bb_plot_genes_in_pseudotime: Plots expression for one or more genes as a function of...
In blaserlab/blaseRtools: R Tools for Blaser Lab Data Analysis

bb_plot_genes_in_pseudotime

R Documentation

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

bb_plot_genes_in_pseudotime(
  cds,
  gene_or_genes,
  pseudotime_dim,
  min_expr = NULL,
  cell_size = 0.75,
  nrow = NULL,
  ncol = 1,
  panel_order = NULL,
  color_cells_by = pseudotime_dim,
  trend_formula_df = 3,
  label_by_short_name = TRUE,
  vertical_jitter = NULL,
  horizontal_jitter = NULL,
  legend_title = NULL
)

Arguments

`cds`	Cell data set to plot.
`gene_or_genes`	Gene or genes for which to plot pseudotime.
`pseudotime_dim`	The column holding the pseudotime dimension to plot along.
`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. Defaults to the value provided for pseudotime_dim.
`trend_formula_df`	degrees of freedom for the model formula used to fit the expression trend over pseudotime. The formulat takes the form of "~ splines::ns(pseudotime_dim, df = trend_formula_df)".
`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.