selected_markers_dimplot: Make a grid of feature plots for selected markers.

In bioinfocz/scdrake: A pipeline for droplet-based single-cell RNA-seq data secondary analysis implemented in the drake Make-like toolkit for R language

Make a grid of feature plots for selected markers.

Description

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.

bioinfocz/scdrake documentation built on Jan. 29, 2024, 10:24 a.m.