draw.NetBID: Create Plot to show Differential Expression and Differential...

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

Create Plot to show Differential Expression and Differential Activity Analysis of Top Drivers

Description

draw.NetBID creates two side-by-side heatmaps to show the result of NetBID analysis. Both the differential expression analysis (the right heatmap) and differential activity analysis (the left heatmap) of top drivers are shown in the plot.

Usage

draw.NetBID(
  DA_list = NULL,
  DE_list = NULL,
  main_id = NULL,
  top_number = 30,
  DA_display_col = "P.Value",
  DE_display_col = "logFC",
  z_col = "Z-statistics",
  digit_num = 2,
  row_cex = 1,
  column_cex = 1,
  text_cex = 1,
  col_srt = 60,
  pdf_file = NULL
)

Arguments

DA_list	list, contains the differential activity (DA) analysis result.
DE_list	list, contains the differential expression (DE) analysis result.
main_id	character, the top genes/drivers from which DA comparison group. Must be one of the names in DA_list. If NULL, the first element name of DA_list will be used. Default is NULL.
top_number	integer, the number of the top significant genes/drivers to be displayed in the plot. Default is 30.
DA_display_col	character, which statistic column from NetBID analysis is to be used as the column of the left heatmap. Default is "P.Value".
DE_display_col	character, which statistic column from NetBID analysis is to be used as the column of the right heatmap. Default is "logFC".
z_col	character, which statistic column from NetBID analysis is to be used as the color scale of the heatmap. Default is "Z-statistics".
digit_num	integer, indicating the number of decimal places (round) or significant digits (signif) to be used. Default is 2.
row_cex	numeric, giving the amount by which the text of row names should be magnified relative to the default. Default is 1.
column_cex	numeric, giving the amount by which the text of column names should be maginified relative to the default. Default is 1.
text_cex	numeric, giving the amount by which the text of in the table cell should be maginified relative to the default. Default is 1.
col_srt	numeric, rotation angle of the column labels at the bottom of heatmap. Default is 60.
pdf_file	character, the path to save the plot as PDF file. If NULL, PDF file will not be generated. Default is NULL.

Value

Return a logical value. If TRUE, the plot is created successfully.

Examples

analysis.par <- list()
analysis.par$out.dir.DATA <- system.file('demo1','driver/DATA/',package = "NetBID2")
NetBID.loadRData(analysis.par=analysis.par,step='ms-tab')
draw.NetBID(DA_list=analysis.par$DA,DE_list=analysis.par$DE)

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