iPAS_bar: Produce bar plots of top iPAS pathways
In uc-bd2k/iPAS: integrative Pathway Activity Signatures (iPAS)

iPAS_bar

R Documentation

Produce bar plots of top iPAS pathways

Description

This function creates bar plots that graph iPAS results. The input to the function is the object returned from the iPAS_enrich function.

Usage

iPAS_bar(
  res,
  experiment = 1,
  num_top = 15,
  col_scale_max = 5,
  pal = "vikO",
  pathway_names = c("names", "identifiers", "both", "none"),
  short_names = TRUE,
  rev = FALSE,
  fill = "z_score",
  bar_height = "neg_log10_p",
  arrange_col = "p_emp",
  category = c("Signaling", "Cancer", "Disease", "Other", "All")
)

Arguments

`res`	output object from the iPAS_enrich function
`experiment`	the sample number or name of the sample from which to graph results.
`num_top`	the number of top pathways (by iPAS score) to plot
`col_scale_max`	a positive number that defines the limits of the color scale. The color scale is defined as c(-col_scale_max, col_scale_max).
`pal`	scico package color palette. See here: https://github.com/thomasp85/scico
`pathway_names`	whether to show the names of KEGG pathways (e.g. "mTOR signaling pathway - Homo sapiens (human)"), their unique identifiers (e.g. "hsa04150") or both. "names" shows pathway names, "identifiers" shows only ID numbers, "both" shows both, "none" shows no names.
`short_names`	if TRUE, show shortened pathway names, not including " - Homo sapiens (human)" at the end
`rev`	T/F whether to reverse the order of the bars in the chart or not
`fill`	the column to be used for the fill (color) of the bars. The default is "z_score", but other options are "score" for the raw iPAS score or "neg_log10_p" for the p-value (negative log10-transformed).
`bar_height`	the column to be used for the height of the bars. The choices are the same as above, the default is "neg_log10_p", the p-value (negative log10-transformed).
`arrange_col`	the column to use to order the bars, by default "p_emp" for the empirical p-value (non-transformed).
`category`	the categories of KEGG pathways for which to calculate iPAS scores. We categorize pathways as "Disease", "Other", "Signaling", or "Cancer". By default all categories/pathways are included.