plot_genes_in_pseudotime: Plots expression for one or more genes as a function of...

In cole-trapnell-lab/monocle3: Clustering, Differential Expression, and Trajectory Analysis for Single-Cell RNA-Seq

Plots expression for one or more genes as a function of pseudotime

Description

Plots expression for one or more genes as a function of pseudotime

Usage

plot_genes_in_pseudotime(
  cds_subset,
  min_expr = NULL,
  cell_size = 0.75,
  nrow = NULL,
  ncol = 1,
  panel_order = NULL,
  color_cells_by = "pseudotime",
  trend_formula = "~ splines::ns(pseudotime, df=3)",
  label_by_short_name = TRUE,
  vertical_jitter = NULL,
  horizontal_jitter = NULL
)

Arguments

cds_subset	subset cell_data_set including only the genes to be plotted.
min_expr	the minimum (untransformed) expression level to plot.
cell_size	the size (in points) of each cell used in the plot.
nrow	the number of rows used when laying out the panels for each gene's expression.
ncol	the number of columns used when laying out the panels for each gene's expression
panel_order	vector of gene names indicating the order in which genes should be laid out (left-to-right, top-to-bottom). If label_by_short_name = TRUE, use gene_short_name values, otherwise use feature IDs.
color_cells_by	the cell attribute (e.g. the column of colData(cds)) to be used to color each cell.
trend_formula	the model formula to be used for fitting the expression trend over pseudotime.
label_by_short_name	label figure panels by gene_short_name (TRUE) or feature ID (FALSE).
vertical_jitter	A value passed to ggplot to jitter the points in the vertical dimension. Prevents overplotting, and is particularly helpful for rounded transcript count data.
horizontal_jitter	A value passed to ggplot to jitter the points in the horizontal dimension. Prevents overplotting, and is particularly helpful for rounded transcript count data.

Value

a ggplot2 plot object

cole-trapnell-lab/monocle3 documentation built on April 7, 2024, 9:24 p.m.