seuratBoxPlot: Boxplot Function:

In LabexCortexBioinformatics/LxCxUtils: Utils Function for Labex Cortex Bioinformatics Platform

Boxplot Function

Description

This function aims at replacing the VlnPlot function from Seurat with box plots.

Usage

seuratBoxPlot(
  seur,
  features,
  group.by = "ident",
  assay = "RNA",
  slot = "data",
  ncol = 2,
  cols = NULL,
  pt.size = 1,
  pt.alpha = 1,
  remove_legend = FALSE,
  remove_x_text = FALSE
)

Arguments

seur	The Seurat object within which the data will be fetched.
features	Vector of features to use. Can be genes, or any other continuous column accessible by Seurat's FetchData.
group.by	Metadata column used to make the groups in the boxplot. Default to "ident"
assay	Assay used to Fetch the data from. Will replace the Default Assay. Default to "RNA"
slot	Slot used within the assay the fetch data from. Default to "data"
ncol	Number of column in the gridExtra object. Default to 2
pt.size	Size of the points to plot. Either set this to 0 or pt.alpha to 0 to remove points. Default to 1
pt.alpha	Transparency of the points. Either set this to 0 or pt.size to 0 to remove points. Default to 1
remove_legend	Whether to remove the color legend. Default to FALSE
remove_x_text	Whether to remove x-axis legend. Default to FALSE

Value

A gridExtra object containing as much plots as there are elements in the features parameter. If there is only one feature, it will return the ggplot object.

LabexCortexBioinformatics/LxCxUtils documentation built on Aug. 2, 2022, 6:23 a.m.