barplot_cluster_abundance: Plot Abundance Comparison Across Sample Clusters

In altairwei/rhapsodykit: A Set of Tools for BD Rhapsody WTA Downstream Analysis

Plot Abundance Comparison Across Sample Clusters

Description

Plot Abundance Comparison Across Sample Clusters

Usage

barplot_cluster_abundance(x, ...)

## S3 method for class 'data.frame'
barplot_cluster_abundance(df, position = c("stack", "dodge"))

## S3 method for class 'SingleCellExperiment'
barplot_cluster_abundance(sce, ...)

## S3 method for class 'Seurat'
barplot_cluster_abundance(srt, ...)

Arguments

...	Args passed to muscat::aggregateData
df	Data frame to plot, must contains columns: frequency the proportion of cells in a cluster in a sample sample_id IDs of samples cluster_id IDs of clusters group_id IDs of sample groups
position	Specify the way to display the bar chart
sce	A SingleCellExperiment object. The following cell metadata (colData) columns have to be provided: sample_id unique sample identifiers cluster_id subpopulation (cluster) assignments group_id experimental group/condition
srt	Seurat object. The sample and group infromation must exist in [e-mail] slot.

Value

A ggplot2 object

Methods (by class)

• data.frame: Plot abundance comparison across sample clusters from a formatted data.frame

• SingleCellExperiment: Calculate the proportion of cells from object SingleCellExperiment

• Seurat: Calculate the proportion of cells from Seurat object.

altairwei/rhapsodykit documentation built on Feb. 1, 2023, 8:52 a.m.