Spatial expression heatmap

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

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.

Author

Wei Liu

Note

nothing

See also

None

Examples

  library(Seurat)
  data(PRECASTObj)
  PRECASTObj <- SelectModel(PRECASTObj)
  seuInt <- IntegrateSpaData(PRECASTObj, species='unknown')
#> Using only PRECAST results to obtain the batch corrected gene expressions since species is unknown or the genelist in PRECASTObj has less than 5 overlapp with the housekeeping genes of given species.
  seuInt <- ScaleData(seuInt)
#> Centering and scaling data matrix
  featurePlot(seuInt, assay='PRE_CAST')