prepareCytoscape {ActivePathways}

Prepare files for building an enrichment map network visualization in Cytoscape

Description

This function writes four text files that are used to build an network using Cytoscape and the EnrichmentMap app. The files are prefixed with cytoscape_file_tag. The four files written are:

pathways.txt

A list of significant terms and the associated p-value. Only terms with adjusted_p_val <= significant are written to this file

subgroups.txt

A matrix indicating whether the significant pathways are found to be significant when considering only one column (i.e., type of omics evidence) from scores. A 1 indicates that that term is significant using only that column to test for enrichment analysis

pathways.gmt

A shortened version of the supplied GMT file, containing only the terms in pathways.txt.

legend.pdf

A legend with colours matching contributions from columns in scores

Usage

prepareCytoscape(
  terms,
  gmt,
  cytoscape_file_tag,
  col_significance,
  color_palette = NULL,
  custom_colors = NULL,
  color_integrated_only = "#FFFFF0"
)

Arguments

terms

A data.table object with the columns 'term_id', 'term_name', 'adjusted_p_val'.

gmt

An abridged GMT object containing only the pathways that were found to be significant in the ActivePathways analysis.

cytoscape_file_tag

The user-defined file prefix and/or directory defining the location of the files.

col_significance

A data.table object with a column 'term_id' and a column for each type of omics evidence indicating whether a term was also found to be significant or not when considering only the genes and p-values in the corresponding column of the scores matrix. If term was not found, NA's are shown in columns, otherwise the relevant lists of genes are shown.

color_palette

Color palette from RColorBrewer::brewer.pal to color each column in the scores matrix. If NULL grDevices::rainbow is used by default.

custom_colors

A character vector of custom colors for each column in the scores matrix.

color_integrated_only

A character vector of length 1 specifying the color of the "combined" pathway contribution.

Value

None