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Seurat

PolyFeaturePlot

Polygon FeaturePlot

Description

Plot cells as polygons, rather than single points. Color cells by any value accessible by FetchData.

Usage

PolyFeaturePlot(
  object,
  features,
  cells = NULL,
  poly.data = "spatial",
  ncol = ceiling(x = length(x = features)/2),
  min.cutoff = 0,
  max.cutoff = NA,
  common.scale = TRUE,
  flip.coords = FALSE
)

Arguments

object

Seurat object
features

Vector of features to plot. Features can come from:

  • An Assay feature (e.g. a gene name - "MS4A1")

  • A column name from meta.data (e.g. mitochondrial percentage - "percent.mito")

  • A column name from a DimReduc object corresponding to the cell embedding values (e.g. the PC 1 scores - "PC_1")

cells

Vector of cells to plot (default is all cells)
poly.data

Name of the polygon dataframe in the misc slot
ncol

Number of columns to split the plot into
min.cutoff

Vector of minimum and maximum cutoff values for each feature, may specify quantile in the form of 'q##' where '##' is the quantile (eg, 'q1', 'q10')
max.cutoff

Vector of minimum and maximum cutoff values for each feature, may specify quantile in the form of 'q##' where '##' is the quantile (eg, 'q1', 'q10')
common.scale

...
flip.coords

Flip x and y coordinates

Value

Returns a ggplot object

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

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