plotCounts: Plot counts

In acidgenomics/minimalism: Acid Genomics Plot Functions and Themes

Plot counts

Description

Plot counts

Usage

plotCounts(object, ...)

plotDots(object, ...)

plotViolin(object, ...)

## S4 method for signature 'SingleCellExperiment'
plotCounts(
  object,
  genes,
  assay = c("logcounts", "normcounts"),
  geom = c("violin", "dots"),
  perSample = TRUE,
  legend = getOption(x = "acid.legend", default = TRUE),
  title = NULL
)

## S4 method for signature 'SummarizedExperiment'
plotCounts(
  object,
  genes,
  assay = 1L,
  interestingGroups = NULL,
  convertGenesToSymbols = TRUE,
  geom = c("point", "violin", "boxplot", "bar"),
  trans = c("identity", "log2", "log10"),
  line = c("none", "median", "mean", "geometricMean"),
  legend = getOption(x = "acid.legend", default = TRUE),
  style = c("facet", "wide"),
  sort = FALSE,
  labels = list(title = NULL, subtitle = NULL, sampleAxis = NULL, countAxis = "counts")
)

## S4 method for signature 'SingleCellExperiment'
plotDots(
  object,
  genes,
  perSample = TRUE,
  colMin = -2.5,
  colMax = 2.5,
  dotMin = 0L,
  dotScale = 6L,
  color = getOption(x = "acid.continuous.color", default =
    ggplot2::scale_color_gradient2(low = "orange", mid = "gray75", high = "purple",
    midpoint = 0L)),
  legend = getOption(x = "acid.legend", default = TRUE),
  title = NULL
)

## S4 method for signature 'SingleCellExperiment'
plotViolin(
  object,
  genes,
  assay = c("logcounts", "normcounts"),
  perSample = TRUE,
  scale = c("count", "width", "area"),
  color = getOption(x = "acid.discrete.color", default =
    AcidPlots::acid_scale_color_synesthesia_d()),
  legend = getOption(x = "acid.legend", default = TRUE),
  title = NULL
)

Arguments

object	Object.
genes	character or missing. Gene identifiers. The function will automatically match identifiers corresponding to the rownames of the object, or gene symbols defined in the object.
assay	vector(1). Assay name or index position.
geom	character(1). Plot type. Uses match.arg() to pick the type. Currently supports "dots" and "violin".
perSample	logical(1). Visualize the distributions per sample.
legend	logical(1). Include plot legend.
title	character(1). Title.
interestingGroups	character. Groups of interest to use for visualization. Corresponds to factors describing the columns of the object.
convertGenesToSymbols	logical(1). Attempt to automatically convert gene identifiers to gene symbols. Only applies when object contains mappings defined in rowRanges.
trans	character(1). Name of the axis scale transformation to apply. For more information: help(topic = "scale_x_continuous", package = "ggplot2")
line	character(1). Include average (median, mean, or geometric mean) line for each interesting group. Disabled by default and if samples are colored by sample name.
style	character(1). Plot style.
sort	logical(1). Sort the genes alphabetically. This setting applies to the gene symbols rather than the gene identifiers when convertGenesToSymbols is TRUE.
labels	list. ggplot2 labels. See ggplot2::labs() for details.
colMin	numeric(1). Minimum scaled average expression threshold. Everything smaller will be set to this.
colMax	numeric(1). Maximum scaled average expression threshold. Everything larger will be set to this.
dotMin	numeric(1). The fraction of cells at which to draw the smallest dot. All cell groups with less than this expressing the given gene will have no dot drawn.
dotScale	numeric(1). Scale the size of the points, similar to cex.
color	ScaleDiscrete. Desired ggplot2 color scale. Must supply discrete values. When set NULL, the default ggplot2 color palette will be used. If manual color definitions are desired, we recommend using ggplot2::scale_color_manual(). To set the discrete color palette globally, use: options("acid.color.discrete" = ggplot2::scale_color_viridis_d())
scale	character(1). If "area" (default), all violins have the same area (before trimming the tails). If "count", areas are scaled proportionally to the number of observartions. If "width", all violins have the same maximum width. See ggplot2::geom_violin for details.
...	Additional arguments.

Value

• style = "facet": ggplot grouped by sampleName, with ggplot2::facet_wrap() applied to panel the samples.

• style = "wide": ggplot in wide format, with genes on the x-axis.

Note

Updated 2023-12-04.

See Also

• Seurat::DotPlot().

• Seurat::VlnPlot().

• Seurat::RidgePlot().

• monocle3::plot_genes_violin().

Examples

data(
    RangedSummarizedExperiment,
    SingleCellExperiment_Seurat,
    package = "AcidTest"
)

## SummarizedExperiment ====
object <- RangedSummarizedExperiment
rownames <- head(rownames(object))
print(rownames)
g2s <- AcidGenomes::GeneToSymbol(object)
geneIds <- head(g2s[[1L]])
print(geneIds)
geneNames <- head(g2s[[2L]])
print(geneNames)

## Rownames, gene IDs, and gene names (symbols) are supported.
plotCounts(object, genes = geneIds, style = "facet")
plotCounts(object, genes = geneNames, style = "wide")

## SingleCellExperiment ====
object <- SingleCellExperiment_Seurat

## Plotting with either gene IDs or gene names (symbols) works.
genes <- head(rownames(object), n = 4L)
print(genes)

## Per sample mode enabled.
plotCounts(object, genes = genes, perSample = TRUE)

## Per sample mode disabled.
plotCounts(object, genes = genes, perSample = FALSE)

acidgenomics/minimalism documentation built on April 1, 2024, 10:34 a.m.