marker_plot: Make a marker plot.

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 marker plot.

Description

A marker plot is composed of:

• Two plots of a dimred: one colored by a clustering, and second colored by expression of a marker (feature plot).

• A plot of summarized marker expression: proportion of cells expressing a marker, colored by average expression.

• A violin plot: expression of a marker in each cluster.

Usage

marker_plot(
  sce,
  dimred_name,
  gene_ensembl_id,
  group,
  cluster_plot_title = NULL,
  cluster_plot_subtitle = NULL,
  cluster_plot_legend_title = NULL,
  cluster_plot_label = TRUE,
  cluster_plot_point_size = 1,
  feature_plot_point_size = 1,
  vln_plot_legend_title = NULL
)

Arguments

sce	A SingleCellExperiment object.
dimred_name	A character scalar.
gene_ensembl_id	A character scalar. ENSEMBL ID of a marker.
group	A character scalar: name of column in colData(sce) by which are cells separated (e.g. clustering). A character vector or factor: assignment of cells to groups (clusters). Must have the same length as the number of cells (columns) in sce.
cluster_plot_title, cluster_plot_subtitle, cluster_plot_legend_title, cluster_plot_label	A character scalar. Applied to the dimred plot which is colored by group.
cluster_plot_point_size	A numeric scalar.
feature_plot_point_size	A numeric scalar. Applied to the feature plot.
vln_plot_legend_title	A character scalar. Applied to the violin plot.

Value

A patchwork object.

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