plotAbundances {CATALYST}R Documentation

Population frequencies across samples & clusters

Description

Plots the relative population abundances of the specified clustering.

Usage

plotAbundances(
  x,
  k = "meta20",
  by = c("sample_id", "cluster_id"),
  group_by = NULL,
  shape_by = NULL
)

Arguments

x

a SingleCellExperiment.

k

character string. Specifies which clustering to use.

by

a character string specifying whether to plot frequencies by samples or clusters.

group_by

a character string. Should corresponds to a column name of rowData(x) other than "sample_id" and "cluster_id". The default NULL will use the first factor available.

shape_by

a character string. Should correspond to a column name of rowData(x) other than "sample_id" and "cluster_id".

Value

a ggplot object.

Author(s)

Helena Lucia Crowell helena.crowell@uzh.ch

References

Nowicka M, Krieg C, Weber LM et al. CyTOF workflow: Differential discovery in high-throughput high-dimensional cytometry datasets. F1000Research 2017, 6:748 (doi: 10.12688/f1000research.11622.1)

Examples

# construct SCE & run clustering
data(PBMC_fs, PBMC_panel, PBMC_md)
sce <- prepData(PBMC_fs, PBMC_panel, PBMC_md)
sce <- cluster(sce)

# plot relative population abundances 
plotAbundances(sce, k="meta12")                 # ...by sample 
plotAbundances(sce, k="meta8", by="cluster_id") # ...by cluster


[Package CATALYST version 1.10.3 Index]