plotSummaryHistograms: Plots cell subtype frequency histograms summarizing each...

In wschen/phemd: Phenotypic EMD for comparison of single-cell samples

Plots cell subtype frequency histograms summarizing each group of samples

Description

Visualizes plots of relative frequency ("weights") of cell subtypes ("bins" or "signatures") summarizing each group of single-cell samples. Each summary histogram is computed by taking the bin-wise mean of all samples in the group

Usage

plotSummaryHistograms(
  myobj,
  cluster_assignments,
  cell_model = c("monocle2", "seurat", "phate"),
  cmap = NULL,
  ncol.plot = 4,
  ax.lab.sz = 2.5,
  title.sz = 3
)

Arguments

myobj	Phemd object containing cell subtype relative frequency in @data_cluster_weights slot
cluster_assignments	Vector containing group assignments for each sample in myobj
cell_model	Method by which cell state was modeled (either "monocle2", "seurat", or "phate")
cmap	Vector containing colors by which histogram bars should be colored (optional)
ncol.plot	Number of columns to use to plot multi-panel histogram plot
ax.lab.sz	Scaling factor for axis labels (default 2.5)
title.sz	Scaling factor for plot title (default 3)

Details

groupSamples must be called before calling this function. Saves plots in directory called "summary_inhibs"

Value

None

wschen/phemd documentation built on Oct. 1, 2024, 4:45 a.m.