Low-dimensional embeddings' plot

Low-dimensional embeddings' plot colored by a specified meta data in the Seurat object.

dimPlot(seuInt, item=NULL, reduction=NULL, point_size=1,text_size=16, 
                    cols=NULL,font_family='', border_col="gray10",
                    fill_col="white", ...)

Arguments

seuInt

an object named "Seurat".

item

the item used for coloring the plot in the meta data of seuInt object.

reduction

the reduction used for plot in the seuInt object. If reduction is null, the last added one is used for plotting.

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.

border_col

the border color in the plot.

fill_col

the color used in backgroup.

...

other arguments passed to plot_scatter

.

Details

Nothing

Value

Return a ggplot2 object.

Author

Wei Liu

Note

nothing

See also

None

Examples

  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.
  dimPlot(seuInt, reduction = 'PRECAST')

  ## or use the Seurat::DimPlot(seuInt, reduction = 'PRECAST')