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:
A list of significant terms and the
associated p-value. Only terms with adjusted_p_val <= significant are
written to this file
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
A shortened version of the supplied GMT file, containing only the terms in pathways.txt.
A legend with colours matching contributions
from columns in scores
prepareCytoscape(
terms,
gmt,
cytoscape_file_tag,
col_significance,
color_palette = NULL,
custom_colors = NULL,
color_integrated_only = "#FFFFF0"
)None
A data.table object with the columns 'term_id', 'term_name', 'adjusted_p_val'.
An abridged GMT object containing only the pathways that were found to be significant in the ActivePathways analysis.
The user-defined file prefix and/or directory defining the location of the files.
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 from RColorBrewer::brewer.pal to color each column in the scores matrix. If NULL grDevices::rainbow is used by default.
A character vector of custom colors for each column in the scores matrix.
A character vector of length 1 specifying the color of the "combined" pathway contribution.