Make a grid of feature plots for selected markers.

Usage

selected_markers_dimplot(
  sce,
  dimred,
  selected_markers_df,
  assay = "logcounts",
  low_color = "lightgrey",
  high_color = "red",
  combine = TRUE
)

Arguments

sce

A SingleCellExperiment object.

dimred

A character scalar: name of dimred to plot.

selected_markers_df

A dataframe-like object with two character columns:

group: marker group.
markers: gene symbols of markers separated by ":". Such dataframe is created from a CSV file defined in the SELECTED_MARKERS_FILE parameter in e.g. 02_norm_clustering.yaml config.

Input target: selected_markers_df or selected_markers_int_df

assay

A character scalar: name of assay in sce to be used.

low_color, high_color

Passed as list(low = low_color, high = high_color) to plotReducedDim_mod().

combine

A logical scalar: if TRUE, combine plots to a single patchwork object, otherwise return list of ggplot2 objects.

Value

See the combine argument.