Plot counts

Plot counts

Usage

plotCounts(object, ...)

plotDots(object, ...)

plotViolin(object, ...)

# S4 method for 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 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 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 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.

Examples

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

## SummarizedExperiment ====
object <- RangedSummarizedExperiment
rownames <- head(rownames(object))
print(rownames)
#> [1] "gene001" "gene002" "gene003" "gene004" "gene005" "gene006"
g2s <- AcidGenomes::GeneToSymbol(object)
geneIds <- head(g2s[[1L]])
print(geneIds)
#> [1] "ENSG00000000003.15" "ENSG00000000005.6"  "ENSG00000000419.12"
#> [4] "ENSG00000000457.14" "ENSG00000000460.17" "ENSG00000000938.13"
geneNames <- head(g2s[[2L]])
print(geneNames)
#> [1] "TSPAN6"   "TNMD"     "DPM1"     "SCYL3"    "C1orf112" "FGR"     

## 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)
#> [1] "ENSG00000156738" "ENSG00000007312" "ENSG00000105369" "ENSG00000204287"

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


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

Usage

Arguments

Value

Note

See also

Examples