R/makeCellexalVRObj.R

In shambam/cellexalvrR: Provides the backend calculations for CellexalVR

#'Creates a cellexalvr objext with the data given
#'@param exdata A matrix of expression values (required). Colnames are cell IDs, rownames are unique gene names
#'@param mds.list A list of 3-column MDS coords (at least one required)
#'@param specie Specify whether data is from mouse of human (required)
#'@param cell.metadata Required meta data for cells
#'@param facs Surface marker intensities from index sorted cells
#'@keywords heatmap
#'@export MakeCellexaVRObj

MakeCellexaVRObj <- function(exdata,mds.list,specie=c("mouse","human"),cell.metadata=NULL,facs.data=NULL){

    ### add the rownames to the given matricies
    for(i in 1:length(mds.list)){
        rownames(mds.list[[i]]) <- colnames(exdata)
    }
    
    if(!is.null(cell.metadata)){
        rownames(cell.metadata) <- colnames(exdata)
    }

    #cellexalobj <- new("cellexalvr",data=as.matrix(exdata),mds=mds.list,meta.cell=as.matrix(cell.metadata),index=facs.data)
    cellexalobj <- new("cellexalvr",data=as.matrix(exdata),mds=mds.list,meta.cell=as.matrix(cell.metadata))

    if(!is.null(facs.data)){
        cellexalobj  <- addFACS2cellexalvr(cellexalobj,facs.data)
    }

    cellexalobj <- set.specie(cellexalobj,specie)

    cellexalobj
}