bb_gene_pseudotime: Plot expression of a gene or genes in pseudotime.
In blaserlab/blaseRtools: R Tools for Blaser Lab Data Analysis

bb_gene_pseudotime

R Documentation

Plot expression of a gene or genes in pseudotime.

Description

Plot expression of a gene or genes in pseudotime.

Usage

bb_gene_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`	A cell data set object subset with only cells and genes of interest
`min_expr`	Lower threshold of expression for plotting
`cell_size`	Size of point for plotting
`nrow`	Number of rows for facetting
`ncol`	Number of columns for facetting
`panel_order`	Character string for order of genes to plot
`color_cells_by`	A cds colData column
`trend_formula`	Formula for the trend line
`label_by_short_name`	Boolean to label by gene name or ID
`vertical_jitter`	Adjustment to vertical jitter. Optional
`horizontal_jitter`	Adjustment to horizontal jitter. Optional