Spatial_selection_of_cells_on_image: Allows to select an area on the spatial image and to isolate...

In Platypus: Single-Cell Immune Repertoire and Gene Expression Analysis

Allows to select an area on the spatial image and to isolate the cells expressed on this part and repeat this process several times.

Description

Allows to select an area on the spatial image and to isolate the cells expressed on this part and repeat this process several times.

Usage

Spatial_selection_of_cells_on_image(
  vgm_VDJ,
  alpha,
  bcs_merge,
  images_tibble,
  sample_names,
  nbpoints,
  title,
  size,
  plotting
)

Arguments

vgm_VDJ	Data frame containing all the data on the cell. It must contain the column clonotype_id which describes the number of the clonotype to which the cell belongs. This data frame can be obtained by the assignment functions (VDJ_assignment_random_based, VDJ_assignment_density_based and VDJ_assignment_germline_based).
alpha	Number that give the transparency coefficient (value between 0 and 1). If it is not given it will automatically be 0.
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.
sample_names	Character vector containing the name of the sample.
nbpoints	Numerical value that limite the maximum number of mouse click for the selection, default = 100.
title	Character vector to name the plot.
size	Number, to define the size of the text, default = 15.
plotting	Character vector to return (TRUE) or not (FALSE) the plot of the selection

Value

If plotting = TRUE, returns a list containing [[1]] the plot of the selected cells according to their group, [[2]] a data frame that contains all the cells but the selected cells are distinguished. If plotting = FALSE it juste returns the dataframe.

Examples

## Not run: 
test<-Spatial_selection_of_cells_on_image(
vgm_VDJ = vgm_spatial_simulated$VDJ$B_cells$random_BCR_assignment,
images_tibble = scaling_parameters[[5]],
bcs_merge = scaling_parameters[[10]],sample_names = sample_names,
plotting = TRUE)

## End(Not run)

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