remove spatial argument from bambu

R/bambu-assignDist.R

@@ -3,7 +3,7 @@
 #' @import data.table
 #' @noRd
 assignReadClasstoTranscripts <- function(readClassList, annotations, isoreParameters, 
-                                        verbose, sampleData, demultiplexed, spatial, 
+                                        verbose, sampleData, demultiplexed,
                                         returnDistTable = FALSE, trackReads = TRUE) {
     if (is.character(readClassList)) readClassList <- readRDS(file = readClassList)
     metadata(readClassList)$readClassDist <- calculateDistTable(readClassList, annotations, isoreParameters, verbose, returnDistTable)

R/bambu.R

@@ -173,7 +173,7 @@ bambu <- function(reads, annotations = NULL, genome = NULL, NDR = NULL,
         annotations <- checkInputs(annotations, reads,
             readClass.outputDir = rcOutDir, 
             genomeSequence = genome, discovery = discovery, 
-            sampleNames = sampleNames, spatial = spatial,quantData = quantData)
+            sampleNames = sampleNames, sampleData = sampleData, quantData = quantData)
     }
     isoreParameters <- setIsoreParameters(isoreParameters = opt.discovery)
     #below line is to be compatible with earlier version of running bambu
@@ -243,7 +243,6 @@ bambu <- function(reads, annotations = NULL, genome = NULL, NDR = NULL,
                 # for bulk data, there is one sampleData (keep sampleData[1]), for single-cell, there is one per sample
                 sampleData = if(length(sampleData) == 1) sampleData[1] else sampleData[i],
                 demultiplexed = demultiplexed, 
-                spatial = spatial, 
                 returnDistTable = returnDistTable,
                 trackReads = trackReads
               )

R/bambu_utilityFunctions.R

@@ -73,7 +73,7 @@ updateParameters <- function(Parameters, Parameters.default) {
 #' @importFrom methods is
 #' @noRd
 checkInputs <- function(annotations, reads, readClass.outputDir, genomeSequence, 
-                        discovery, sampleNames, spatial, quantData){
+                        discovery, sampleNames, quantData){
     # ===# Check annotation inputs #===#
     if (!is.null(annotations)) {
         if (is(annotations, "CompressedGRangesList")) {
@@ -156,12 +156,12 @@ checkInputs <- function(annotations, reads, readClass.outputDir, genomeSequence,
         }
     }
 
-    if(!is.null(spatial)){
-        #if(!all(grepl(".tsv^", spatial))){stop("Not all paths for spatial are .tsv files")}
-        if(length(spatial)==1 & length(reads)>1){
-            warning("Using the same whitelist and coordinates for all input samples")
-        } else if(length(reads)!=length(spatial)){
-            stop("There are not the same number spatial whitelist paths as input files to reads. ",
+    if(!is.null(sampleData)){
+        if(!all(grepl(".csv^", sampleData))){stop("Not all paths for sample metadata files are .csv files")}
+        if(length(sampleData)==1 & length(reads)>1){
+            warning("Using the same sample metadata file for all input samples")
+        } else if(length(reads)!=length(sampleData)){
+            stop("There are not the same number sample metadata files paths as input files to reads. ",
             "Make sure these two arguments are vectors of the same length")
         }
     }