featurePlot.Rd
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")
an object named "Seurat". The object of class "Seurat" must include slot "scale.data".
an optional string, specify the name of feature to be plotted. If it is null, the first feature will be plotted.
colors used in the plot
the size of point in the spatial heatmap plot.
the title size used for the plot.
the quantile value to generate the gradient color map.
the assay selected for plot.
the Reduc object for plot.
Nothing
Return a ggplot2 object.
nothing
None
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.
#> Start integration...
#> 2025-09-29 12:46:04.96664 : ***** Data integration finished!, 0 mins elapsed.
#> Put the data into a new Seurat object...
#> 2025-09-29 12:46:05.024299 : ***** New Seurat object is generated!, 0.001 mins elapsed.
seuInt <- ScaleData(seuInt)
#> Centering and scaling data matrix
featurePlot(seuInt, assay='PRE_CAST')