加载上一步的数据

    1. rm(list = ls()) 
    2. library(ggplot2)
    3. library(tinyarray)
    4. load("TCGA-HNSC.Rdata")
    5. load("TCGA-HNSC_DEG.Rdata")
    6. exp[1:4,1:4]
    7. ncol(exp)

    去除文库大小的影响

    1. # cpm 去除文库大小的影响
    2. library(edgeR)
    3. dat = log2(cpm(exp)+1)
    4. pca.plot = draw_pca(dat,Group);pca.plot
    5. save(pca.plot,file = paste0(proj,"_pcaplot.Rdata"))

    挑选差异性比较大的“up”和”down”行

    1. cg1 = rownames(DEG1)[DEG1$change !="NOT"]
    2. cg2 = rownames(DEG2)[DEG2$change !="NOT"]
    3. cg3 = rownames(DEG3)[DEG3$change !="NOT"]

    画热图

    1. h1 = draw_heatmap(dat[cg1,],Group,n_cutoff = 2)
    2. h2 = draw_heatmap(dat[cg2,],Group,n_cutoff = 2)
    3. h3 = draw_heatmap(dat[cg3,],Group,n_cutoff = 2)

    画火山图

    1. logFC_t = 2
    2. pvalue_t = 0.05
    3. v1 = draw_volcano(DEG1,pkg = 1,logFC_cutoff = logFC_t)
    4. v2 = draw_volcano(DEG2,pkg = 2,logFC_cutoff = logFC_t)
    5. v3 = draw_volcano(DEG3,pkg = 3,logFC_cutoff = logFC_t)

    拼图加导出

    1. library(patchwork)
    2. (h1 + h2 + h3) / (v1 + v2 + v3) +plot_layout(guides = 'collect') &theme(legend.position = "none")
    3. ggsave(paste0(proj,"_heat_vo.png"),width = 15,height = 10)