question about R language 'for' loop

Question

[13719756608]

When I type in the following code, the resulting picture is blank

samples <- c("m5C","m6A","m7G")
group <- c("Control","Treatment")
for(sa in samples){
for(gr in group){
  genelist = bitr(geneID = metG.expr[[sa]][[gr]]$Symbol,fromType = "SYMBOL",toType = "ENTREZID",OrgDb = org.Dr.eg.db)
  kegg <- enrichKEGG(gene = genelist$ENTREZID,
                     keyType = "kegg",organism = "dre",
                     pvalueCutoff = 0.05,pAdjustMethod = "BH")
  png(paste("./exprProfile/enrich/",sa,".",gr,".kegg",".png",sep=""),width = 1500,height = 1000,res = 200)
  ggplot(kegg@result[c(1:10),],mapping = aes(x = Description,y = -log10(pvalue),fill = pvalue))+
    geom_bar(stat = "identity",show.legend = T)+ 
    coord_flip()+scale_fill_gradient2(high="blue",mid = "red")
  dev.off()
}}

but when i assign values to two variables 'sa' and 'gr'

sa<-"m5C"
gr<-"Control"

then run

genelist = bitr(geneID = metG.expr[[sa]][[gr]]$Symbol,fromType = "SYMBOL",toType = "ENTREZID",OrgDb = org.Dr.eg.db)
  kegg <- enrichKEGG(gene = genelist$ENTREZID,
                     keyType = "kegg",organism = "dre",
                     pvalueCutoff = 0.05,pAdjustMethod = "BH")
  png(paste("./exprProfile/enrich/",sa,".",gr,".kegg",".png",sep=""),width = 1500,height = 1000,res = 200)
  ggplot(kegg@result[c(1:10),],mapping = aes(x = Description,y = -log10(pvalue),fill = pvalue))+
    geom_bar(stat = "identity",show.legend = T)+ 
    coord_flip()+scale_fill_gradient2(high="blue",mid = "red")
  dev.off()

the picture is successfully produced,so i wonder what cause this situation and how i can fix that,thanks

Answer 1

[rpolicastro]

Within the for loop, save the plot to a variable, and then pass that variable to the print function while the graphics device is open. R usually won't plot in a for loop unless you do so.

Alternatively you can use the ggsave function instead which will work without any problems in loops.

[13719756608]

very useful advice,thank you very much

Answer 2

[MatthewP]

Use ggsave function to save ggplot picture.

[13719756608]

thank you very much.