From 58b3b9dba5c740af825d713668c7bcd0fd08a39f Mon Sep 17 00:00:00 2001
From: John Lafin <john.lafin@utsouthwestern.edu>
Date: Wed, 12 Feb 2025 16:39:53 -0600
Subject: [PATCH] Update labels to include JUN/FOS epi
---
scripts/04_annotation.R | 21 ++++++++-------
scripts/05_female_only.R | 56 ++++++++++++++++++++++------------------
2 files changed, 43 insertions(+), 34 deletions(-)
diff --git a/scripts/04_annotation.R b/scripts/04_annotation.R
index 467d10f..5e98f6e 100644
--- a/scripts/04_annotation.R
+++ b/scripts/04_annotation.R
@@ -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$Leukocyte <- c(4,9)
## Remove stressed clusters and reprocess
for (lin in names(lin.list)) {
+ if (!(lin %in% names(stressed.cells))) {
+ Idents(lin.list[[lin]]) <- "cellannotation"
+ next
+ }
lin.list[[lin]] <- subset(lin.list[[lin]],
idents = stressed.cells[[lin]],
invert = TRUE)
diff --git a/scripts/05_female_only.R b/scripts/05_female_only.R
index 2a5e2eb..fd6a7e7 100644
--- a/scripts/05_female_only.R
+++ b/scripts/05_female_only.R
@@ -64,22 +64,29 @@ lin.list <- subset(seu, subset = Sex == "female") %>%
SplitObject(split.by="Lineage")
## Preprocess each lineage
-lin.list <- future_lapply(lin.list, preprocess, default.res="cellannotation")
+lin.list <- future_lapply(lin.list, preprocess, default.res="cellannotation", future.seed=TRUE)
# Update annotation -------------------------------------------------------
## Epithelia
-Idents(lin.list$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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