plot_coexpression_matrix: Not sure we're ready to release this one quite yet: Plot the...

In monocle: Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq

Description

Not sure we're ready to release this one quite yet: Plot the branch genes in pseduotime with separate branch curves

Usage

plot_coexpression_matrix(cds, rowgenes, colgenes, relative_expr = TRUE,
  min_expr = NULL, cell_size = 0.85, label_by_short_name = TRUE,
  show_density = TRUE, round_expr = FALSE)

Arguments

cds	CellDataSet for the experiment
rowgenes	Gene ids or short names to be arrayed on the vertical axis.
colgenes	Gene ids or short names to be arrayed on the horizontal axis
relative_expr	Whether to transform expression into relative values
min_expr	The minimum level of expression to show in the plot
cell_size	A number how large the cells should be in the plot
label_by_short_name	a boolean that indicates whether cells should be labeled by their short name
show_density	a boolean that indicates whether a 2D density estimation should be shown in the plot
round_expr	a boolean that indicates whether cds_expr values should be rounded or not

Value

a ggplot2 plot object

monocle documentation built on Nov. 8, 2020, 5:06 p.m.