RVA (version 0.0.5)

plot_volcano: Plot volcanoplot

Description

This function processes the summary statistics table generated by differential expression analysis like limma or DESeq2 to show on the volcano plot with the highlight gene set option (like disease related genes from Disease vs Healthy comparison).

Usage

plot_volcano(
  data = data,
  comp.names = NULL,
  geneset = NULL,
  geneset.FCflag = "logFC",
  highlight.1 = NULL,
  highlight.2 = NULL,
  upcolor = "#FF0000",
  downcolor = "#0000FF",
  plot.save.to = NULL,
  xlim = c(-4, 4),
  ylim = c(0, 12),
  FCflag = "logFC",
  FDRflag = "adj.P.Val",
  highlight.FC.cutoff = 1.5,
  highlight.FDR.cutoff = 0.05,
  title = "Volcano plot",
  xlab = "log2 Fold Change",
  ylab = "log10(FDR)"
)

Arguments

data

Summary statistics table or a list contain 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. Required if data is list. No default.

geneset

Summary statistic table that contains the genes which needed to be highlighted, the gene name format (in row names) needs to be consistent with the main summary statistics table). For example, this summary statistics table could be the output summary statistics table from the Disease vs Healthy comparison (Only contains the subsetted significant genes to be highlighted).

geneset.FCflag

The column name of fold change in geneset, Default = "logFC".

highlight.1

Genes to be highlighted, in the format of a vector consists of gene names. The gene name format needs to be consistent to the main summary statistics table.

highlight.2

Genes to be highlighted, in the format of a vector consists of gene names. The gene name format needs to be consistent to the main summary statistics table.

upcolor

The color of the gene names in highlight.1 or the positive fold change gene in geneset, default = "#FDE725FF" (viridis color palette).

downcolor

The color of the gene names in highlight.2 or the negative fold change gene in geneset, default = "#440154FF" (viridis color palette).

plot.save.to

The file name and address where to save the volcano plot, e.g. "~/address_to_folder/volcano_plot.png".

xlim

Range of x axis. Default = c(-3,3).

ylim

Range of x axis. Default = c(0,6).

FCflag

Column name of log2FC in the summary statistics table. Default = "logFC".

FDRflag

Column name of FDR in the summary statistics table. Default = "adj.P.Val".

highlight.FC.cutoff

Fold change cutoff line want to be shown on the plot. Default = 1.5.

highlight.FDR.cutoff

FDR cutoff shades want to be shown on the plot. Default = 0.05.

title

The plot title. Default "Volcano plot".

xlab

The label for x-axis. Default "log2 Fold Change".

ylab

The label for y-axis. Default "log10(FDR)".

Value

The function return a volcano plot as a ggplot object.

Details

The function takes the summary statistics table and returns a ggplot, with the option to highlight genes, e.g. disease signature genes, the genes which are up-regulated and down-regulated in diseased subjects.

References

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

Examples

# NOT RUN {
plot_volcano(data = Sample_summary_statistics_table,
             geneset = Sample_disease_gene_set)

plot_volcano(data = list(Sample_summary_statistics_table, Sample_summary_statistics_table1),
            comp.names = c("A", "B"),
            geneset = Sample_disease_gene_set)
# }