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Commit 58b3b9db authored by John Lafin's avatar John Lafin
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Update labels to include JUN/FOS epi

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scripts/04_annotation.R
+ 12
− 9
View file @ 58b3b9db
......@@ -84,11 +84,11 @@ annot.list$Epithelia <- c("transitional basal epithelia of urethra",
"transitional intermediate epithelia of urethra",
"squamous intermediate epithelia of urethra",
"luminal epithelia of prostate",
"club epithelia of urethra",
"transitional luminal epithelia of urethra",
"transitional intermediate epithelia of urethra",
"club epithelia of urethra",
"stressed cells",
"stressed cells",
"transitional luminal epithelia of urethra",
"transitional basal (JUN/FOS hi) epithelia of urethra",
"transitional basal (JUN/FOS hi) epithelia of urethra",
"squamous intermediate epithelia of urethra",
"squamous intermediate epithelia of urethra",
"basal epithelia of prostate",
......@@ -96,7 +96,7 @@ annot.list$Epithelia <- c("transitional basal epithelia of urethra",
"basal epithelia of prostate",
"proliferative cells",
"squamous luminal epithelia of urethra",
"stressed cells",
"transitional basal (JUN/FOS hi) epithelia of urethra",
"transitional basal epithelia of urethra",
"basal epithelia of prostate")
annot.list$Leukocyte <- c("T cell",
......@@ -121,11 +121,11 @@ annot.list$Stroma <- c("pericyte",
"periepithelial fibroblast of urethra",
"stressed cell",
"pericyte",
"glia",
"satellite glial cell",
"smooth muscle cell",
"endoneurial fibroblast",
"pericyte",
"glia")
"satellite glial cell")
## Set epithelia and stroma to higher resolutions
Idents(lin.list$Epithelia) <- "RNA_snn_res.1.5"
......@@ -150,7 +150,7 @@ VlnPlot(lin.list$Epithelia, "NE.score", group.by = "orig.ident") +
ggsave(paste0(annotdir, "NE_score_cutoff.png"))
lin.list$Epithelia@meta.data <- lin.list$Epithelia@meta.data %>%
mutate(cellannotation = if_else(NE.score > 0.3, "neuroendocrine cell", cellannotation))
mutate(cellannotation = if_else(NE.score > 0.3, "neuroendocrine epithelia", cellannotation))
## Add ionocytes
VlnPlot(lin.list$Epithelia, "FOXI1", group.by = "orig.ident") +
......@@ -197,13 +197,16 @@ for (lin in names(lin.list)) {
## Define stressed clusters based on violin plots
stressed.cells <- list()
stressed.cells$Epithelia <- c(11,12,20)
stressed.cells$Stroma <- c(2,10,15)
stressed.cells$Endothelia <- c(4,10)
stressed.cells$Leukocyte <- c(4,9)
## Remove stressed clusters and reprocess
for (lin in names(lin.list)) {
if (!(lin %in% names(stressed.cells))) {
Idents(lin.list[[lin]]) <- "cellannotation"
next
}
lin.list[[lin]] <- subset(lin.list[[lin]],
idents = stressed.cells[[lin]],
invert = TRUE)
......
scripts/05_female_only.R
+ 31
− 25
View file @ 58b3b9db
......@@ -64,22 +64,29 @@ lin.list <- subset(seu, subset = Sex == "female") %>%
SplitObject(split.by="Lineage")
## Preprocess each lineage
lin.list <- future_lapply(lin.list, preprocess, default.res="cellannotation")
lin.list <- future_lapply(lin.list, preprocess, default.res="cellannotation", future.seed=TRUE)
# Update annotation -------------------------------------------------------
## Epithelia
Idents(lin.list$Epithelia) <- "RNA_snn_res.0.5"
cluster.ids <- c("0" = "intermediate cell of transitional epithelia",
"1" = "basal cell of transitional epithelia",
"2" = "basal cell of squamous epithelia",
"3" = "intermediate cell of squamous epithelia",
"4" = "club cell",
"5" = "intermediate cell of squamous epithelia",
"6" = "intermediate cell of squamous epithelia",
"7" = "luminal cell of squamous epithelia",
"8" = "proliferative cells",
"9" = "basal cell of transitional epithelia")
Idents(lin.list$Epithelia) <- "RNA_snn_res.1"
