qSeuViolin: Create a Violin Plot for a Seurat Object Feature and save the...

In vertesy/Seurat.utils: Seurat.utils - utility functions for Seurat

Create a Violin Plot for a Seurat Object Feature and save the file.

Description

Generates a violin plot for a specified feature in a Seurat object, allowing for the data to be split by a specified grouping variable. The function supports customization options such as logarithmic scaling, custom titles, and more.

Usage

qSeuViolin(
  obj,
  feature = "nFeature_RNA",
  ident = GetNamedClusteringRuns(obj = obj, v = FALSE)[1],
  assay = "RNA",
  slot = "data",
  split.by = NULL,
  colors = NULL,
  clip.outliers = TRUE,
  replace.na = FALSE,
  pt.size = 0,
  sub = NULL,
  suffix = NULL,
  suffix.2.title = FALSE,
  caption = try(.parseKeyParams(obj), silent = TRUE),
  logY = TRUE,
  hline = FALSE,
  ylab = "Expression",
  ylimit = NULL,
  legend = TRUE,
  legend.pos = NULL,
  legend.title = NULL,
  show_plot = TRUE,
  grid = TRUE,
  w = NULL,
  h = 7,
  ...
)

Arguments

obj	A Seurat object to be plotted.
feature	A character string specifying the name of the feature to plot.
ident	A character vector specifying the identities to be used in the plot.
split.by	A character string specifying the grouping variable for splitting the plot.
colors	A character vector specifying the colors to use for the plot.
clip.outliers	A logical indicating whether to clip outliers.
replace.na	A logical indicating whether NA values should be replaced.
pt.size	The size of the individual datapoints in the plot. Default: 0 for simple violin plot.
sub	Subtitle of the plot. Default: feature by ident.
suffix	An optional string to append to the title of the plot.
suffix.2.title	A logical indicating whether to append the suffix to the plot title.
caption	A character string or logical for the plot caption. If FALSE, no caption is displayed.
logY	A logical indicating whether to use a logarithmic scale for the y-axis.
hline	A numeric or logical value; if numeric, the value where a horizontal line should be drawn.
ylab	Y-axis label. Default: "Expression".
ylimit	A numeric vector specifying the limits of the y-axis.
legend	Show legend; Default: opposite of label.
legend.pos	Position of legend; Default: 'NULL'.
legend.title	Title of legend; Default: 'split.by'.
show_plot	A logical indicating whether to display the plot.
grid	A logical indicating whether to display grid lines.
w	Width of the plot.
h	Height of the plot.
...	Additional arguments passed to VlnPlot.

Value

A ggplot object representing the violin plot.

Examples

# Assuming `seurat_obj` is a valid Seurat object
qSeuViolin(obj = seurat_obj, feature = "nFeature_RNA")

vertesy/Seurat.utils documentation built on Dec. 4, 2024, 5:20 p.m.