View source: R/Spatial_vgm_formation.R
Spatial_vgm_formation | R Documentation |
Addition of the spatial information to the VGM matrix, output of VDJ_GEX_matrix()
Spatial_vgm_formation( vgm, tissue_lowres_image_path, scalefactors_json_path, tissue_positions_list_path, cluster_path, matrix_path )
vgm |
Large list, output of VDJ_GEX_matrix() |
tissue_lowres_image_path |
Path to file containing the image of the tissue in png format |
scalefactors_json_path |
Path to a file for converting pixel positions in the original, full-resolution image to pixel positions in the histological image in json format |
tissue_positions_list_path |
Path to a text file containing a table with rows that correspond to spots in csv format |
cluster_path |
Path to 10X Genomic clustering file that is not specific for immune cells, in csv format |
matrix_path |
Path to the filtered feature barcode matrix containing barcode from fixed list of known-good barcode sequences in the h5 format |
Returns the input VGM matrix (output of VDJ_GEX_matrix()) with an additional list containing the spatial information.
## Not run: #Needed spatial files tissue_lowres_image_path<-list() tissue_lowres_image_path[[1]]<-c("c:/.../tissue_lowres_image.png") scalefactors_json_path<-list() scalefactors_json_path[[1]]<-c("c:/.../scalefactors_json.json") tissue_positions_list_path<-list() tissue_positions_list_path[[1]]<-c("c:/.../tissue_positions_list.csv") cluster_path<-list() cluster_path[[1]]<-c("c:/.../analysis/clustering/graphclust/clusters.csv") matrix_path<-list() matrix_path[[1]]<-c("c:/.../filtered_feature_bc_matrix/filtered_feature_bc_matrix.h5") #VGM formation with spatial data vgm_spatial<-Spatial_vgm_formation(vgm = vgm_without_spatial_data_and_VDJ, tissue_lowres_image_path = tissue_lowres_image_path, tissue_positions_list_path = tissue_positions_list_path, scalefactors_json_path = scalefactors_json_path, cluster_path = cluster_path, matrix_path = matrix_path) ## End(Not run)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.