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Copy pathDE_svm.R
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DE_svm.R
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# DEPENDENCIES: total_labels
# must have been created from seurat_svm.R file
library(Seurat)
library(dplyr)
library(ggplot2)
library(cowplot)
library(data.table)
integrated<- readRDS(file = "integrated.rds")
#total_labels
cardio <- filter(total_labels, x == "Cardiomyocytes")
cardio["Cells"] <- attr(cardio, "row.names")
cardio_sham<-cardio[ cardio$Cells %like% "sham",]
cardio_sham[,2] <- NULL #Removing the first column
cardio_sham_seurat <- attr(cardio_sham, "row.names")
cardio_mi<-cardio[rownames(cardio) %like% "mi",]
cardio_mi[,2] <- NULL #Removing the first column
cardio_mi_seurat <- attr(cardio_mi, "row.names")
fibro <- filter(total_labels, x == "Fibroblasts" )
#fibro["Cells"] <- attr(cardio, "row.names")
fibro_seurat <- attr(fibro, "row.names")
endo <- filter(total_labels, x == "Endothelial")
endo_seurat <- attr(endo, "row.names")
immun <- filter(total_labels, x == "Immune" )
immun_seurat <- attr(immun, "row.names")
integrated_seurat <- SetIdent(object = integrated,cells = cardio_sham_seurat,value = 'cardio_sham')
integrated_seurat <- SetIdent(object = integrated_seurat,cells = cardio_mi_seurat,value = 'cardio_mi')
integrated_seurat <- SetIdent(object = integrated_seurat,cells = fibro_seurat,value = 'fibro')
integrated_seurat <- SetIdent(object = integrated_seurat,cells = endo_seurat,value = 'endo')
integrated_seurat <- SetIdent(object = integrated_seurat,cells = immun_seurat,value = 'immun')
# Visualization
p1 <- DimPlot(integrated_seurat, reduction = "umap", group.by = "protocol")
p2 <- DimPlot(integrated_seurat, reduction = "umap", label = TRUE)
plot_grid(p1, p2)
DimPlot(integrated_seurat, reduction = "umap", split.by = "protocol")
# Markers
markers_cardio_sham_seurat <- FindMarkers(integrated_seurat, ident.1 = "cardio_sham",only.pos = TRUE)
markers_cardio_mi_seurat <- FindMarkers(integrated_seurat, ident.1 = "cardio_mi",only.pos = TRUE)
markers_fibro_seurat <- FindMarkers(integrated_seurat, ident.1 = "fibro",only.pos = TRUE)
markers_endo_seurat <- FindMarkers(integrated_seurat, ident.1 = "endo",only.pos = TRUE)
markers_immun_seurat <- FindMarkers(integrated_seurat, ident.1 = "immun",only.pos = TRUE)
sham_markers_seurat <- FindMarkers(integrated_seurat, ident.1 = "cardio_sham",ident.2 = "cardio_mi",only.pos = TRUE)
mi_markers_seurat <- FindMarkers(integrated_seurat, ident.1 = "cardio_mi",ident.2 = "cardio_sham",only.pos = TRUE )
# Markers Mast
markers_mast_cardio_sham_seurat <- FindMarkers(integrated_seurat, ident.1 = "cardio_sham", test.use = "MAST",only.pos = TRUE)
markers_mast_cardio_mi_seurat <- FindMarkers(integrated_seurat, ident.1 = "cardio_mi", test.use = "MAST",only.pos = TRUE)
markers_mast_fibro_seurat <- FindMarkers(integrated_seurat, ident.1 = "fibro", test.use = "MAST",only.pos = TRUE)
markers_mast_endo_seurat <- FindMarkers(integrated_seurat, ident.1 = "endo", test.use = "MAST",only.pos = TRUE)
