FeatureScatter: Scatter plot of single cell data

In lambdamoses/SeuratBasics: Slimmed down version of Seurat

Description

Creates a scatter plot of two features (typically feature expression), across a set of single cells. Cells are colored by their identity class. Pearson correlation between the two features is displayed above the plot.

Usage

FeatureScatter(
  object,
  feature1,
  feature2,
  cells = NULL,
  group.by = NULL,
  cols = NULL,
  pt.size = 1,
  shape.by = NULL,
  span = NULL,
  smooth = FALSE,
  slot = "data"
)

Arguments

object	Seurat object
feature1	First feature to plot. Typically feature expression but can also be metrics, PC scores, etc. - anything that can be retreived with FetchData
feature2	Second feature to plot.
cells	Cells to include on the scatter plot.
group.by	Name of one or more metadata columns to group (color) cells by (for example, orig.ident); pass 'ident' to group by identity class
cols	Colors to use for identity class plotting.
pt.size	Size of the points on the plot
shape.by	Ignored for now
span	Spline span in loess function call, if NULL, no spline added
smooth	Smooth the graph (similar to smoothScatter)
slot	Slot to pull data from, should be one of 'counts', 'data', or 'scale.data'

Value

A ggplot object

Examples

FeatureScatter(object = pbmc_small, feature1 = 'CD9', feature2 = 'CD3E')

lambdamoses/SeuratBasics documentation built on May 6, 2020, 9:32 a.m.