plotAbundances {CATALYST}R Documentation

Population frequencies across samples & clusters

Description

Plots the relative population abundances of the specified clustering.

Usage

plotAbundances(x, ...)

## S4 method for signature 'daFrame'
plotAbundances(x, k = "meta20", by = c("sample_id",
  "cluster_id"), group_by = NULL, shape_by = NULL)

Arguments

x

a daFrame.

...

optional arguments.

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

data(PBMC_fs, PBMC_panel, PBMC_md)
re <- daFrame(PBMC_fs, PBMC_panel, PBMC_md)
# run clustering
re <- cluster(re)
# plot relative population abundances 
plotAbundances(re, k="meta12")                 # ...by sample 
plotAbundances(re, k="meta8", by="cluster_id") # ...by cluster


[Package CATALYST version 1.8.6 Index]