模式物種進(jìn)行GO富集分析繪圖

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? ? ?今天通過clusterProfiler包對模式物種進(jìn)行GO富集分析，并繪制富集分析圖片,今天以小鼠數(shù)據(jù)為例進(jìn)行，代碼如下：

1.?安裝所需的R包

Install.packages(“BiocManager”)

Install.packages(“clusterProfiler”)

Install.packages(“ggplot2”)

Install.packages(“tidyverse”)

2.導(dǎo)入所需的R包

library(clusterProfiler)

library(ggplot2)

1.?差異分析結(jié)果文件

2.?富集分析

#讀取小鼠基因差異分析結(jié)果數(shù)據(jù)

gsym.fc <- read.csv("easy_input_Mm.csv", as.is = T)

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#獲取基因名與ENTREZID的對應(yīng)關(guān)系。

gsym.id <- bitr(gsym.fc$SYMBOL, #基因名

????????????????fromType = "SYMBOL", #從gene symbol

????????????????toType = "ENTREZID", #提取ENTREZ ID

????????????????OrgDb = "org.Mm.eg.db") #相應(yīng)物種

idvec <- gsym.id$ENTREZID

names(idvec) <- gsym.id$SYMBOL

gsym.fc$ENTREZID <- idvec[gsym.fc$SYMBOL]

write.csv(gsym.fc[,c(3,2)], "very_easy_input_Mm.csv", quote = F, row.names = F)

id.fc <- read.csv("very_easy_input_Mm.csv", as.is = T)

#enrich進(jìn)行富集分析

ego <- enrichGO(gene = id.fc$ENTREZID,

????????????????#小鼠用這行

????????????????OrgDb = org.Mm.eg.db,

????????????????#人類用這行

????????????????#OrgDb = org.Hs.eg.db,

????????????????#非模式生物用這行，例如玉米

????????????????#OrgDb = maize.db,

????????????????ont = "BP", #或MF或CC

????????????????pAdjustMethod = "BH",

????????????????#pvalueCutoff ?= 0.001,

????????????????qvalueCutoff ?= 0.01)

write.csv(ego,"enrichGO_output.csv",quote = F)

egox <- setReadable(ego, 'org.Mm.eg.db', #物種

????????????????????'ENTREZID')

geneList <- id.fc$log2fc

names(geneList)<- gsym.fc$SYMBOL

#繪制圈圖，通過circular來確定。

cnetplot(egox,

?????????foldChange = geneList,

?????????#foldChange = NULL, #不展示倍數(shù)

?????????circular = TRUE,

?????????#node_label = FALSE, #如果太多，就不要顯示基因名了

?????????showCategory = 4, #顯示富集的term數(shù)量，默認(rèn)5

?????????colorEdge = TRUE)

ggsave("clusterProfiler_circle.pdf", width = 8, height = 5)

cnetplot(egox,

?????????foldChange = geneList,

?????????#foldChange = NULL, #不展示倍數(shù)

?????????#circular = TRUE,

?????????#node_label = FALSE, #不顯示基因名

?????????showCategory = 4, #顯示的富集term數(shù)量，默認(rèn)5

?????????colorEdge = TRUE)

ggsave("clusterProfiler_not_circle.pdf", width = 8, height = 5)

3.?Go富集分析結(jié)果

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