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Strand Lab
sc-TissueMapper
Commits
af6cb761
Commit
af6cb761
authored
Feb 16, 2020
by
Gervaise Henry
🤠
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Change singler to res 5 and fine
parent
dbb4d204
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-14
r.scripts/SingleR.R
r.scripts/SingleR.R
+19
-14
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r.scripts/SingleR.R
View file @
af6cb761
...
@@ -68,22 +68,27 @@ lin.se <- lin.se[common,]
...
@@ -68,22 +68,27 @@ lin.se <- lin.se[common,]
sc10x.se
<-
sc10x.se
[
common
,]
sc10x.se
<-
sc10x.se
[
common
,]
rm
(
common
)
rm
(
common
)
singler.lin
<-
SingleR
(
sc10x.se
,
ref
=
lin.se
,
method
=
"cluster"
,
clusters
=
sc10x.se
$
integrated_snn_res.
0.5
,
labels
=
lin.se
$
label.main
,
BPPARAM
=
MulticoreParam
(
workers
=
10
))
singler.lin
<-
SingleR
(
sc10x.se
,
ref
=
lin.se
,
method
=
"cluster"
,
clusters
=
sc10x.se
$
integrated_snn_res.
5
,
labels
=
lin.se
$
label.fine
,
BPPARAM
=
MulticoreParam
(
workers
=
10
))
sc10x
$
lin
<-
singler.lin
$
labels
[
match
(
sc10x.se
$
integrated_snn_res.
0.
5
,
singler.lin
@
rownames
)]
sc10x
$
lin
<-
singler.lin
$
labels
[
match
(
sc10x.se
$
integrated_snn_res.5
,
singler.lin
@
rownames
)]
#singler.lin <- SingleR(sc10x.se,ref=lin.se,method="single",labels=lin.se$label.main,BPPARAM=MulticoreParam(workers=10))
#singler.lin <- SingleR(sc10x.se,ref=lin.se,method="single",labels=lin.se$label.main,BPPARAM=MulticoreParam(workers=10))
#sc10x$lin <- singler.lin$labels
#sc10x$lin <- singler.lin$labels
if
(
opt
$
s
==
"hu"
){
sc10x
$
lin
[
sc10x
$
lin
%in%
unique
(
lin.se
@
colData
[
lin.se
@
colData
[,
"label.main"
]
%in%
c
(
sc10x
$
lin
[
sc10x
$
lin
%in%
c
(
"DC"
,
"B_cell"
,
"Neutrophil"
,
"T_cells"
,
"Monocyte"
,
"Macrophage"
,
"NK_cell"
,
"Neutrophils"
,
"CMP"
,
"GMP"
,
"MEP"
,
"Myelocyte"
,
"Pre-B_cell_CD34-"
,
"Pro-B_cell_CD34+"
,
"Pro-Myelocyte"
,
"HSC_-G-CSF"
,
"HSC_CD34+"
)]
<-
"Leu"
c
(
"DC"
,
"B_cell"
,
"Neutrophil"
,
"T_cells"
,
"Monocyte"
,
"Macrophage"
,
"NK_cell"
,
"Neutrophils"
,
"CMP"
,
"GMP"
,
"MEP"
,
"Myelocyte"
,
"Pre-B_cell_CD34-"
,
"Pro-B_cell_CD34+"
,
"Pro-Myelocyte"
,
"HSC_-G-CSF"
,
"HSC_CD34+"
),
sc10x
$
lin
[
sc10x
$
lin
%in%
c
(
"Endothelial_cells"
,
"Erythroblast"
,
"Platelets"
)]
<-
"Endo"
c
(
"Macrophages"
,
"Monocytes"
,
"B cells"
,
"DC"
,
"Eosinophils"
,
"Neutrophils"
,
"T cells"
,
"ILC"
,
"NK cells"
,
"Basophils"
,
"Mast cells"
,
"Tgd"
,
"NKT"
,
"B cells, pro"
,
"Microglia"
)
sc10x
$
lin
[
sc10x
$
lin
%in%
c
(
"Smooth_muscle_cells"
,
"Fibroblasts"
,
"Chondrocytes"
,
"Osteoblasts"
,
"MSC"
,
"Tissue_stem_cells"
)]
<-
"FMSt"
),
c
(
"label.main"
,
"label.fine"
)])
$
label.fine
]
<-
"Leu"
sc10x
$
lin
[
sc10x
$
lin
%in%
c
(
"Epithelial_cells"
,
"Keratinocytes"
,
"Neuroepithelial_cell"
)]
<-
"Epi"
sc10x
$
lin
[
sc10x
$
lin
%in%
unique
(
lin.se
@
colData
[
lin.se
@
colData
[,
"label.main"
]
%in%
c
(
}
else
if
(
opt
$
s
==
"mu"
){
c
(
"Endothelial_cells"
,
"Erythroblast"
,
"Platelets"
),
sc10x
$
lin
[
sc10x
$
lin
%in%
c
(
"Macrophages"
,
"Monocytes"
,
"B cells"
,
"DC"
,
"Eosinophils"
,
"Neutrophils"
,
"T cells"
,
"ILC"
,
"NK cells"
,
"Basophils"
,
"Mast cells"
,
"Tgd"
,
"NKT"
,
"B cells, pro"
,
"Microglia"
)]
<-
"Leu"
c
(
"Endothelial cells"
)
sc10x
$
lin
[
sc10x
$
lin
%in%
c
(
"Endothelial cells"
)]
<-
"Endo"
),
c
(
"label.main"
,
"label.fine"
)])
$
label.fine
]
<-
"Endo"
sc10x
$
lin
[
sc10x
$
lin
%in%
c
(
"Stromal cells"
,
"Fibroblasts"
)]
<-
"FMSt"
sc10x
$
lin
[
sc10x
$
lin
%in%
unique
(
lin.se
@
colData
[
lin.se
@
colData
[,
"label.main"
]
%in%
c
(
sc10x
$
lin
[
sc10x
$
lin
%in%
c
(
"Epithelial cells"
)]
<-
"Epi"
c
(
"Smooth_muscle_cells"
,
"Fibroblasts"
,
"Chondrocytes"
,
"Osteoblasts"
,
"MSC"
,
"Tissue_stem_cells"
),
}
c
(
"Stromal cells"
,
"Fibroblasts"
)
#DimPlot(sc10x,group.by="lin",reduction="umap",label=TRUE,repel=TRUE)+theme(legend.position="none")
),
c
(
"label.main"
,
"label.fine"
)])
$
label.fine
]
<-
"FMSt"
sc10x
$
lin
[
sc10x
$
lin
%in%
unique
(
lin.se
@
colData
[
lin.se
@
colData
[,
"label.main"
]
%in%
c
(
c
(
"Epithelial_cells"
,
"Keratinocytes"
,
"Neuroepithelial_cell"
),
c
(
"Epithelial cells"
)
),
c
(
"label.main"
,
"label.fine"
)])
$
label.fine
]
<-
"Epi"
DimPlot
(
sc10x
,
group.by
=
"lin"
,
reduction
=
"umap"
,
label
=
TRUE
,
repel
=
TRUE
)
+
theme
(
legend.position
=
"none"
)
Idents
(
sc10x
)
<-
"lin"
Idents
(
sc10x
)
<-
"lin"
sc10x.epi
<-
subset
(
sc10x
,
idents
=
"Epi"
)
sc10x.epi
<-
subset
(
sc10x
,
idents
=
"Epi"
)
...
...
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