plot_gene_express: Plot the gene expression of a list of genes in a SCE object
In lahuuki/DeconvoBuddies: Helper Functions for LIBD Deconvolution

plot_gene_express

R Documentation

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

Description

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.

Usage

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")

## 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))

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
)

lahuuki/DeconvoBuddies documentation built on July 4, 2025, 11:27 p.m.