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.

Value

a ggplot2 plot object