plot_cluster_by_markers: "Barcode" plot

In JCVenterInstitute/FRmatch: Cell type matching in single-cell RNA-sequencing data using FR-Match

"Barcode" plot

Description

This function plots expression pattern of a cluster by marker genes, a.k.a. barcode plot.

Usage

plot_cluster_by_markers(
  sce.E1,
  sce.E2 = NULL,
  cluster.name,
  nsamp = 30,
  name.self = "E1.",
  name.cross = "E2.",
  use.common.markergenes = TRUE,
  scale.colorbar = FALSE,
  cellheight = 10,
  cellwidth = 5,
  main = NULL,
  filename = NA,
  ...
)

Arguments

sce.E1, sce.E2	Data objects of the SingleCellExperiment data class. If only sce.E1, then the "barcode" is a self plot, i.e. both cluster (cluster.name) and marker genes are from the same experiment. If both sce.E1 and sce.E2 are provided, then the "barcode" is a cross-experiment plot, i.e. marker genes are from sce.E1 (reference) and cluster (cluster.name) is from sce.E2 (query).
cluster.name	Name of the cluster to be plotted.
nsamp	Number of randomly selected cells to plot for a large cluster. Default: 30.
name.self, name.cross	Prefix name of experiment for self and cross-experiment plots. Default: "E1." and "E2.", respectively.
use.common.markergenes	Boolean variable indicating if to plot only common marker genes in a cross-experiment plot.
scale.colorbar	Boolean variable indicating if to scale the color bar to [0,1] for normalized gene expression values. Default: "FALSE".
cellwidth, cellheight, main, filename, ...	Plotting parameters passed to pheatmap.

JCVenterInstitute/FRmatch documentation built on Dec. 15, 2022, 2:30 p.m.