draw.volcanoPlot: Draw Volcano Plot for Top DE (differentiated expressed) Genes...

In jyyulab/NetBID: Network-based Bayesian Inference of Drivers, version 2

Draw Volcano Plot for Top DE (differentiated expressed) Genes or DA (differentiated activity) Drivers

Description

draw.volcanoPlot draws the volcano plot to identify and visualize DE genes or DA drivers with fold change threshold and significant P-value from the input dataset. The function will return a data.frame of these highlighted genes/drivers.

Usage

draw.volcanoPlot(
  dat = NULL,
  label_col = NULL,
  logFC_col = NULL,
  Pv_col = NULL,
  logFC_thre = 0.1,
  Pv_thre = 0.01,
  show_plot = TRUE,
  xlab = "log2 Fold Change",
  ylab = "P-value",
  show_label = FALSE,
  label_cex = 0.5,
  legend_cex = 0.8,
  label_type = "distribute",
  main = "",
  pdf_file = NULL
)

Arguments

dat	data.frame, the master table created by function generate.masterTable. Or a table with columns of the following parameters.
label_col	character, the name of the column in dat contains gene/driver names.
logFC_col	character, the name of the column in dat contains logFC values.
Pv_col	character, the name of the column in dat contains P-values.
logFC_thre	numeric, the threshold of logFC. Genes or drivers with absolute logFC value higher than the threshold will be kept. Default is 0.1.
Pv_thre	numeric, the threshold of P-values. Genes or drivers with P-values lower than the threshold will be kept. Default is 0.01.
show_plot	logical, if TRUE, the plot will be shown in the plot pane. Default is TRUE.
xlab	character, a title for the X axis.
ylab	character, a title for the Y axis.
show_label	logical, if TRUE, labels of selected genes or drivers will be displayed in the plot. Default is FALSE.
label_cex	numeric, giving the amount by which the text of genes/drivers label should be magnified relative to the default. Default is 0.5.
legend_cex	numeric, giving the amount by which the text of legend should be magnified relative to the default. Default is 0.7.
label_type	character, users can choose between "origin" and "distribute". If "origin", all the labels will be displayed without location modification. If "distribute", location of labels will be rearranged to avoid overlap. Default is "distribute".
main	character, an overall title for the plot.
pdf_file	character, the path to save the plot as PDF file. If NULL, no PDF file will be created. Default is NULL.

Details

Top genes or drivers will be colored (blue for down-regulated and red for up-regulated) and labeled with their names. This function requires the input of master table and two thresholds of logFC and P-value.

Value

Return a data.frame of selected significant genes or drivers, with columns contain label_col, logFC_col and Pv_col.

Examples

analysis.par <- list()
analysis.par$out.dir.DATA <- system.file('demo1','driver/DATA/',package = "NetBID2")
NetBID.loadRData(analysis.par=analysis.par,step='ms-tab')
ms_tab <- analysis.par$final_ms_tab
sig_driver <- draw.volcanoPlot(dat=ms_tab,label_col='gene_label',
                               logFC_col='logFC.G4.Vs.others_DA',
                               Pv_col='P.Value.G4.Vs.others_DA',
                               logFC_thre=0.4,
                               Pv_thre=1e-7,
                               main='Volcano Plot for G4.Vs.others_DA',
                               show_label=FALSE,
                               label_type = 'origin',
                               label_cex = 0.5)

## Not run: 
analysis.par <- list()
analysis.par$out.dir.DATA <- system.file('demo1','driver/DATA/',package = "NetBID2")
NetBID.loadRData(analysis.par=analysis.par,step='ms-tab')
ms_tab <- analysis.par$final_ms_tab
analysis.par$out.dir.PLOT <- getwd() ## directory for saving the pdf files
sig_driver <- draw.volcanoPlot(dat=ms_tab,label_col='gene_label',
                               logFC_col='logFC.G4.Vs.others_DA',
                               Pv_col='P.Value.G4.Vs.others_DA',
                               logFC_thre=0.4,
                               Pv_thre=1e-7,
                               main='Volcano Plot for G4.Vs.others_DA',
                               show_label=FALSE,
                               label_type = 'origin',
                               label_cex = 0.5)
sig_gene <- draw.volcanoPlot(dat=ms_tab,label_col='geneSymbol',
                               logFC_col='logFC.G4.Vs.others_DE',
                               Pv_col='P.Value.G4.Vs.others_DE',
                               logFC_thre=2,Pv_thre=1e-3,
                               main='Volcano Plot for G4.Vs.others_DE',
                               show_label=FALSE,
                               pdf_file=sprintf('%s/vocalno_nolabel_DE.pdf',
                               analysis.par$out.dir.PLOT))

## End(Not run)

jyyulab/NetBID documentation built on Dec. 23, 2024, 6:34 a.m.