【生信技能树】2019-12-28作业1：复现富集分析的5幅图

Jimmy老师今天发在群里的作业：

公众号文章地址：https://mp.weixin.qq.com/s/MnoT1zL8r0nr2ayBsBZgsQ
y叔为clusterprofile包写的书：https://yulab-smu.github.io/clusterProfiler-book/
所以作业就是复现富集分析的几个图。

rm(list = ls())
options(stringsAsFactors = F)
gene_up <- read.table("up_gene.txt",sep = '\n')
colnames(gene_up) <- "SYMBOL"
nrow(gene_up)
#[1] 120  ##上调基因数量

##基因多名情况取第1个名字
gene_up$SYMBOL <- apply(gene_up,1,function(x) {
  trimws(strsplit(x,'///')[[1]][1])
})

library(clusterProfiler)
library(org.Hs.eg.db)
df <- bitr(gene_up$SYMBOL,
           fromType = "SYMBOL",
           toType = c("ENTREZID"),
           OrgDb = org.Hs.eg.db)
gene_up <- df$ENTREZID  ##KEGG分析需要使用ENTREZID

kk_up <- enrichKEGG(gene = gene_up,
                       organism = 'hsa',
                       pvalueCutoff = 0.1,
                       qvalueCutoff = 0.1)
head(kk_up)[,1:6]
#               ID             Description GeneRatio  BgRatio       pvalue    p.adjust
#hsa04657 hsa04657 IL-17 signaling pathway      7/62  94/7923 7.633936e-06 0.001022947
#hsa04310 hsa04310   Wnt signaling pathway      8/62 160/7923 3.109488e-05 0.002083357
#hsa05210 hsa05210       Colorectal cancer      5/62  86/7923 5.334629e-04 0.023828009
#hsa05213 hsa05213      Endometrial cancer      4/62  58/7923 1.051629e-03 0.027373514
#hsa05146 hsa05146              Amoebiasis      5/62 102/7923 1.159510e-03 0.027373514
#hsa04390 hsa04390 Hippo signaling pathway      6/62 154/7923 1.225680e-03 0.027373514
dotplot(kk_up)
browseKEGG(kk_up, 'hsa04657')
enrichKK=DOSE::setReadable(kk_up, OrgDb='org.Hs.eg.db',keyType='ENTREZID')

气泡图

条带图

(gg_barplot <- barplot(enrichKK,showCategory=20))

barplot.png

通路与基因之间的关系可视化

cnetplot(enrichKK, categorySize="pvalue", foldChange=gene_up,colorEdge = TRUE)
cnetplot(enrichKK, foldChange=gene_up, circular = TRUE, colorEdge = TRUE)

cnetplot_type_1.png cnetplot_type_2.png

通路与通路之间的连接展示

emapplot(enrichKK)

emapplot.png

热图展现通路与基因之间的关系

heatplot(enrichKK)

heatplot.png