In Tong-Chen/YSX: For Yishengxin Training

widedataframe2boxplot

df = generateAbundanceDF()
head(df)

widedataframe2boxplot(df)

widedataframe2boxplot(df, saveplot="widedataframe2boxplot.pdf", width=10, height=10, units=c("cm"))

rankPlot

输入数据格式

a <- data.frame(log2FoldChange=rnorm(1000), row.names=paste0("YSX",1:1000))
head(a)

Raw plot

rankPlot(a)

Label top 10

rankPlot(a, label=10)

Label specified points

rankPlot(a, label=c("YSX1","YSX2","YSX10"))

Label specified points with new names

b <- c("A","B","C")
names(b) <- c("YSX1","YSX2","YSX10")
rankPlot(a, label=b)

volcanoPlot

Prepare data

res_output <- data.frame(log2FoldChange=rnorm(3000), row.names=paste0("YSX",1:3000))
res_output$padj <- 20 ^ (-1*(res_output$log2FoldChange^2))
padj = 0.05
log2FC = 1
res_output$level <- ifelse(res_output$padj<=padj,
                      ifelse(res_output$log2FoldChange>=log2FC,
                             paste("groupA","UP"),
                      ifelse(res_output$log2FoldChange<=(-1)*(log2FC),
                             paste("groupB","UP"), "NoDiff")) , "NoDiff")
head(res_output)

Plot

volcanoPlot(res_output, colour="level")

Tong-Chen/YSX documentation built on Jan. 25, 2021, 2:49 a.m.