plot2: Plot a pair of COMPASSResults

In RGLab/COMPASS: Combinatorial Polyfunctionality Analysis of Single Cells

Plot a pair of COMPASSResults

Description

This function can be used to visualize the mean probability of response – that is, the probability that there is a difference in response between samples subjected to the 'treatment' condition, and samples subjected to the 'control' condition.

Usage

plot2(
  x,
  y,
  subset,
  threshold = 0.01,
  minimum_dof = 1,
  maximum_dof = Inf,
  must_express = NULL,
  row_annotation = NULL,
  palette = NA,
  show_rownames = FALSE,
  show_colnames = FALSE,
  ...
)

Arguments

x	An object of class COMPASSResult.
y	An object of class COMPASSResult.
subset	An R expression, evaluated within the metadata, used to determine which individuals should be kept.
threshold	A numeric threshold for filtering under-expressed categories. Any categories with mean score < threshold are removed.
minimum_dof	The minimum degree of functionality for the categories to be plotted.
maximum_dof	The maximum degree of functionality for the categories to be plotted.
must_express	A character vector of markers that should be included in each subset plotted. For example, must_express=c("TNFa & IFNg") says we include only subsets that are positive for both TNFa or IFNg, while must_express=c("TNFa", "IFNg") says we should keep subsets which are positive for either TNFa or IFNg.
row_annotation	A vector of names, pulled from the metadata, to be used for row annotation.
palette	The colour palette to be used.
show_rownames	Boolean; if TRUE we display row names (ie, the individual ids).
show_colnames	Boolean; if TRUE we display column names (ie, the column name associated with a cytokine; typically not needed)
...	Optional arguments passed to pheatmap.

Value

The plot as a grid object (grob). It can be redrawn with e.g. grid::grid.draw().

RGLab/COMPASS documentation built on Feb. 11, 2025, 4:40 p.m.