html_from_graph: Html generation

In ubioinformat/TraRe: Transcriptional Rewiring

Html generation

Description

From input Gene Regulatory Network, an html is generated containing a table with driver to target phenotype dependent relationships. It is a brief summary containing drivers normalized xor sum, which is the ratio between drivers-targets connections present only in one of both phenotypes over all possible connections, and cliques, which are driver genes that are highly correlated (over a user-decision threshold), and may have been lost during the fitting process of the LINKER method.

Usage

html_from_graph(
  gpath = NULL,
  wpath = paste0(tempdir()),
  report_name = "rewiring",
  user_mode = TRUE,
  cliquesbool = TRUE,
  ...
)

Arguments

gpath	path to the graph object ('refinedsumm.rds'). (RDS format)
wpath	writing path, where the html and txts file will be saved. (Default: temp directory)
report_name	name of the folder where the rewiring data will be saved. (Default: "rewiring")
user_mode	boolean indicating if this function is called from user or internaly. (Default: TRUE)
cliquesbool	indicating if cliques method should be added to the summary table. (Default: TRUE)
...	every argument you should pass to generatecliques() in case cliquesbool is TRUE.

Details

This functions takes place inside the runrewiring function, so it is not recommended to run it on its own.

Value

Html and txts containing the mentioned files.

Examples

## For this example, we are going to use a generated 'refinedsumm.rds' from the su2c dataset
## (see vignette of TraRe for more information), which is at the external data folder
## of this package.

gpath <- paste0(system.file('extdata',package='TraRe'),'/refinedsumm.rds')
wpath <- paste0(system.file('extdata',package='TraRe'))

## We are going to use the drivers dataset from the external data folder as well.
## For more information about generatecliques() please check the help page of it.

dataset<-readRDS(paste0(system.file('extdata',package='TraRe')
                 ,'/tfs_linker_example_eg.rds'))
html_from_graph(gpath=gpath,wpath=wpath,dataset=dataset)

ubioinformat/TraRe documentation built on March 10, 2024, 1:11 a.m.