Plot expression profiles along a pseudotime trajectory

Plots the expression profiles of one or more genes along a pseudotime trajectory per species.

Usage

plotExprAlongPseudotime(
  genes,
  sce,
  pseudotime_column = "pseudotime",
  cell_type_column = "cell_type",
  species_colors = NULL,
  cell_type_colors = NULL,
  font_size = 14,
  ncol = 1
)

Arguments

genes

Character vector, the names of the genes for which the expression profiles should be plotted.

sce

SingleCellExperiment object containing the expression data (raw counts, logcounts and metadata) for all network genes. Required metadata columns:

species

Character, the name of the species.

{{pseudotime_column}}

Numeric, inferred pseudotime.

{{cell_type_column}}

Character, cell type annotation (optional).

pseudotime_column

Character, the name of the pseudotime column in the metadata of sce (default: "pseudotime").

cell_type_column

Character, the name of the cell type annotation column in the metadata of sce (default: "cell_type", if there is no cell type annotation available or the user wants to omit the cell type rug plot, this parameter should be set to NULL).

species_colors

Character vector, colors per species.

cell_type_colors

Character vector, colors per cell type.

font_size

Numeric, font size (default: 14).

ncol

Integer, the number of columns the genes (facets) should be organized into (default: 1).

Value

A curve plot as a ggplot object showing the expression profiles of the genes along the pseudotime trajectory per species.

Details

The function plots the expression profiles as smoothed curves colored by species and faceted by gene.

The species, pseudotime and cell type information are taken from the metadata slot of the input sce object, and the expression data are taken from the logcounts assay of the input sce object.

The smoothed expression profiles are fitted per species and gene using loess with the formula "expression ~ pseusotime". The 95% confidence intervals of the fitted lines are calculated using predict and shown as lightly colored areas around the lines.

If a cell type metadata column is specified by the parameter cell_type_column, the cell are shown as a rug plot along the pseudotime axis colored by cell types. The colors for the rug can be be controlled by the parameter cell_type_colors.

See also

Other functions to plot gene expression profiles: plotExprHeatmap(), plotExprViolin(), plotSumExprHeatmap(), plotSumExprLine()

Examples

plotExprAlongPseudotime(regulators, sce)