plot_markers: Plot marker metrics

In cole-trapnell-lab/garnett: Automated cell type classification

Plot marker metrics

Description

This function takes as input the output of the check_markers function and generates a plot to visualize the most important metrics.

Usage

plot_markers(marker_check_df, amb_marker_cutoff = 0.5, label_size = 2)

Arguments

marker_check_df	Marker check data.frame - output of check_markers.
amb_marker_cutoff	Numeric. Cutoff at which to label ambiguous markers. Default 0.5.
label_size	Numeric, size of the text labels for ambiguous markers and unplotted markers.

Value

A ggplot object of the marker plot.

Examples

library(org.Hs.eg.db)

marker_file_path <- system.file("extdata", "pbmc_test.txt",
                                package = "garnett")
data(test_cds)
marker_check <- check_markers(test_cds,
                              marker_file_path,
                              db=org.Hs.eg.db,
                              cds_gene_id_type = "SYMBOL",
                              marker_file_gene_id_type = "SYMBOL")

plot_markers(marker_check)

cole-trapnell-lab/garnett documentation built on Jan. 6, 2025, 2:18 p.m.