Seurat: DimHeatmap – R documentation

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DimHeatmap

Dimensional reduction heatmap

Description

Draws a heatmap focusing on a principal component. Both cells and genes are sorted by their principal component scores. Allows for nice visualization of sources of heterogeneity in the dataset.

Usage

DimHeatmap(
  object,
  dims = 1,
  nfeatures = 30,
  cells = NULL,
  reduction = "pca",
  disp.min = -2.5,
  disp.max = NULL,
  balanced = TRUE,
  projected = FALSE,
  ncol = NULL,
  fast = TRUE,
  raster = TRUE,
  slot = "scale.data",
  assays = NULL,
  combine = TRUE
)

PCHeatmap(object, ...)

Arguments

`object`	Seurat object
`dims`	Dimensions to plot
`nfeatures`	Number of genes to plot
`cells`	A list of cells to plot. If numeric, just plots the top cells.
`reduction`	Which dimmensional reduction to use
`disp.min`	Minimum display value (all values below are clipped)
`disp.max`	Maximum display value (all values above are clipped); defaults to 2.5 if `slot` is 'scale.data', 6 otherwise
`balanced`	Plot an equal number of genes with both + and - scores.
`projected`	Use the full projected dimensional reduction
`ncol`	Number of columns to plot
`fast`	If true, use `image` to generate plots; faster than using ggplot2, but not customizable
`raster`	If true, plot with geom_raster, else use geom_tile. geom_raster may look blurry on some viewing applications such as Preview due to how the raster is interpolated. Set this to FALSE if you are encountering that issue (note that plots may take longer to produce/render).
`slot`	Data slot to use, choose from 'raw.data', 'data', or 'scale.data'
`assays`	A vector of assays to pull data from
`combine`	Combine plots into a single `patchworked` ggplot object. If `FALSE`, return a list of ggplot objects
`...`	Extra parameters passed to `DimHeatmap`

Value

No return value by default. If using fast = FALSE, will return a patchworked ggplot object if combine = TRUE, otherwise returns a list of ggplot objects

Examples

data("pbmc_small")
DimHeatmap(object = pbmc_small)

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