html_from_graph {TraRe} | R Documentation

## Html generation

### Description

From input Gene Regulatory Network, an html is generated containing a table with driver to target phenotype dependent relationships. 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()),
      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)
`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.

### 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)

[Package TraRe version 1.2.0 Index]