enhancedFeaturePlot: enhancedFeaturePlot

In milescsmith/enhancedDimPlot: Generate Scatterplots of scRNAseq Data

Description

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

Usage

enhancedFeaturePlot(object, ...)

## S3 method for class 'Seurat'
enhancedFeaturePlot(object, feature, reduction = "tsne",
  grouping_var = NULL, subset_labels = NULL, group_plot = NULL,
  split_by = NULL, lower.cutoff = 0.05, upper.cutoff = 0.95,
  dim_1 = 1, dim_2 = 2, pt_size = 1, alpha = 0.5, force = 1,
  label = TRUE, label_size = 3, label_text_color = "black",
  scale_colors = c("grey90", "red"), fill_palette = NULL, ...)

Arguments

object	scRNAseq data object
...	Additional parameters
feature	Feature to use for coloring. Anything FetchData can extract.
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
subset_labels	A list of the groups in grouping_var to display. By default, all are displayed. 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
lower.cutoff	Remove expression values below this quantile. Expressed as decimal. Default: 0.05
upper.cutoff	Remove expression values above this quantile. Expressed as decimal. Default: 0.95
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
scale_colors	Colors to use for expression gradient. Takes a list of c(low, high). Default: c("grey90","red")
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.