featurePlot: Spatial expression heatmap
In PRECAST: Embedding and Clustering with Alignment for Spatial Datasets

featurePlot

R Documentation

Spatial expression heatmap

Description

Plot spatial heatmap for a feature of Seurat object with spatial transcriptomics data.

Usage

  featurePlot(seu, feature=NULL, cols=NULL, pt_size=1, title_size =16, quant=0.5, 
  assay='RNA' , reduction="position")

Arguments

`seu`	an object named "Seurat". The object of class "Seurat" must include slot "scale.data".
`feature`	an optional string, specify the name of feature to be plotted. If it is null, the first feature will be plotted.
`cols`	colors used in the plot
`pt_size`	the size of point in the spatial heatmap plot.
`title_size`	the title size used for the plot.
`quant`	the quantile value to generate the gradient color map.
`assay`	the assay selected for plot.
`reduction`	the Reduc object for plot.

Details

Nothing

Value

Return a ggplot2 object.

Note

nothing

Author(s)

Wei Liu

Examples


  library(Seurat)
  data(PRECASTObj)
  PRECASTObj <- SelectModel(PRECASTObj)
  seuInt <- IntegrateSpaData(PRECASTObj, species='unknown')
  seuInt <- ScaleData(seuInt)
  featurePlot(seuInt, assay='PRE_CAST')

PRECAST documentation built on May 29, 2024, 3 a.m.