R/PlatypusDB_VGM_to_AIRR.R
PlatypusDB_VGM_to_AIRR.RdExports AIRR compatible tables supplemented with VDJ and GEX information from the Platypus VGM object and the cellranger output airr_rearrangements.tsv
PlatypusDB_VGM_to_AIRR(
VGM,
VDJ.features.to.append,
GEX.features.to.append,
airr.rearrangements,
airr.integrate
)Output object of the VDJ_GEX_matrix function generated with VDJ.combine = T, GEX.combine = T (to merge all samples) and integrate.VDJ.to.GEX = T (to integrate VDJ and GEX data)
Character vector. Defaults to "none". Can be either "all" or column names of the VGM VDJ matrix (VGM[[1]]) to append to the AIRR compatible table.
Character vector. Defaults to "none". Can be either "all" or GEX metadata column names or Gene names of the VGM GEX object (VGM[[2]])(passed to Seurat::FetchData()) to append to the AIRR compatible table. For a list of available features run: names(VGM[[2]]@meta.data) and rownames(VGM[[2]])
Source of the airr_rearrangements.tsv file as generated by Cellranger. There are 3 available input options: 1. R list object from Platypus_DB_load_from_disk or Platypus_DB_fetch / 2. List with local paths to airr_rearrangements.tsv / 3. List of airr_rearrangements.tsv loaded in as R objects within the current R enviroment. ! Order of input list must be identical to that of sample_ids in the VGM ! If not provided or set to "none" CIGAR strings in output will be empty.
Boolean. Defaults to TRUE, whether to integrate output AIRR tables
A list of length of samples in VGM containing a AIRR-compatible dataframe for each sample if airr.integrate = F or a single dataframe if airr.integrate = T ! Cave the format: VGM object => 1 cell = 1 row; AIRR table 1 cell = as many rows as VDJ and VJ chains available for that cell. GEX cell-level information is attached to all rows containing a chain of that cell.
if (FALSE) {
#complete workflow below
#usage with airr rearrangement tables from PlatypusDB_load_from_disk
#or PlatypusDB_fetch list object
airr.list.out <- PlatypusDB_VGM_to_AIRR(VGM = VGM
, VDJ.features.to.append = c("VDJ_cdr3s_aa")
, GEX.features.to.append = c("CTLA4", "TOX"), airr.rearrangements = Data.in)
#usage with airr rearrangement tables from disk
airr.list.out <- PlatypusDB_VGM_to_AIRR(VGM = VGM
, VDJ.features.to.append = c("VDJ_cdr3s_aa")
, GEX.features.to.append = c("CTLA4", "TOX"),
airr.rearrangements =list("~/path_to/s1/airr.rearrangement.tsv"
,"~/path_to/s2/airr_rearrangement.tsv"))
#usage with airr rearrangement tables from objects in R environment
airr.list.out <- PlatypusDB_VGM_to_AIRR(VGM = VGM
, VDJ.features.to.append = c("VDJ_cdr3s_aa")
, GEX.features.to.append = c("CTLA4", "TOX"),
airr.rearrangements = list(airr_rearrangements.s1, airr_rearrangements_2))
#Complete workflow
#set paths of cellranger directories containing
#also the airr_rearrangements.tsv file
VDJ.out.directory.list <- list()
VDJ.out.directory.list[[1]] <- c("~/cellrangerVDJ/s1")
VDJ.out.directory.list[[2]] <- c("~/cellrangerVDJ/s2")
GEX.out.directory.list <- list()
GEX.out.directory.list[[1]] <- c("~/cellrangerGEX/s1")
GEX.out.directory.list[[2]] <- c("~/cellrangerGEX/s2")
#Run VGM with GEX and VDJ integration
VGM <- VDJ_GEX_matrix(VDJ.out.directory.list = VDJ.out.directory.list,
GEX.out.directory.list = GEX.out.directory.list,
GEX.integrate = TRUE, VDJ.combine = TRUE, integrate.GEX.to.VDJ = TRUE
, integrate.VDJ.to.GEX = TRUE,
get.VDJ.stats = FALSE, trim.and.align = FALSE)
#Generate AIRR compatible table supplemented by GEX information
airr.list.out <- PlatypusDB_VGM_to_AIRR(VGM = VGM,
VDJ.features.to.append = c("VDJ_sequence_nt_trimmed","VJ_sequence_nt_trimmed"),
GEX.features.to.append = c("UMAP_1","UMAP_2","CTLA4", "TOX"),
airr.rearrangements = c("~/cellrangerVDJ/s1/airr_rearrangement.tsv"
,"~/cellrangerVDJ/s2/airr_rearrangement.tsv"))
#To save a dataframe as .tsv
write.table(airr_dataframe, file = "supplemented_airr_rearrangements.tsv"
, sep='\t', row.names = FALSE, quote=FALSE)
}