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Square stacked violin plot of gene expression in each identity

Source: R/Grid_VlnPlot.R
Grid_VlnPlot.Rd

This function is a stacked violin plot optimized to display the average expression of features in a Seurat object in a grid fashion (square) instead of a single column like other stacked violin functions available in other packages.

Usage

Grid_VlnPlot(
  seurat_object,
  assay = "RNA",
  layer = "data",
  features,
  idents = NULL,
  scale = TRUE,
  rotate.axis = FALSE,
  colors = NULL,
  order.idents = NULL,
  order.colors = TRUE,
  idents.text.size = 9,
  show.idents = FALSE,
  features.text.size = 9,
  legend.text.size = 7,
  legend.side = "bottom",
  show.legend = TRUE,
  ncol = "square"
)

Arguments

seurat_object

A Seurat object.

assay

Character. The name of an assay containing the layer with the expression matrix. If the seurat_object contains multiple 'RNA' assays, you may specify which one to use (for example, 'RNA2' if you have created a second 'RNA' assay you named 'RNA2'. See Seurat v5 vignettes for more information). You may also use another assay, such as 'SCT', to pull feature expression from.

layer

Character. The name of a layer (formerly known as slot) which stores the expression matrix. It is recommended to use 'data'.

features

Character. The names of one or several features to plot the cell expression from.

idents

Character. The names of one or several identities in the active.ident metadata to select. If NULL, all identities are used.

scale

Logical. If TRUE, scales the violins to have the same max height between features.

rotate.axis

Logical. If TRUE, flips the axis, displaying violins vertically instead of horizontally.

colors

Character. The color names for each identity of the active.ident metadata or in idents. If NULL, uses Seurat's default colors.

order.idents

Character or Numeric. Either 'reverse', or the identities (as names or as numeric values corresponding to the indices) of the active.ident metadata or in idents to order the cells.

order.colors

Logical. If TRUE, the colors will automatically be ordered according to order.prop. Ignored if order.prop = NULL.

idents.text.size

Numeric. The font size of the identity names. Ignored if show.idents = FALSE.

show.idents

Logical. If TRUE, shows the identity names on the plot.

features.text.size

Numeric. The font size of the feature names.

legend.text.size

Numeric. The font size of the legend text. Ignored if show.legend = FALSE.

legend.side

Character. The side where the legend will be displayed, either 'left', 'right', 'top' or 'bottom'. Ignored if show.legend = FALSE.

show.legend

Logical. If TRUE, shows the legend.

ncol

Numeric. The number of columns to use. If 'square', will display features in a square grid or as close as possible depending on the number of features.

Value

A ggplot2 object.

Examples

# Prepare data
pbmc3k <- Right_Data("pbmc3k")
pbmc3k.markers <- c("CCR7", "CD14", "CD40LG",
                    "CD79A", "CD8A", "CDKN1C",
                    "GNLY", "CLEC10A", "PPBP")

# Example 1: default parameters
Grid_VlnPlot(pbmc3k,
             features = pbmc3k.markers)