NetBID.lazyMode.DriverVisualization: Lazy mode for NetBID2 result visualization

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

Lazy mode for NetBID2 result visualization

Description

NetBID.lazyMode.DriverVisualization is an integrated function to draw visualization plots for top drivers.

Usage

NetBID.lazyMode.DriverVisualization(
  analysis.par = NULL,
  intgroup = NULL,
  use_comp = NULL,
  main_id_type = "external_gene_name",
  transfer_tab = NULL,
  use_gs = c("H", "CP:BIOCARTA", "CP:REACTOME", "CP:KEGG"),
  min_Size = 30,
  max_Size = 1000,
  top_number = 30,
  top_strategy = "Both",
  logFC_thre = 0.05,
  Pv_thre = 0.05
)

Arguments

analysis.par	list, stores all related datasets from driver analysis step.
intgroup	character, one interested phenotype group from the analysis.par$cal.eset.
use_comp	character, the name of the comparison of interest, should be included in the colnames of analysis.par$DA and analysis.par$DE.
main_id_type	character, the type of driver's ID. It comes from the attribute name in biomaRt package. Such as "ensembl_gene_id", "ensembl_gene_id_version", "ensembl_transcript_id", "ensembl_transcript_id_version" or "refseq_mrna". For details, user can call biomaRt::listAttributes() to display all available attributes in the selected dataset.
transfer_tab	data.frame, the ID conversion table. Users can call get_IDtransfer to get this table.
use_gs	a vector of characters, names of major gene set collections. Users can call all_gs2gene_info to see all the available collections. Default is c("H", "CP:BIOCARTA", "CP:REACTOME", "CP:KEGG").
min_Size	numeric, minimum size for the target genes. Default is 30.
max_Size	numeric, maximum size for the target genes. Default is 1000.
top_number	number for the top significant genes/drivers in the combine results to be displayed on the plot. Default is 30.
top_strategy	character, choose from "Both", "Up", "Down". If set to "Both", top drivers with highest absolute Z statistics will be displayed. If set to "Up", only top up-regulated drivers will be displayed. If set to "Down", only top down-regulated drivers will be displayed. Default is "Both".
logFC_thre	numeric, the threshold of logFC. Genes or drivers with absolute logFC value higher than the threshold will be kept. Default is 0.05.
Pv_thre	numeric, the threshold of P-values. Genes or drivers with P-values lower than the threshold will be kept. Default is 0.05.

Details

User need to strictly follow the NetBID2 pipeline to get the complicated list object analysis.par. "intgroup", "use_comp" should be specified; "transfer_tab" could be set to NULL with "main_id_type" specified, but it is suggested to input by hand if available.

Examples

## Not run: 
analysis.par <- list()
analysis.par$out.dir.DATA <- system.file('demo1','driver/DATA/',package = "NetBID2")
NetBID.loadRData(analysis.par=analysis.par,step='ms-tab')
analysis.par$out.dir.PLOT <- 'test/'
NetBID.lazyMode.DriverVisualization(analysis.par=analysis.par,
                                    intgroup='subgroup',use_comp='G4.Vs.others',
                                    transfer_tab=analysis.par$transfer_tab,
                                    logFC_thre=0.2,Pv_thre=1e-4)

## End(Not run)

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