress"),
make_option("--res.prestress",action="store",default=1,type='numeric',help="Resolution to cluster, pre-stress"),
make_option("--st",action="store",default="TRUE",type='logical',help="Remove stressed cells?"),
make_option("--stg",action="store",default="dws",type='character',help="Geneset to use for stress ID"),
make_option("--hpc.poststress",action="store",default=0.85,type='numeric',help="Max variance cutoff for PCs to use, post-stress"),
make_option("--hpc.poststress",action="store",default=0.8,type='numeric',help="Max variance cutoff for PCs to use, post-stress"),
make_option("--res.poststress",action="store",default=0.5,type='numeric',help="Resolution to cluster, post-stress"),
make_option("--ds",action="store",default=0,type='integer',help="Number of cells to downsample"),
make_option("--hpc.epi",action="store",default=0.75,type='numeric',help="Max variance cutoff for PCs to use, Epi"),
......@@ -203,7 +203,7 @@ if (any(levels(sc10x@ident)=="Unknown")){
#rm(results)
sc10x.Epi <- scCluster(sc10x.Epi,pc.use=pc.use.poststress,res.use=0.1,folder="epi")
sc10x.Epi <- scCluster(sc10x.Epi,pc.use=pc.use.poststress,res.use=0.2,folder="epi")
sc10x.Epi <- scCluster(sc10x.Epi,pc.use=pc.use.poststress,res.use=0.5,folder="epi")
sc10x.Epi <- scCluster(sc10x.Epi,pc.use=pc.use.poststress,res.use=opt$res.epi,folder="epi")
gene.set1 <- read_delim("./genesets/genes.deg.BE.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
......
r.scripts/sc-TissueMapper_RUN.D17.R
+ 3
− 3
View file @ 792f5605
......@@ -88,11 +88,11 @@ option_list=list(
make_option("--ly",action="store",default=0.5,type='numeric',help="y low threshold for hvg selection"),
make_option("--cc",action="store",default=TRUE,type='logical',help="Scale cell cycle?"),
make_option("--pc",action="store",default=25,type='integer',help="Number of PCs to cacluate"),
make_option("--hpc",action="store",default=0.75,type='numeric',help="Max variance cutoff for PCs to use, pre-stress"),
make_option("--hpc",action="store",default=0.8,type='numeric',help="Max variance cutoff for PCs to use, pre-stress"),
make_option("--res.prestress",action="store",default=1,type='numeric',help="Resolution to cluster, pre-stress"),
make_option("--st",action="store",default="TRUE",type='logical',help="Remove stressed cells?"),
make_option("--stg",action="store",default="go",type='character',help="Geneset to use for stress ID"),
make_option("--hpc.poststress",action="store",default=0.85,type='numeric',help="Max variance cutoff for PCs to use, post-stress"),
make_option("--hpc.poststress",action="store",default=0.8,type='numeric',help="Max variance cutoff for PCs to use, post-stress"),
make_option("--res.poststress",action="store",default=0.5,type='numeric',help="Resolution to cluster, post-stress"),
make_option("--ds",action="store",default=0,type='integer',help="Number of cells to downsample"),
make_option("--hpc.epi",action="store",default=0.75,type='numeric',help="Max variance cutoff for PCs to use, Epi"),
......@@ -181,7 +181,7 @@ if (any(levels(sc10x@ident)=="Unknown")){
#rm(results)
sc10x.Epi <- scCluster(sc10x.Epi,pc.use=pc.use.poststress,res.use=0.1,folder="epi")
sc10x.Epi <- scCluster(sc10x.Epi,pc.use=pc.use.poststress,res.use=0.2,folder="epi")
sc10x.Epi <- scCluster(sc10x.Epi,pc.use=pc.use.poststress,res.use=0.5,folder="epi")
sc10x.Epi <- scCluster(sc10x.Epi,pc.use=pc.use.poststress,res.use=opt$res.epi,folder="epi")
gene.set1 <- read_delim("./genesets/DEG_BE_5FC.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
......
r.scripts/sc-TissueMapper_RUN.D27.R
+ 3
− 3
View file @ 792f5605
......@@ -88,11 +88,11 @@ option_list=list(
make_option("--ly",action="store",default=0.5,type='numeric',help="y low threshold for hvg selection"),
make_option("--cc",action="store",default=TRUE,type='logical',help="Scale cell cycle?"),
make_option("--pc",action="store",default=25,type='integer',help="Number of PCs to cacluate"),
make_option("--hpc",action="store",default=0.75,type='numeric',help="Max variance cutoff for PCs to use, pre-stress"),
make_option("--hpc",action="store",default=0.8,type='numeric',help="Max variance cutoff for PCs to use, pre-stress"),
make_option("--res.prestress",action="store",default=1,type='numeric',help="Resolution to cluster, pre-stress"),
make_option("--st",action="store",default="TRUE",type='logical',help="Remove stressed cells?"),
make_option("--stg",action="store",default="dws",type='character',help="Geneset to use for stress ID"),
make_option("--hpc.poststress",action="store",default=0.85,type='numeric',help="Max variance cutoff for PCs to use, post-stress"),
make_option("--hpc.poststress",action="store",default=0.80,type='numeric',help="Max variance cutoff for PCs to use, post-stress"),
make_option("--res.poststress",action="store",default=0.5,type='numeric',help="Resolution to cluster, post-stress"),
make_option("--ds",action="store",default=0,type='integer',help="Number of cells to downsample"),
make_option("--hpc.epi",action="store",default=0.75,type='numeric',help="Max variance cutoff for PCs to use, Epi"),
......@@ -183,7 +183,7 @@ if (any(levels(sc10x@ident)=="Unknown")){
#rm(results)
sc10x.Epi <- scCluster(sc10x.Epi,pc.use=pc.use.poststress,res.use=0.1,folder="epi")
sc10x.Epi <- scCluster(sc10x.Epi,pc.use=pc.use.poststress,res.use=0.2,folder="epi")
sc10x.Epi <- scCluster(sc10x.Epi,pc.use=pc.use.poststress,res.use=0.5,folder="epi")
sc10x.Epi <- scCluster(sc10x.Epi,pc.use=pc.use.poststress,res.use=opt$res.epi,folder="epi")
gene.set1 <- read_delim("./genesets/genes.deg.BE.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
......
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