Skip to content
GitLab
Menu
Projects
Groups
Snippets
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Sign in / Register
Toggle navigation
Menu
Open sidebar
Strand Lab
sc-TissueMapper
Commits
8a31b27b
Commit
8a31b27b
authored
May 13, 2019
by
Gervaise Henry
🤠
Browse files
Add/update singler scmatch code
parent
7a6eac0e
Changes
5
Hide whitespace changes
Inline
Side-by-side
genesets/cibersort.rda
View file @
8a31b27b
No preview for this file type
r.scripts/SingleR.R
0 → 100644
View file @
8a31b27b
load
(
"./genesets/scDWS.250.rda"
)
load
(
"./genesets/cibersort.rda"
)
singler
=
CreateSinglerObject
(
GetAssayData
(
sc10x
,
assay
=
"RNA"
),
annot
=
NULL
,
"PdPbPc_deep"
,
min.genes
=
0
,
technology
=
"10X"
,
species
=
"Human"
,
citation
=
""
,
ref.list
=
list
(
scDWS.250
),
normalize.gene.length
=
F
,
variable.genes
=
"de"
,
fine.tune
=
T
,
do.signatures
=
T
,
clusters
=
NULL
,
do.main.types
=
T
,
reduce.file.size
=
T
,
numCores
=
SingleR.numCores
)
cells.epi
<-
names
(
singler
$
singler
[[
1
]]
$
SingleR.single.main
$
labels
[
singler
$
singler
[[
1
]]
$
SingleR.single.main
$
labels
[,
1
]
==
"Epi"
,])
cells.fmst
<-
names
(
singler
$
singler
[[
1
]]
$
SingleR.single.main
$
labels
[
singler
$
singler
[[
1
]]
$
SingleR.single.main
$
labels
[,
1
]
==
"FMSt"
,])
cells.endo
<-
names
(
singler
$
singler
[[
1
]]
$
SingleR.single.main
$
labels
[
singler
$
singler
[[
1
]]
$
SingleR.single.main
$
labels
[,
1
]
==
"Endo"
,])
cells.st
<-
c
(
cells.fmst
,
cells.endo
)
cells.leu
<-
names
(
singler
$
singler
[[
1
]]
$
SingleR.single.main
$
labels
[
singler
$
singler
[[
1
]]
$
SingleR.single.main
$
labels
[,
1
]
==
"Leu"
,])
cells.be
<-
names
(
singler
$
singler
[[
1
]]
$
SingleR.single.main
$
labels
[
singler
$
singler
[[
1
]]
$
SingleR.single
$
labels
[,
1
]
==
"BE"
,])
cells.le
<-
names
(
singler
$
singler
[[
1
]]
$
SingleR.single.main
$
labels
[
singler
$
singler
[[
1
]]
$
SingleR.single
$
labels
[,
1
]
==
"LE"
,])
cells.hillock
<-
names
(
singler
$
singler
[[
1
]]
$
SingleR.single.main
$
labels
[
singler
$
singler
[[
1
]]
$
SingleR.single
$
labels
[,
1
]
==
"Hillock"
,])
cells.club
<-
names
(
singler
$
singler
[[
1
]]
$
SingleR.single.main
$
labels
[
singler
$
singler
[[
1
]]
$
SingleR.single
$
labels
[,
1
]
==
"Club"
,])
cells.ne
<-
names
(
singler
$
singler
[[
1
]]
$
SingleR.single.main
$
labels
[
singler
$
singler
[[
1
