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

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,
  plot_type = c("violin", "boxplot")
)

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 palette 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.
plot_type: A character(1) specifying whether to plot a 'violin' (default) or 'boxplot'.

Value

A ggplot() violin plot for selected genes.

Examples

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

plot_gene_express(sce = sce_ab, genes = c("G-D1_A"), plot_type = "boxplot")


# Access example data
if (!exists("sce_DLPFC_example")) sce_DLPFC_example <- fetch_deconvo_data("sce_DLPFC_example")
#> 2025-07-03 15:02:45.330359 Access ExperimentHub EH9626
#> see ?DeconvoBuddies and browseVignettes('DeconvoBuddies') for documentation
#> loading from cache

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


## plot as boxplot
plot_gene_express(
    sce = sce_DLPFC_example,
    category = "cellType_broad_hc",
    genes = c("GAD2", "CD22"),
    plot_type = "boxplot"
)


## 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
)


## with boxplot
plot_gene_express(
    sce = sce_DLPFC_example,
    category = "cellType_broad_hc",
    genes = c("GAD2", "CD22"), 
    plot_points = TRUE,
    plot_type = "boxplot"
)


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


## Add color pallet
my_cell_colors <- create_cell_colors(cell_types = levels(sce_DLPFC_example$cellType_broad_hc))
#> Creating classic palette for 7 broad cell types

plot_gene_express(
    sce = sce_DLPFC_example,
    category = "cellType_broad_hc",
    genes = c("GAD2", "CD22"),
    color_pal =  my_cell_colors,
    plot_type = "boxplot",
    plot_points = TRUE
)

Arguments

Value

See also

Examples