plotDR {CATALYST} | R Documentation

## Plot reduced dimensions

### Description

Dimension reduction plot colored by expression, cluster, sample or group ID.

### Usage

    plotDR(x, dr = NULL, color_by = "condition")

### Arguments

`x` | a `SingleCellExperiment`.
`dr` | character string specifying which dimension reduction to use. Should be one of `reducedDimNames(x)`; default to the 1st available.
`color_by` | character string corresponding to a `colData(x)` column. Specifies the color coding.

### Value

a `ggplot` object.

### Author(s)

Helena Lucia Crowell

### 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)

    library(scater)
    sce <- runUMAP(sce, exprs_values = "exprs")

    # color by pS6 expression, split by group
    plotDR(sce, color_by = "pS6") +
      facet_wrap("condition")

    # color by 8 metaclusters, split by sample
    plotDR(sce, color_by = "meta8") +
      facet_wrap("sample_id", ncol = 4)

[Package CATALYST version 1.10.3 Index]