R Markdown

差异基因的pheatmap绘图

library(dplyr)
library(pheatmap)
library(tibble)
de_result <- arrange(de_result, desc(abs(log2FoldChange)))

top_de_exp <- dplyr::slice(de_result,1:20)%>%
  select(-c(2:12))%>%
  column_to_rownames(var = 'id')
pheatmap(top_de_exp)

进行优化（类比想象：马云工资和普通人工资

对数据取log（对数）（基因与基因间的表达量，仍可进行比较

pheatmap(log10(top_de_exp + 1))#有些数值为0 ，不能取对数，报错，故+1

进行标准化（同一基因不同样本间，可进行比较。基因之间不能进相比较

pheatmap(top_de_exp,
         scale = 'row',
         )

上色，图裂开

pheatmap(log10(top_de_exp + 1),
         #cluster_rows = F,
         #cluster_cols = F,
         show_colnames = F,#列名不显示
         annotation_col = select(sample_info,stage),
         cutree_rows = 3)

设置stage的颜色

cols <- list(stage = c(S1 = '#ADFF2F', S2 = '#FFFF00',S3 = '#FF6347',S4 = '#FF0000'))
pheatmap(log10(top_de_exp + 1),
         color = colorRampPalette(c("#006400","white","#FF0000"))(100),
         #cluster_rows = F,
         #cluster_cols = F,
         show_colnames = F,#列名不显示
         annotation_col = select(sample_info,stage),
         annotation_colors = cols,
         cutree_rows = 3)