plot_qq: Plot qqplot

In RVA: RNAseq Visualization Automation

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"))

RVA documentation built on Nov. 2, 2021, 1:06 a.m.