| #BiocManager::install('clusterProfiler') |
| #BiocManager::install("pathview") |
| #install.packages('tidyverse') |
| library(clusterProfiler) |
| library(tidyverse) |
| data1<-read.table("K2.txt",header = TRUE,row.names = 1) |
| #head(data1) |
| data1.2<-data1 %>% select_if(is.numeric) |
| data1.2$Group <- factor(data1$Group,levels=c("CCFM16","Placebo")) |
| |
| |
| ''' |
| shapiro.test的零假设是变量符合正态分布, |
| 当结果的p-value > 0.05时,不能拒绝原假设,表明变量服从正态分布 |
| dim(data1) |
| diff_test <- data1 %>% |
| select_if(is.numeric) |
| shapiro.test(diff_test[,1]) |
| Shapiro-Wilk normality test |
| data: diff_test[, 1] |
| W = 0.97972, p-value = 0.297 |
| ''' |
| |
| diff <- data1.2 %>% |
| select_if(is.numeric) %>% |
| map_df(~ broom::tidy(t.test(. ~ Group,data = data1.2)), .id = 'var') |
| |
| diff$q.value <- p.adjust(diff$p.value,"fdr") |
| diff$FC<-diff$estimate1/diff$estimate2 |
| diff$logFC<-log2(diff$FC) |
| p1<-diff[,c(1,14,6)] |
| newdata1<-na.omit(p1) |
| |
| |
| p2 <- p1[p1$logFC!= "-Inf",] |
| p3 <- p2[p2$logFC!= "Inf",] |
| write.csv(newdata3,"p1.csv") |
| |
| |
| flt <- p3[p3$logFC > 1.1 & p3$p.value < 0.05,] |
| up_gene<-na.omit(flt) |
| library("pathview") |
| library(clusterProfiler) |
| ekegg <- enrichKEGG(gene =up_gene$var, |
| organism = "ko", |
| keyType = "kegg") |
| View(as.data.frame(ekegg)) |
| dotplot(ekegg) |
| #browseKEGG(ekegg, "rno05146") |
| barplot(ekegg, showCategory = 20) |
| dotplot(ekegg, x = "GeneRatio", |
| color = "p.adjust", |
| showCategory = 30, |
| split = NULL, font.size = 12,) |
| browseKEGG(ekegg, "ko02025") |
| |
| flt <- p3[p3$logFC < 1.1 & p3$p.value < 0.05,] |
| down_gene<-na.omit(flt) |
| library("pathview") |
| library(clusterProfiler) |
| ekegg <- enrichKEGG(gene =down_gene$var, |
| organism = "ko", |
| keyType = "kegg") |
| View(as.data.frame(ekegg)) |
| dotplot(ekegg) |
| dotplot(ekegg, x = "GeneRatio", |
| color = "p.adjust", |
| showCategory = 30, |
| split = NULL, font.size = 12,) |
| browseKEGG(ekegg, "ko00720") |