Merge pull request #2235 from GreenleafLab/ia/suppress-archr-warnings

remove seurat/harmony warnings

Author: immanuelazn

R/Clustering.R

@@ -435,7 +435,7 @@ addClusters <- function(
 
   clustParams <- tryCatch({
 
-    obj <- Seurat::CreateSeuratObject(tmp, project='scATAC', min.cells=0, min.features=0)
+    obj <- suppressWarnings(Seurat::CreateSeuratObject(tmp, project='scATAC', min.cells=0, min.features=0))
     obj[['pca']] <- Seurat::CreateDimReducObject(embeddings=mat, key='PC_', assay='RNA')
     clustParams$object <- obj
     clustParams$reduction <- "pca"
@@ -469,7 +469,7 @@ addClusters <- function(
         colnames(tmp) <- rownames(mat)
         rownames(tmp) <- paste0("t",seq_len(nrow(tmp)))
 
-        obj <- Seurat::CreateSeuratObject(tmp, project='scATAC', min.cells=0, min.features=0)
+        obj <- suppressWarnings(Seurat::CreateSeuratObject(tmp, project='scATAC', min.cells=0, min.features=0))
         obj[['pca']] <- Seurat::CreateDimReducObject(embeddings=mat, key='PC_', assay='RNA')
         clustParams$object <- obj
         clustParams$reduction <- "pca"

R/Harmony.R

@@ -80,7 +80,7 @@ addHarmony <- function(
   harmonyParams$plot_convergence <- FALSE
 
   #Call Harmony
-  harmonyMat <- do.call(HarmonyMatrix, harmonyParams)
+  harmonyMat <- suppressWarnings(do.call(HarmonyMatrix, harmonyParams))
   harmonyParams$data_mat <- NULL
   ArchRProj@reducedDims[[name]] <- SimpleList(
     matDR = harmonyMat, 
@@ -89,7 +89,6 @@ addHarmony <- function(
     scaleDims = NA, #Do not scale dims after
     corToDepth = NA
   )
-
   ArchRProj
 
 }

R/RNAIntegration.R

@@ -220,7 +220,7 @@ addGeneIntegrationMatrix <- function(
 
   #Set up RNA
   if(inherits(seRNA, "SummarizedExperiment")){
-    seuratRNA <- CreateSeuratObject(counts = assay(seRNA))
+    seuratRNA <- suppressWarnings(CreateSeuratObject(counts = assay(seRNA)))
     if(groupRNA %ni% colnames(colData(seRNA))){
       .logMessage("groupRNA not in colData of seRNA", logFile = logFile)
       stop("groupRNA not in colData of seRNA")
@@ -475,7 +475,7 @@ addGeneIntegrationMatrix <- function(
 
     #Log-Normalize 
     mat <- log(mat + 1) #use natural log
-    seuratATAC <- Seurat::CreateSeuratObject(counts = mat[head(seq_len(nrow(mat)), 5), , drop = FALSE])
+    seuratATAC <- supressWarninggs(Seurat::CreateSeuratObject(counts = as.matrix(mat[head(seq_len(nrow(mat)), 5), , drop = FALSE])))
     seuratATAC[["GeneScore"]] <- Seurat::CreateAssayObject(counts = mat)
 
     #Clean Memory