plotScatter {CATALYST} | R Documentation

## Scatter plot

### Description

Bivariate scatter plots including visualization of (group-specific) gates, their boundaries and percentage of selected cells.

### Usage

    plotScatter(
      x,
      chs,
      color_by = NULL,
      facet_by = NULL,
      bins = 100,
      assay = "exprs",
      label = c("target", "channel", "both"),
      zeros = FALSE,
      k_pal = CATALYST:::.cluster_cols
    )

### Arguments

`x` | a `SingleCellExperiment`.
`chs` | character string pecifying which channels to plot. Valid values are antigens: `rownames(x)`, channel names: `channels(x)` or non-mass channels stored in `names([int_]colData(x))`, and should correspond to numeric variables.
`color_by` | character string specifying a cell metadata column to color by; valid values are `names(colData(x))`, `names(int_colData(x))`; `names(cluster_codes(x))` (if `cluster` has been run); or NULL to color by density.
`facet_by` | character string specifying a non-numeric cell metadata column to facet by; valid values are `names(colData(x))`. When `length(chs) == 1`, 2 facetting variables may be provided, otherwise 1 only.
`bins` | numeric of length 1 giving the number of bins for `geom_hex` when coloring by density.
`assay` | character string specifying which assay data to use. Should be one of `assayNames(x)`.
`label` | character string specifying axis labels should include antigen targets, channel names, or a concatenation of both.
`zeros` | logical specifying whether to include 0 values.
`k_pal` | character string specifying the cluster color palette; ignored when `color_by` is not one of `names(cluster_codes(x))`. If less than `nlevels(cluster_ids(x, k))` are supplied, colors will be interpolated via `colorRampPalette`.

### Value

a `ggplot` object.

### Author(s)

Helena L Crowell helena.crowell@uzh.ch

### Examples

    data(raw_data)
    sce <- prepData(raw_data)

    dna_chs <- c("DNA1", "DNA2")
    plotScatter(sce, dna_chs, label = "both")

    plotScatter(sce,
      chs = sample(rownames(sce), 4),
      color_by = "sample_id")

    sce <- prepData(sample_ff)
    ids <- sample(rownames(sample_key), 3)
    sce <- assignPrelim(sce, sample_key[ids, ])
    sce <- sce[, sce$bc_id %in% ids]

    chs <- sample(rownames(sce), 5)
    plotScatter(sce, chs, color_by = "bc_id")
    plotScatter(sce, chs, color_by = "delta")

[Package CATALYST version 1.18.1 Index]