enhancedDimPlot: enhancedDimPlot

In milescsmith/enhancedDimPlot: Generate Scatterplots of scRNAseq Data

Description

A customized version of Seurat's DimPlot. Used for plotting dimensional reductions.

Usage

enhancedDimPlot(object, ...)

## S3 method for class 'Seurat'
enhancedDimPlot(object, reduction = "tsne",
  grouping_var = NULL, group_plot = NULL, split_by = NULL,
  dim_1 = 1, dim_2 = 2, pt_size = 1, alpha = 1, force = 1,
  label = TRUE, label_size = 3, label_text_color = "black",
  color_palette = NULL, fill_palette = NULL, ...)

Arguments

object	scRNAseq data object
...	Additional parameters
reduction	dimensional reduction to use. Default: tsne
grouping_var	Metadata variable to use in grouping data. If none is provided, the current ident will be used. Default: NULL
group_plot	If provided, only this identity group will be displayed. Default: NULL
split_by	Metadata variable to use in faceting the plots. Default: NULL
dim_1	Dimension to display along the x-axis. Default: 1
dim_2	Dimension to display along the y-axis. Default: 2
pt_size	Point size. Default: 1
alpha	Point alpha. Default: 1 (i.e. fully opaque)
force	Force parameter to pass to ggrepel. See geom_label_repel
label	Should labels be shown? Default: TRUE
label_size	Label font size. Default: 3
label_text_color	Label font color. Default: black
color_palette	Palette to use. If fill_palette is provided, this controls the color surrounding objects and the background of labels. Default: palette "bold_color" from package "rcartocolor"
fill_palette	Palette to use for point fill. By default, this matches color_palette

milescsmith/enhancedDimPlot documentation built on March 17, 2021, 4:20 a.m.