plot_marker_express: Plot gene expression violin plots for top marker genes for...
In lahuuki/DeconvoBuddies: Helper Functions for LIBD Deconvolution

plot_marker_express

R Documentation

Plot gene expression violin plots for top marker genes for one cell type

Description

This function plots the top n marker genes for a specified cell type based off of the stats table from get_mean_ratio2(). The gene expression is plotted as violin plot with plot_gene_express and adds annotations to each plot.

Usage

plot_marker_express(
  sce,
  stats,
  cell_type,
  n_genes = 4,
  rank_col = "MeanRatio.rank",
  anno_col = "MeanRatio.anno",
  gene_col = "gene",
  cellType_col = "cellType",
  color_pal = NULL,
  plot_points = FALSE,
  ncol = 2
)

Arguments

`sce`	SummarizedExperiment-class object
`stats`	A `data.frame()` generated by `get_mean_ratio()` and/or `findMarkers_1vAll()`.
`cell_type`	A `character()` target cell type to plot markers for
`n_genes`	An `integer(1)` of number of markers you'd like to plot
`rank_col`	The `character(1)` name of column to rank genes by in `stats`.
`anno_col`	The `character(1)` name of column containing annotation in `stats`.
`gene_col`	The `character(1)` name of column containing gene name in `stats` should be the same syntax as `rownames(sce)`.
`cellType_col`	The `character(1)` name of `colData()` column containing cell type for `sce` data. It should match `cellType.target` in `stats`.
`color_pal`	A named `character(1)` vector that contains a color pallet matching the `cell_type` values.
`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 ggplot2 object created with plot_gene_express(). It is a scater::plotExpression() style violin plot for selected marker genes.

Examples

## Download the processed study data from
## <https://github.com/LieberInstitute/Human_DLPFC_Deconvolution>.
if (!exists("sce_DLPFC_example")) sce_DLPFC_example <- fetch_deconvo_data("sce_DLPFC_example")

## load example marker stats
data("marker_test")

## Plot the top markers for Astrocytes
plot_marker_express(
    sce = sce_DLPFC_example,
    stat = marker_test,
    cellType_col = "cellType_broad_hc",
    cell_type = "Astro",
    gene_col = "gene"
)

lahuuki/DeconvoBuddies documentation built on Dec. 18, 2024, 6:24 a.m.