]]
$
SingleR.single
$
labels
[,
1
]
==
"NE"
,])
cells.fib
<-
names
(
singler
$
singler
[[
1
]]
$
SingleR.single.main
$
labels
[
singler
$
singler
[[
1
]]
$
SingleR.single
$
labels
[,
1
]
==
"Fib"
,])
cells.sm
<-
names
(
singler
$
singler
[[
1
]]
$
SingleR.single.main
$
labels
[
singler
$
singler
[[
1
]]
$
SingleR.single
$
labels
[,
1
]
==
"SM"
,])
Idents
(
sc10x
,
cells
=
cells.epi
)
<-
"Epi"
Idents
(
sc10x
,
cells
=
cells.fmst
)
<-
"FMSt"
Idents
(
sc10x
,
cells
=
cells.endo
)
<-
"Endo"
Idents
(
sc10x
,
cells
=
cells.leu
)
<-
"Leu"
sc10x
$
lin
<-
Idents
(
sc10x
)
sc10x.epi
<-
subset
(
sc10x
,
idents
=
"Epi"
)
sc10x.fmst
<-
subset
(
sc10x
,
idents
=
"FMSt"
)
sc10x.st
<-
subset
(
sc10x
,
idents
=
c
(
"FMSt"
,
"Endo"
))
sc10x.leu
<-
subset
(
sc10x
,
idents
=
"Leu"
)
Idents
(
sc10x.epi
,
cells
=
cells.be
)
<-
"BE"
Idents
(
sc10x.epi
,
cells
=
cells.le
)
<-
"LE"
Idents
(
sc10x.epi
,
cells
=
cells.hillock
)
<-
"Hillock"
Idents
(
sc10x.epi
,
cells
=
cells.club
)
<-
"Club"
Idents
(
sc10x.epi
,
cells
=
cells.ne
)
<-
"NE"
sc10x.epi
$
epi.pops
<-
Idents
(
sc10x.epi
)
Idents
(
sc10x.fmst
,
cells
=
cells.fib
)
<-
"Fib"
Idents
(
sc10x.fmst
,
cells
=
cells.sm
)
<-
"SM"
sc10x.fmst
$
fmst.pops
<-
Idents
(
sc10x.fmst
)
Idents
(
sc10x.st
,
cells
=
cells.fib
)
<-
"Fib"
Idents
(
sc10x.st
,
cells
=
cells.sm
)
<-
"SM"
Idents
(
sc10x.st
,
cells
=
cells.endo
)
<-
"Endo"
sc10x.st
$
st.pops
<-
Idents
(
sc10x.st
)
results
<-
scPC
(
sc10x.epi
,
pc
=
100
,
hpc
=
0.9
,
file
=
"epi"
,
print
=
"2"
)
sc10x.epi
<-
results
[[
1
]]
pc.use.epi
<-
results
[[
2
]]
rm
(
results
)
sc10x.epi
<-
scCluster
(
sc10x.epi
,
res
=
res
,
red
=
"pca"
,
dim
=
pc.use.epi
,
print
=
"2"
,
folder
=
"epi"
)
results
<-
scPC
(
sc10x.fmst
,
pc
=
100
,
hpc
=
0.9
,
file
=
"fmst"
,
print
=
"2"
)
sc10x.fmst
<-
results
[[
1
]]
pc.use.fmst
<-
results
[[
2
]]
rm
(
results
)
sc10x.fmst
<-
scCluster
(
sc10x.fmst
,
res
=
res
,
red
=
"pca"
,
dim
=
pc.use.st
,
print
=
"2"
,
folder
=
"fmst"
)
results
<-
scPC
(
sc10x.st
,
pc
=
100
,
hpc
=
0.9
,
file
=
"st"
,
print
=
"2"
)
sc10x.st
<-
results
[[
1
]]
pc.use.st
<-
results
[[
2
]]
rm
(
results
)
sc10x.st
<-
scCluster
(
sc10x.st
,
res
=
res
,
red
=
"pca"
,
dim
=
pc.use.st
,
print
=
"2"
,
folder
=
"st"
)
results
<-
scPC
(
sc10x.leu
,
pc
=
100
,
hpc
=
0.9
,
file
=
"leu"
,
print
=
"2"
)
sc10x.leu
<-
results
[[
1
]]
pc.use.leu
<-
results
[[
2
