draw.combineDE: Plot for combined DE (differentiated expressed)/DA...

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

Plot for combined DE (differentiated expressed)/DA (differentiated activity) Vs. original DE/DA

Description

draw.combineDE draw the image for the combined DE/DA Vs. original DE/DA.

Usage

draw.combineDE(
  DE_list = NULL,
  main_id = NULL,
  top_number = 30,
  display_col = "P.Value",
  z_col = "Z-statistics",
  digit_num = 2,
  row_cex = 1,
  column_cex = 1,
  text_cex = 1,
  pdf_file = NULL
)

Arguments

DE_list	list, a list of DE/DA results, with one more component named "combine" that include the combined results. Strongly suggest to use the output from combineDE.
main_id	character, the main id for display in the figure, must be one of the name in DE_list. If NULL, will use the first name. Default is NULL.
top_number	number for the top significant genes/drivers in the combine results to be displayed on the plot. Default is 30.
display_col	character, column names used to display. Default is 'P.Value'.
z_col	character, column names for Z statistics used for background color bar. Default is 'Z-statistics'.
digit_num	integer, number of digits to display on the plot. Default is 2.
row_cex	numeric, cex for the row labels displayed on the plot. Default is 1
column_cex	numeric, cex for the col labels displayed on the plot. Default is 1
text_cex	numeric, cex for the text displayed on the plot. Default is 1
pdf_file	character, file path for the pdf file to save the figure into pdf format.If NULL, will not generate pdf file. Default is NULL.

Details

This plot function need to input the output from combineDE.

Value

logical value indicating whether the plot has been successfully generated

Examples

analysis.par <- list()
analysis.par$out.dir.DATA <- system.file('demo1','driver/DATA/',package = "NetBID2")
NetBID.loadRData(analysis.par=analysis.par,step='ms-tab')
phe_info <- Biobase::pData(analysis.par$cal.eset)
each_subtype <- 'G4'
G0  <- rownames(phe_info)[which(phe_info$`subgroup`!=each_subtype)] # get sample list for G0
G1  <- rownames(phe_info)[which(phe_info$`subgroup`==each_subtype)] # get sample list for G1
DE_gene_limma_G4 <- getDE.limma.2G(eset=analysis.par$cal.eset,
                                   G1=G1,G0=G0,
                                   G1_name=each_subtype,
                                   G0_name='other')
each_subtype <- 'SHH'
G0  <- rownames(phe_info)[which(phe_info$`subgroup`!=each_subtype)] # get sample list for G0
G1  <- rownames(phe_info)[which(phe_info$`subgroup`==each_subtype)] # get sample list for G1
DE_gene_limma_SHH <- getDE.limma.2G(eset=analysis.par$cal.eset,
                                    G1=G1,G0=G0,
                                    G1_name=each_subtype,
                                    G0_name='other')
DE_list <- list(G4=DE_gene_limma_G4,SHH=DE_gene_limma_SHH)
res2 <- combineDE(DE_list,transfer_tab=NULL)
draw.combineDE(res2)

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