--- a
+++ b/c_VisualizationScript/Visulz_bulkRNA_heatmap.R
@@ -0,0 +1,126 @@
+
+# MESSAGE -----------------------------------------------------------------
+#
+# author: Yulin Lyu
+# email: lvyulin@pku.edu.cn
+#
+# require: R whatever
+#
+# ---
+
+# 1. Load packages --------------------------------------------------------
+
+setwd("exampleData/RNA")
+
+# grammar
+library(tidyverse)
+library(magrittr)
+library(glue)
+library(data.table)
+
+# analysis
+library(DESeq2)
+
+# graphics
+library(ComplexHeatmap)
+library(circlize)
+library(RColorBrewer)
+library(ggsci)
+library(scales)
+
+# 2. Load data ------------------------------------------------------------
+
+vsd <- readRDS("mid/vsd.rds")
+vsdMtx <- assay(vsd)
+
+diffData <- fread("mid/ES_vs_Fib.DEG.csv")
+colnames(diffData)[1] <- "gene"
+
+diffData[is.na(padj), padj := 1][]
+diffData[, p := -log10(padj)][]
+
+# 3. Plot -----------------------------------------------------------------
+
+diffData[, type := "ns"][]
+diffData[log2FoldChange > 3 & padj < 0.05, type := "up"][log2FoldChange < -3 & padj < 0.05, type := "down"][]
+
+upGene <- diffData[order(p, decreasing = T)][type == "up"][1:10, gene]
+downGene <- diffData[order(p, decreasing = T)][type == "down"][1:10, gene]
+
+# heatmap with many genes
+
+diffGene <- diffData[type != "ns", gene]
+geneType <- diffData[type != "ns", type]
+markGene <- c(upGene, downGene)
+
+heatData <- vsdMtx[diffGene, ]
+heatData %<>% apply(1, scale) %>% t() %>% set_colnames(colnames(vsdMtx))
+
+colorFun <- colorRamp2(seq(1.5, -1.5, len = 9), brewer.pal(9, "RdBu"))
+
+pdf("plot/heatmapMany.pdf", width = 6, height = 8)
+
+Heatmap(
+  heatData, col = colorFun, border = T,
+  cluster_rows = T, cluster_columns = T,
+  show_row_names = F, show_column_names = T,
+  show_row_dend = F, show_column_dend = T,
+  column_names_rot = 45,
+  row_split = geneType,
+  column_split = rep(c("Fib", "CiPS", "ES"), each = 2),
+  left_annotation = rowAnnotation(
+    type = anno_block(
+      width = unit(.1, "in"), gp = gpar(fill = pal_nejm()(2)[2:1]))),
+  right_annotation = rowAnnotation(
+    gene = anno_mark(
+      match(markGene, diffGene), markGene,
+      labels_gp = gpar(fontface = "italic", fontsize = 10))),
+  heatmap_legend_param = list(
+    title = "Scaled expression",
+    title_position = "lefttop-rot",
+    legend_height = unit(1.5, "in")),
+  width = unit(3, "in"),
+  height = unit(6, "in")
+)
+
+dev.off()
+
+# heatmap with few genes
+
+setkey(diffData, gene)
+
+usedGene <- c(upGene, downGene)
+geneType <- diffData[usedGene, type]
+
+heatData <- vsdMtx[usedGene, ]
+heatData %<>% apply(1, scale) %>% t() %>% set_colnames(colnames(vsdMtx))
+
+colorFun <- colorRamp2(seq(1.5, -1.5, len = 9), brewer.pal(9, "RdBu"))
+
+pdf("plot/heatmapFew.pdf", width = 6, height = 6)
+
+Heatmap(
+  heatData, col = colorFun, border = F,
+  cluster_rows = T, cluster_columns = T,
+  show_row_names = T, show_column_names = T,
+  show_row_dend = F, show_column_dend = T,
+  column_names_rot = 45,
+  row_names_gp = gpar(fontface = "italic"),
+  row_split = geneType,
+  column_split = rep(c("Fib", "CiPS", "ES"), each = 2),
+  cell_fun = function(j, i, x, y, width, height, fill){
+    grid.rect(x = x, y = y, width = width, height = height, 
+              gp = gpar(col = "white", fill = NA))},
+  left_annotation = rowAnnotation(
+    type = anno_block(
+      width = unit(.1, "in"), gp = gpar(fill = pal_nejm()(2)[2:1]))),
+  heatmap_legend_param = list(
+    title = "Scaled expression",
+    title_position = "lefttop-rot",
+    legend_height = unit(1.5, "in")),
+  width = unit(3, "in"),
+  height = unit(4, "in")
+)
+
+dev.off()
+