plot_qq {RVA}

Plot qqplot

Description

This function generates a QQ-plot object with confidence interval from summary statistics table generated by differential expression analysis like limma or DESeq2.

Usage

plot_qq(
  data = data,
  comp.names = NULL,
  p.value.flag = "P.Value",
  ci = 0.95,
  plot.save.to = NULL
)

Arguments

data

Summary statistics table or a list that contains multiple summary statistics tables from limma or DEseq2, where each row is a gene.

comp.names

A character vector that contains the comparison names which correspond to the same order as data. No default.

p.value.flag

The column name of P-VALUE (NOT FDR, NO multiplicity adjusted p-value) in the summary statistics table. Default = "P.Value".

ci

Confidence interval. Default = 0.95

plot.save.to

The file name and the address where to save the qq-plot "~/address_to_folder/qqplot.png". Default = NULL.

Details

The function produces the qqplot to evaluate the result from differential expression analysis. The output is a ggplot object.

Value

The function return a ggplot object of qqplot

References

Xingpeng Li & Tatiana Gelaf Romer & Olya Besedina, RVA - RNAseq Visualization Automation tool.

Examples

plot_qq(data = Sample_summary_statistics_table)
plot_qq(data = list(Sample_summary_statistics_table, Sample_summary_statistics_table1),
        comp.names = c("A","B"))