GSE84563

GSE84563

Kidney MSC perfused (4) vs non-perfused (5)

Efferocytosis

MSC perfused vs. Control

Note merged Gene Symbol – Probe ID as some probes map to same transcript

cts <- as.data.frame(counts[SPL_CTRL$Row.names,])
colnames(cts) <- c(rep("CTRL", 5), rep("MSC", 4))

SPL_CTRL$probe <- paste0(SPL_CTRL$GENE_SYMBOL, "--", SPL_CTRL$Row.names)

cts <- t(cts)
cts <- scale(cts, center=T, scale = T)
cts <- t(cts)

SPL_CTRL <- SPL_CTRL[,c(1, 9)]
cts <- merge(cts, SPL_CTRL, by.x = 0, by.y= "Row.names")

## Warning in merge.data.frame(as.data.frame(x), as.data.frame(y), ...): column
## names 'CTRL', 'CTRL', 'CTRL', 'CTRL', 'MSC', 'MSC', 'MSC' are duplicated in the
## result

cts <- cts[,2:11]
cts <- tibble::column_to_rownames(cts, "probe")

annot_col <- data.frame(row.names = colnames(cts), status = factor(c(rep("CTRL", 5), rep("MSC", 4))))

cols <- c("blue", "red")
names(cols) <- c("CTRL", "MSC")
annot_colors <- list(status = cols)

library(viridis)

## Loading required package: viridisLite

pheatmap::pheatmap(cts, cluster_cols = F, cluster_rows = T, show_rownames = T,
                   show_colnames = T, annotation_col = annot_col,
                   annotation_colors = annot_colors,
                   col = hcl.colors(100, "Purple-Green",rev=F),
                   main = "DE Efferocytosis MSC v CTRL\nP.Value <= 0.05",
                   cutree_cols = 2)

Fibrosis

MSC perfused vs. Control