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.