cluster_mr_heatmap: Generates a heatmap of cluster-specific MR activity....

In califano-lab/PISCES: Protein Activity Inferecne in Single Cells

Generates a heatmap of cluster-specific MR activity. Alternatively, can be provided with a pre-selected set of proteins, typically canonical markers.

Description

Generates a heatmap of cluster-specific MR activity. Alternatively, can be provided with a pre-selected set of proteins, typically canonical markers.

Usage

cluster_mr_heatmap(
  dat.mat,
  dat.type = c("gexp", "pact"),
  clust.vec,
  mr.list,
  num.mrs = 10,
  reg.class = c("regulator", "marker"),
  marker.set = NULL,
  group.means = FALSE,
  scale.rows = FALSE,
  plot.title = NULL,
  clust.rows = FALSE
)

Arguments

dat.mat	Matrix of either scaled expresison data or PES generated by NaRnEA (featues X samples).
dat.type	One of ‘c(’gexp', 'pact')', specifying expression or activity data. ASsumes activity if not specified.
clust.vec	Named clustering vector.
num.mrs	Number of master regulators to display. Default of 10.
marker.set	Optional list of markers to use in lieu of master regulators.
group.means	Flag to plot the mean of each group rather than each sample. Default of FALSE.
scale.rows	Flag to scale rows for plot color. Default of FALSE.
plot.title	Optional plot title argument. Will be generated according to other arguments if not specified.
clust.rows	Clusters rows if set to true. Default of FALSE.
mr.obj	Master regulator object, such as that generated by 'cluster_signature_mrs'. Should be a list with a 'cluster.narnea' element, containing cluster-specific NaRnEA results (NES and PES matrices).

Value

A ComplexHeatmap object.

califano-lab/PISCES documentation built on Jan. 11, 2023, 5:34 a.m.