Spatial_scaling_parameters: Scaling of the spatial parameters to be able to express the...

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

Scaling of the spatial parameters to be able to express the gene expression on the spatial image.

Description

Scaling of the spatial parameters to be able to express the gene expression on the spatial image.

Usage

Spatial_scaling_parameters(vgm_spatial, GEX.out.directory.list, sample_names)

Arguments

vgm_spatial	List containing the output of VDJ_GEX_matrix function from Platypus with at least the gene expression data and the addition of spatial parameters: image, scalefacor, tissue, cluster and matrix.
GEX.out.directory.list	Path to the filtered feature bc matrix data.
sample_names	Character vector containing the name of the sample.

Value

Returns a list containing all parameters to scale the data on the spatial image. List element [[1]]: images_cl. List element [[2]]: height of the image. List element [[3]]: width of the image. List element [[4]]: grobs. List element [[5]]: images_tibble. List element [[6]]: scales. List element [[7]]: cluster. List element [[8]]: bcs. List element [[9]]: matrix. List element [[10]]: bcs_merge.

Examples

## Not run: 
scaling_parameters<-Spatial_scaling_parameters(vgm_spatial = vgm_spatial,
GEX.out.directory.list = GEX.out.directory.list,
sample_names = sample_names)

## End(Not run)

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