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]