plot_gene_express: Plot the gene expression of a list of genes in a SCE object
In LieberInstitute/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
)

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.

Examples

## Using Symbol as rownames makes this more human readable
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")

## 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")

LieberInstitute/DeconvoBuddies documentation built on Oct. 17, 2024, 4:24 a.m.