]]
rm
(
results
)
sc10x.leu
<-
scCluster
(
sc10x.leu
,
res
=
res
,
red
=
"pca"
,
dim
=
pc.use.leu
,
print
=
"2"
,
folder
=
"leu.lin"
)
singler.leu
=
CreateSinglerObject
(
GetAssayData
(
sc10x.leu
,
assay
=
"RNA"
),
annot
=
NULL
,
"PdPbPc_deep"
,
min.genes
=
0
,
technology
=
"10X"
,
species
=
"Human"
,
citation
=
""
,
ref.list
=
list
(
cibersort
),
normalize.gene.length
=
F
,
variable.genes
=
"de"
,
fine.tune
=
T
,
do.signatures
=
T
,
clusters
=
NULL
,
do.main.types
=
T
,
reduce.file.size
=
T
,
numCores
=
SingleR.numCores
)
save
(
singler
,
file
=
'./analysis/singler_object.RData'
)
\ No newline at end of file
r.scripts/scmatch.R
0 → 100644
View file @
8a31b27b
write.csv
(
GetAssayData
(
sc10x
,
assay
=
"RNA"
),
file
=
paste0
(
"./analysis/"
,
project.name
,
".csv"
))
r.scripts/singler.R
View file @
8a31b27b
...
...
@@ -2,17 +2,17 @@
# load("./genesets/scDWS.100.rda")
# load("./genesets/scDWS.200.rda")
load
(
"./genesets/scDWS.250.rda"
)
load
(
"./genesets/scDWS.lin.rda"
)
load
(
"./genesets/scDWS.epi.rda"
)
load
(
"./genesets/scDWS.fmst.rda"
)
#
load("./genesets/scDWS.lin.rda")
#
load("./genesets/scDWS.epi.rda")
#
load("./genesets/scDWS.fmst.rda")
load
(
"./genesets/cibersort.rda"
)
load
(
"./genesets/blueprint_encode.rda"
)
load
(
"./genesets/hpca.rda"
)
singler
=
CreateSinglerObject
(
GetAssayData
(
object
=
sc10x
),
annot
=
NULL
,
"PdPbPc_deep"
,
min.genes
=
0
,
singler
=
CreateSinglerObject
(
GetAssayData
(
sc10x
,
assay
=
"RNA"
),
annot
=
NULL
,
"PdPbPc_deep"
,
min.genes
=
0
,
technology
=
"10X"
,
species
=
"Human"
,
citation
=
""
,
ref.list
=
list
(
cibersort
),
normalize.gene.length
=
F
,
variable.genes
=
"de"
,
fine.tune
=
T
,
do.signatures
=
T
,
clusters
=
NULL
,
do.main.types
=
T
,
ref.list
=
list
(
scDWS.250
,
cibersort
,
blueprint_encode
),
normalize.gene.length
=
F
,
variable.genes
=
"de"
,
fine.tune
=
F
,
do.signatures
=
T
,
clusters
=
NULL
,
do.main.types
=
T
,
reduce.file.size
=
T
,
numCores
=
SingleR.numCores
)
singler
$
seurat
<-
sc10x
...
...
@@ -21,7 +21,7 @@ singler$meta.data$ALL.POPS <- sc10x$ALL.POPS
singler
$
meta.data
$
xy
<-
sc10x
[[
"umap"
]]
@
cell.embeddings
save
(
singler
,
file
=
'./analysis/singler_object.RData'
)
save
(
singler
,
file
=
'./analysis/singler_
test
object.RData'
)
p
<-
SingleR.PlotTsne
(
singler
$
singler
[[
1
]]
$
SingleR.single
,
singler
$
meta.data
$
xy
)
...
...
