Seurat: FeatureScatter – R documentation

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FeatureScatter

Scatter plot of single cell data

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,
  combine = TRUE,
  slot = "data",
  plot.cor = TRUE,
  raster = NULL
)

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)
`combine`	Combine plots into a single `patchworked`
`slot`	Slot to pull data from, should be one of 'counts', 'data', or 'scale.data'
`plot.cor`	Display correlation in plot title
`raster`	Convert points to raster format, default is `NULL` which will automatically use raster if the number of points plotted is greater than 100,000

Value

A ggplot object

Examples

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

Seurat

Tools for Single Cell Genomics

v4.0.1

GPL-3 | file LICENSE

Authors

Andrew Butler [ctb] (<https://orcid.org/0000-0003-3608-0463>), Saket Choudhary [ctb] (<https://orcid.org/0000-0001-5202-7633>), Charlotte Darby [ctb] (<https://orcid.org/0000-0003-2195-5300>), Jeff Farrell [ctb], Christoph Hafemeister [ctb] (<https://orcid.org/0000-0001-6365-8254>), Yuhan Hao [ctb] (<https://orcid.org/0000-0002-1810-0822>), Paul Hoffman [aut, cre] (<https://orcid.org/0000-0002-7693-8957>), Jaison Jain [ctb] (<https://orcid.org/0000-0002-9478-5018>), Efthymia Papalexi [ctb] (<https://orcid.org/0000-0001-5898-694X>), Patrick Roelli [ctb], Rahul Satija [ctb] (<https://orcid.org/0000-0001-9448-8833>), Karthik Shekhar [ctb], Avi Srivastava [ctb] (<https://orcid.org/0000-0001-9798-2079>), Tim Stuart [ctb] (<https://orcid.org/0000-0002-3044-0897>), Kristof Torkenczy [ctb] (<https://orcid.org/0000-0002-4869-7957>), Shiwei Zheng [ctb] (<https://orcid.org/0000-0001-6682-6743>), Satija Lab and Collaborators [fnd]

Initial release

2021-03-17