markers_mast_immun_seurat <- FindMarkers(integrated_seurat, ident.1 = "immun", test.use = "MAST")
sham_markers_mast_seurat <- FindMarkers(integrated_seurat, ident.1 = "cardio_sham",ident.2 = "cardio_mi", test.use = "MAST",only.pos = TRUE)
mi_markers_mast_seurat <- FindMarkers(integrated_seurat, ident.1 = "cardio_mi",ident.2 = "cardio_sham", test.use = "MAST",only.pos = TRUE)
library("writexl")
# Markers
m1 <- cbind(" "=rownames(markers_cardio_sham_seurat), markers_cardio_sham_seurat)
#m1 <- m1[order(m1$p_val,decreasing = TRUE),]
write_xlsx(m1,"markers_svm/wilcoxon/markers_cardio_sham_seurat.xlsx")
m2 <- cbind(" "=rownames(markers_cardio_mi_seurat), markers_cardio_mi_seurat)
#m2 <- m2[order(m2$p_val,decreasing = TRUE),]
write_xlsx(m2,"markers_svm/wilcoxon/markers_cardio_mi_seurat.xlsx")
m3 <- cbind(" "=rownames(markers_fibro_seurat), markers_fibro_seurat)
#m3 <- m3[order(m3$p_val,decreasing = TRUE),]
write_xlsx(m3,"markers_svm/wilcoxon/markers_fibro_seurat.xlsx")
m4 <- cbind(" "=rownames(markers_endo_seurat), markers_endo_seurat)
#m4 <- m4[order(m4$p_val,decreasing = TRUE),]
write_xlsx(m4,"markers_svm/wilcoxon/markers_endo_seurat.xlsx")
m5 <- cbind(" "=rownames(markers_immun_seurat), markers_immun_seurat)
#m5 <- m5[order(m5$p_val,decreasing = TRUE),]
write_xlsx(m5,"markers_svm/wilcoxon/markers_immun_seurat.xlsx")
m6 <- cbind(" "=rownames(sham_markers_seurat), sham_markers_seurat)
#m6 <- m6[order(m6$p_val,decreasing = TRUE),]
write_xlsx(m6,"markers_svm/wilcoxon/sham_vs_mi/sham_markers_seurat.xlsx")
m7 <- cbind(" "=rownames(mi_markers_seurat), mi_markers_seurat)
#m7 <- m7[order(m7$p_val,decreasing = TRUE),]
write_xlsx(m7,"markers_svm/wilcoxon/sham_vs_mi/mi_markers_seurat.xlsx")
# Markers Mast ###############################
m1 <- cbind(" "=rownames(markers_mast_cardio_sham_seurat), markers_mast_cardio_sham_seurat)
#m1 <- m1[order(m1$p_val,decreasing = TRUE),]
write_xlsx(m1,"markers_svm/mast/markers_mast_cardio_sham_seurat.xlsx")
m2 <- cbind(" "=rownames(markers_mast_cardio_mi_seurat), markers_mast_cardio_mi_seurat)
#m2 <- m2[order(m2$p_val,decreasing = TRUE),]
write_xlsx(m2,"markers_svm/mast/markers_mast_cardio_mi_seurat.xlsx")
m3 <- cbind(" "=rownames(markers_mast_fibro_seurat), markers_mast_fibro_seurat)
#m3 <- m3[order(m3$p_val,decreasing = TRUE),]
write_xlsx(m3,"markers_svm/mast/markers_mast_fibro_seurat.xlsx")
m4 <- cbind(" "=rownames(markers_mast_endo_seurat), markers_mast_endo_seurat)
#m4 <- m4[order(m4$p_val,decreasing = TRUE),]
write_xlsx(m4,"markers_svm/mast/markers_mast_endo_seurat.xlsx")
m5 <- cbind(" "=rownames(markers_mast_immun_seurat), markers_mast_immun_seurat)
#m5 <- m5[order(m5$p_val,decreasing = TRUE),]
write_xlsx(m5,"markers_svm/mast/markers_mast_immun_seurat.xlsx")
m6 <- cbind(" "=rownames(sham_markers_mast_seurat), sham_markers_mast_seurat)
#m6 <- m6[order(m6$p_val,decreasing = TRUE),]
write_xlsx(m6,"markers_svm/mast/sham_vs_mi/sham_markers_mast_seurat.xlsx")
m7 <- cbind(" "=rownames(mi_markers_mast_seurat), mi_markers_mast_seurat)
#m7 <- m7[order(m7$p_val,decreasing = TRUE),]
write_xlsx(m7,"markers_svm/mast/sham_vs_mi/mi_markers_mast_seurat.xlsx")