@@ -119,3 +119,4 @@ rm(gene.set)
save
(
sc10x
,
file
=
paste0
(
"./analysis/"
,
project.name
,
".RData"
))
save.image
(
file
=
"./analysis/Data.RData"
)
r.scripts/singler.create.ref.R
View file @
8a31b27b
library
(
tidyverse
)
library
(
readxl
)
library
(
genefilter
)
library
(
jsonlite
)
library
(
SingleR
)
load
(
"/work/urology/ghenry/RNA-Seq/SingleCell/PIPELINE/RUN/Pd/PUBLISH/Pd/sc-TissueMapper_Pr/analysis/sc10x.Rda"
)
sc10x
<-
UpdateSeuratObject
(
sc10x
)
...
...
@@ -148,9 +151,42 @@ types = as.character(colnames(cibersort))
main_types
=
cibersort.main
ref
=
list
(
name
=
name
,
data
=
expr
,
types
=
types
,
main_types
=
main_types
)
ref
$
de.genes
=
CreateVariableGeneSet
(
expr
,
types
,
2
00
)
ref
$
de.genes.main
=
CreateVariableGeneSet
(
expr
,
main_types
,
3
00
)
ref
$
de.genes
=
CreateVariableGeneSet
(
expr
,
types
,
3
00
)
ref
$
de.genes.main
=
CreateVariableGeneSet
(
expr
,
main_types
,
5
00
)
cibersort
<-
ref
save
(
cibersort
,
file
=
'./genesets/cibersort.rda'
)
#fantom5 <- read.csv("./genesets/9606_symbol.csv")
fantom5
<-
read_csv
(
"./genesets/9606_symbol.csv"
)
fantom5
<-
as_data_frame
(
as.matrix
(
fantom5
))
fantom5
<-
column_to_rownames
(
fantom5
,
var
=
"symbol"
)
colnames
(
fantom5
)
<-
gsub
(
"\\.."
,
""
,
colnames
(
fantom5
))
fantom5.main.oto
<-
read_json
(
"./genesets/human_samples_oto.txt"
,
simplifyVector
=
TRUE
)
# fantom5.main.oto <- lapply(fantom5.main.oto,function(y) gsub(":",".",y))
# fantom5.main.oto <- lapply(fantom5.main.oto,function(y) gsub("-",".",y))
# fantom5.main.oto <- lapply(fantom5.main.oto,function(y) gsub(" ",".",y))
fantom5.main.oto
<-
lapply
(
fantom5.main.oto
,
function
(
x
)
gsub
(
"\\.."
,
""
,
x
))
fantom5
<-
fantom5
[,
!
(
colnames
(
fantom5
)
%in%
unlist
(
unname
(
unlist
((
fantom5.main.oto
[
grep
(
"DOID"
,
names
(
fantom5.main.oto
))])))))]
fantom5
<-
fantom5
[,
!
(
colnames
(
fantom5
)
%in%
unlist
(
unname
(
unlist
((
fantom5.main.oto
[
grep
(
"UBERON"
,
names
(
fantom5.main.oto
))])))))]
fantom5.main
<-
colnames
(
fantom5
)
name
=
'fantom5'
expr
<-
mapply
(
fantom5
,
FUN
=
as.numeric
)
expr
<-
matrix
(
data
=
expr
,
ncol
=
ncol
(
fantom5
),
nrow
=
nrow
(
fantom5
))
rownames
(
expr
)
<-
rownames
(
fantom5
)
colnames
(
expr
)
<-
colnames
(
fantom5
)
types
=
as.character
(
colnames
(
fantom5
))
main_types
=
fantom5.main
ref
=
list
(
name
=
name
,
data
=
expr
,
types
=
types
,
main_types
=
main_types
)
ref
$
de.genes
=
CreateVariableGeneSet
(
expr
,
types
,
200
)
ref
$
de.genes.main
=
CreateVariableGeneSet
(
expr
,
main_types
,
300
)
fantom5
<-
ref
save
(
fantom5
,
file
=
'./genesets/fantom5.rda'
)
\ No newline at end of file
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment