Spatial_celltype_plot: Plotting celltype assign to cell according to their phenotype...
In Platypus: Single-Cell Immune Repertoire and Gene Expression Analysis

Spatial_celltype_plot

R Documentation

Plotting celltype assign to cell according to their phenotype on the spatial image.

Description

Plotting celltype assign to cell according to their phenotype on the spatial image.

Usage

Spatial_celltype_plot(
  sample_names,
  bcs_merge,
  images_tibble,
  vgm_GEX,
  title,
  size,
  legend_title,
  unclassified_cells = c(TRUE, FALSE),
  specific_celltype = c("T", "B", "No", "Unclassified"),
  density = c(TRUE, FALSE)
)

Arguments

`sample_names`	Character vector containing the name of the sample.
`bcs_merge`	Data frame containing imagerow, imagecol and barcode of the cells belonging to the spatial image. It can also be created by the function scaling_spatial_image_parameter by selecting the output parameter 10.
`images_tibble`	Tbl-df containing the sample name, grob, height and width of the spatial image. It can also be created by the function scaling_spatial_image_parameter by selecting the output parameter 5.
`vgm_GEX`	Data frame containing GEX information (VGM[[2]]). It must have a barcode column containing GEX_barcode and a cell.state column (output from GEX_phenotype).
`title`	Character vector to name the plot.
`size`	Number, to define the size of the text, default = 15.
`legend_title`	Character vector to name the legend scale.
`unclassified_cells`	Booleans, if TRUE the unclassified cells are also plot and if FALSE they aren't plot exept if the parameter specific_celltype = "Unclassified". In this case the unclassified cells are displayed even unclassified_cells = FALSE. Default = FALSE.
`specific_celltype`	Character vector, the user can choose to express a specific celltype like T, B or Unclassified cells. Default = No.
`density`	Booleans, if TRUE a density map is made. Default = FALSE

Value

Returns a ggplot of the celltypes and if density = TRUE a density map of the cells on the spatial image.

Examples

## Not run: 
Spatial_celltype_plot(bcs_merge = scaling_parameters[[10]],
vgm_GEX = vgm_spatial$GEX@meta.data,images_tibble = scaling_parameters[[5]],
sample_names = sample_names,title="B and T celltype", legend_title = "Celltype",
unclassified_cells = FALSE, specific_celltype = "Unclassified")

## End(Not run)

Platypus documentation built on Aug. 15, 2022, 9:08 a.m.