PRECAST (version 1.6.5)

SpaPlot: Spatial heatmap

Description

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

Usage

SpaPlot(seuInt, batch=NULL, item=NULL, point_size=2,text_size=12, 
                    cols=NULL,font_family='', border_col="gray10",
                    fill_col='white', ncol=2, combine = TRUE,
                    title_name="Sample", ...)

Value

Return a ggplot2 object or list of ggplots objects.

Arguments

seuInt

an object named "Seurat".

batch

an optional positive integer or integer vector, specify the batches to be extracted. Users can check the batches' names by unique(seuInt$batch).

item

an optional string, which column is plotted in the meta data of seuInt. Users can check the meta data by head([e-mail]). If item takes value from ("RGB_UMAP", "RGB_tSNE"), this function will plot the RGB plot.

point_size

the size of point in the scatter plot.

text_size

the text size in the plot.

cols

colors used in the plot

font_family

the font family used for the plot, default as Times New Roman.

border_col

the border color in the plot.

fill_col

the color used in backgroup.

ncol

the number of columns in the layout of plots.

combine

an optional logical value, whether plot all on a figure. If TRUE, all figures are plotted; otherwise, return a list with each plot as component.

title_name

an optional string, title name in the plot.

...

other arguments passed to plot_scatter

.

Author

Wei Liu

Details

Nothing

See Also

None

Examples

  data(PRECASTObj)
  PRECASTObj <- SelectModel(PRECASTObj)
  seuInt <- IntegrateSpaData(PRECASTObj, species='unknown')
  SpaPlot(seuInt)