cluster.ids <- c("0" = "transitional basal epithelia of urethra",
"1" = "squamous intermediate epithelia of urethra",
"2" = "transitional luminal epithelia of urethra",
"3" = "transitional intermediate epithelia of urethra",
"4" = "transitional basal (JUN/FOS hi) epithelia of urethra",
"5" = "squamous basal epithelia of urethra",
"6" = "transitional intermediate epithelia of urethra",
"7" = "squamous intermediate epithelia of urethra",
"8" = "squamous intermediate epithelia of urethra",
"9" = "squamous luminal epithelia of urethra",
"10" = "proliferative cells",
"11" = "transitional basal epithelia of urethra",
"12" = "squamous luminal epithelia of urethra",
"13" = "transitional basal epithelia of urethra"
)
names(cluster.ids) <- seq(0, length(cluster.ids)-1, 1)
lin.list$Epithelia <- RenameIdents(lin.list$Epithelia, cluster.ids) %>%
StashIdent("cellannotation")
......@@ -91,7 +98,7 @@ lin.list$Epithelia <- AddModuleScore(lin.list$Epithelia,
name = "NE.score")
lin.list$Epithelia@meta.data <- rename(lin.list$Epithelia@meta.data, NE.score = NE.score1)
lin.list$Epithelia@meta.data <- lin.list$Epithelia@meta.data %>%
mutate(cellannotation = if_else(NE.score > 0.3, "neuroendocrine cell", cellannotation))
mutate(cellannotation = if_else(NE.score > 0.3, "neuroendocrine epithelia", cellannotation))
Idents(lin.list$Epithelia) <- "cellannotation"
## Endothelia
......@@ -100,8 +107,8 @@ cluster.ids <- c("0" = "venous endothelia",
"1" = "venous endothelia",
"2" = "venous endothelia",
"3" = "venous endothelia",
"4" = "capillary endothelia",
"5" = "arterial endothelia",
"4" = "arterial endothelia",
"5" = "capillary endothelia",
"6" = "lymphatic endothelia",
"7" = "venous endothelia")
lin.list$Endothelia <- RenameIdents(lin.list$Endothelia, cluster.ids) %>%
......@@ -109,8 +116,8 @@ lin.list$Endothelia <- RenameIdents(lin.list$Endothelia, cluster.ids) %>%
## Leukocytes
Idents(lin.list$Leukocyte) <- "RNA_snn_res.0.4"
cluster.ids <- c("0" = "macrophage",
"1" = "T cell",
cluster.ids <- c("0" = "T cell",
"1" = "macrophage",
"2" = "NK cell",
"3" = "mast cell",
"4" = "B cell",
......@@ -120,9 +127,9 @@ lin.list$Leukocyte <- RenameIdents(lin.list$Leukocyte, cluster.ids) %>%
## Stroma
Idents(lin.list$Stroma) <- "RNA_snn_res.1"
cluster.ids <- c("0" = "smooth muscle cell",
cluster.ids <- c("0" = "minor interstitial fibroblast",
"1" = "pericyte",
"2" = "minor interstiital fibroblast",
"2" = "smooth muscle cell",
"3" = "major interstitial fibroblast",
"4" = "smooth muscle cell",
"5" = "smooth muscle cell",
......@@ -131,12 +138,11 @@ cluster.ids <- c("0" = "smooth muscle cell",
"8" = "periepithelial fibroblast of urethra",
"9" = "smooth muscle cell",
"10" = "endoneurial fibroblast",
"11" = "glial cell",
"11" = "satellite glial cell",
"12" = "pericyte",
"13" = "major interstitial fibroblast",
"14" = "pericyte",
"15" = "smooth muscle cell",
"16" = "glial cell")
"13" = "pericyte",
"14" = "smooth muscle cell",
"15" = "satellite glial cell")
lin.list$Stroma <- RenameIdents(lin.list$Stroma, cluster.ids) %>%
StashIdent("cellannotation")
......@@ -152,7 +158,7 @@ plotdir <- paste0(outdir, "dot_plots/")
dir.create(plotdir, showWarnings=FALSE)
gene.list <- list(
"Epithelia" = strsplit("AKR1C1 AKR1C2 MKI67 TOP2A PIGR LCN2 KRT6A CHGA KRT5 BCAM", split=" ")[[1]],
"Epithelia" = strsplit("AKR1C1 AKR1C2 MKI67 TOP2A PIGR LCN2 KRT6A CHGA KRT5 BCAM JUN FOS", split=" ")[[1]],
"Endothelia" = strsplit("LYVE1 EFNB2 ACKR1 TXNIP VWF", split=" ")[[1]],
"Leukocyte" = strsplit("LYVE1 C1QA CD163 PTPRC IL7R CD8A GZMK HLA-DRA KIT MS4A1 CD79A JCHAIN GNLY GZMB", split = " ")[[1]],
"Stroma" = strsplit("C7 SFRP4 STC1 APOE APOD NGFR THY1 CD36 DES ACTG2 PRUNE2 MCAM BCAM RGS5 DLK1 MYF5 CDH19 GPM6B", split = " ")[[1]]
......
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