| title | output | ||||
|---|---|---|---|---|---|
rna-seq-volcano_plots |
|
Loading libraries
Read in expression data
path=readtext("C:/Users/jwang/Desktop/DiffExpression-path.txt") # get filename from path
df <- read_excel(path$text, sheet = 2)
df <- arrange(df, desc(abs(stat)))#noduplicates
df <- df[!duplicated(df$GeneID),]
#add boundaries for logfc and pval
df$fdr<- p.adjust(df$pvalue, method="fdr")
df <- dplyr::rename(df, logFC= colnames(df)[4])
#set boundaries on logfc and pvalue
pthresh= 10^-8
fcthresh= 6
df$logFC[df$logFC>fcthresh]= fcthresh
df$logFC[df$logFC< -fcthresh]= -fcthresh
df$pvalue[df$pvalue< pthresh]= pthresh
head(df[,1:9])## # A tibble: 6 x 9
## GeneID GeneName IsCoding logFC lfcSE stat pvalue padj healthy_s110
## <chr> <chr> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 ENSG00000~ ERAP2 TRUE 5.24 0.476 11.0 1.00e-8 5.99e-24 20.6
## 2 ENSG00000~ LAMA1 TRUE 2.75 0.294 9.36 1.00e-8 8.01e-17 57.7
## 3 ENSG00000~ IGFBP4 TRUE 1.06 0.170 6.24 1.00e-8 2.51e- 6 7064.
## 4 ENSG00000~ ANKRD2 TRUE -3.03 0.487 -6.22 1.00e-8 2.51e- 6 657.
## 5 ENSG00000~ HOXC10 TRUE 0.921 0.166 5.56 2.73e-8 1.07e- 4 634.
## 6 ENSG00000~ KLHL4 TRUE -0.732 0.135 -5.41 6.28e-8 1.93e- 4 786.
p <- EnhancedVolcano(df, lab=rep("",nrow(df)), x= "logFC", y="fdr",pCutoff=.05, FCcutoff=1, pointSize = 1.5, labSize = 3.0, xlab = bquote(~Log[2]~ "Fold Change (IO/Healthy)"), ylab = bquote(~-Log[10]~italic("FDR")), ylim=c(0,5), legend = c("d","d","d","FDR<.05 |FC|>1"), title="",subtitle="",col=c('black','red','royalblue','green') ) #,colCustom = keyvals #for mouse coloring
p+ ggplot2::coord_cartesian(xlim=c(-6, 6)) +
ggplot2::scale_x_continuous(
breaks=seq(-6,6, 2))
