plot2 {COMPASS} | R Documentation |
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.
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, ...)
x |
An object of class |
y |
An object of class |
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 < |
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, |
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 |
show_colnames |
Boolean; if |
... |
Optional arguments passed to |
The plot as a grid
object (grob
). It can be redrawn
with e.g. grid::grid.draw()
.