Plot the gene expression of a list of genes in a SCE object

Source: R/plot_gene_express.R

This function plots the expression of one or more genes as a violin plot, over a user defined category, typically a cell type annotation. The plots are made using ggplot2.

plot_gene_express(
  sce,
  genes,
  assay_name = "logcounts",
  category = "cellType",
  color_pal = NULL,
  title = NULL,
  plot_points = FALSE,
  ncol = 2
)

Arguments

sce

A SummarizedExperiment-class object or one inheriting it.

genes

A character() vector specifying the genes to plot, this should match the format of rownames(sce).

assay_name

A character(1) specifying the name of the assay() in the sce object to use to rank expression values. Defaults to logcounts since it typically contains the normalized expression values.

category

A character(1) specifying the name of the categorical variable to group the cells or nuclei by. Defaults to cellType.

color_pal

A named character(1) vector that contains a color pallet matching the category values.

title

A character(1) to title the plot.

plot_points

A logical(1) indicating whether to plot points over the violin, defaults to FALSE as these often become over plotted and quite large (especially when saved as PDF).

ncol

An integer(1) specifying the number of columns for the facet in the final plot. Defaults to 2.

Value

A ggplot() violin plot for selected genes.

See also

Other expression plotting functions: plot_marker_express(), plot_marker_express_ALL(), plot_marker_express_List()

Examples

## Using Symbol as rownames makes this more human readable
data(sce_ab)
plot_gene_express(sce = sce_ab, genes = c("G-D1_A"))


# Access example data
if (!exists("sce_DLPFC_example")) sce_DLPFC_example <- fetch_deconvo_data("sce_DLPFC_example")
#> 2024-12-16 18:01:03.645353 loading file /github/home/.cache/R/BiocFileCache/30161ee4ad2_sce_DLPFC_example.Rdata%3Frlkey%3Dv3z4u8ru0d2y12zgdl1az07q9%26st%3D1dcfqc1i%26dl%3D1

## plot expression of two genes
plot_gene_express(
    sce = sce_DLPFC_example,
    category = "cellType_broad_hc",
    genes = c("GAD2", "CD22")
)


## plot points - note this creates large images and is easy to over plot
plot_gene_express(
    sce = sce_DLPFC_example,
    category = "cellType_broad_hc",
    genes = c("GAD2", "CD22"), plot_points = TRUE
)


## Add title
plot_gene_express(
    sce = sce_DLPFC_example,
    category = "cellType_broad_hc",
    genes = c("GAD2", "CD22"),
    title = "My Genes"
)