Set GeneScoreMatrix as default for ATAC in ArchR objects

Author: catpetersen

R/CHOIR.R

@@ -236,7 +236,10 @@
 #' indicating which matrix or matrices to use in the provided object. The
 #' default value, \code{NULL}, will use the “GeneScoreMatrix” for ATAC-seq data
 #' or the “GeneExpressionMatrix” for RNA-seq data. For multi-omic datasets,
-#' provide a vector with a value corresponding to each modality.
+#' provide a vector with a value corresponding to each modality. When
+#' "GeneScoreMatrix" is provided, the "GeneScoreMatrix" will be used as input
+#' to the random forest classifiers, but the "TileMatrix" will be used for the
+#' initial dimensionality reduction(s).
 #' @param ArchR_depthcol For \code{ArchR} objects, a character string or vector
 #' indicating which column to use for correlation with sequencing depth. The
 #' default value, \code{NULL}, will use the “nFrags” column for ATAC-seq data or

R/HelperUtils.R

@@ -303,7 +303,7 @@ getRecords <- function(object,
   if (is.null(use_matrix)) {
     # Matrix to pull from
     if (is.null(ArchR_matrix)) {
-      ArchR_matrix <- "TileMatrix"
+      ArchR_matrix <- "GeneScoreMatrix"
     }
     if (ArchR_matrix == "GeneScoreMatrix") {
       gene_score_matrix <- ArchR::getMatrixFromProject(object, useMatrix = "GeneScoreMatrix")

R/TreeUtils.R

@@ -343,7 +343,7 @@
         }
       } else if (atac == TRUE) {
         if (is.null(ArchR_matrix)) {
-          ArchR_matrix <- "TileMatrix"
+          ArchR_matrix <- "GeneScoreMatrix"
         }
         if (is.null(ArchR_depthcol)) {
           ArchR_depthcol <- "nFrags"
@@ -2131,7 +2131,7 @@
               "tree_records" = tree_records))
 }
 
-#' Infer clustering tree ---------------------------
+#' Infer clustering tree from pre-generated clusters
 #'
 #' Generate clustering tree from provided, pre-generated clusters. Provide a set
 #' of cluster labels and either a dimensionality reduction or distance matrix.

R/buildParentTree.R

@@ -102,7 +102,10 @@
 #' indicating which matrix or matrices to use in the provided object. The
 #' default value, \code{NULL}, will use the “GeneScoreMatrix” for ATAC-seq data
 #' or the “GeneExpressionMatrix” for RNA-seq data. For multi-omic datasets,
-#' provide a vector with a value corresponding to each modality.
+#' provide a vector with a value corresponding to each modality. When
+#' "GeneScoreMatrix" is provided, the "GeneScoreMatrix" will be used as input
+#' to the random forest classifiers, but the "TileMatrix" will be used for the
+#' initial dimensionality reduction(s).
 #' @param ArchR_depthcol For \code{ArchR} objects, a character string or vector
 #' indicating which column to use for correlation with sequencing depth. The
 #' default value, \code{NULL}, will use the “nFrags” column for ATAC-seq data or

R/buildTree.R

@@ -205,7 +205,10 @@
 #' indicating which matrix or matrices to use in the provided object. The
 #' default value, \code{NULL}, will use the “GeneScoreMatrix” for ATAC-seq data
 #' or the “GeneExpressionMatrix” for RNA-seq data. For multi-omic datasets,
-#' provide a vector with a value corresponding to each modality.
+#' provide a vector with a value corresponding to each modality. When
+#' "GeneScoreMatrix" is provided, the "GeneScoreMatrix" will be used as input
+#' to the random forest classifiers, but the "TileMatrix" will be used for the
+#' initial dimensionality reduction(s).
 #' @param ArchR_depthcol For \code{ArchR} objects, a character string or vector
 #' indicating which column to use for correlation with sequencing depth. The
 #' default value, \code{NULL}, will use the “nFrags” column for ATAC-seq data or

R/combineTrees.R

@@ -156,6 +156,18 @@
 #' object. The default value, \code{NULL}, will choose the current active assay
 #' for \code{Seurat} objects and the \code{logcounts} assay for
 #' \code{SingleCellExperiment} objects.
+#' @param use_slot For \code{Seurat} objects, a character string or vector
+#' indicating the layers(s)—previously known as slot(s)—to use in the provided
+#' object. The default value, \code{NULL}, will choose a layer/slot based on the
+#' selected assay. If an assay other than "RNA", "sketch”, "SCT”, or
+#' "integrated" is provided, you must specify a value for \code{use_slot}. For
+#' multi-omic datasets, provide a vector with a value corresponding to each
+#' provided value of \code{use_assay} in the same order.
+#' @param ArchR_matrix For \code{ArchR} objects, a character string or vector
+#' indicating which matrix or matrices to use in the provided object. The
+#' default value, \code{NULL}, will use the “GeneScoreMatrix” for ATAC-seq data
+#' or the “GeneExpressionMatrix” for RNA-seq data. For multi-omic datasets,
+#' provide a vector with a value corresponding to each modality.
 #' @param countsplit A Boolean value indicating whether or not to use count
 #' split input data (see \code{countsplit} package), such that one matrix of
 #' counts is used for clustering tree generation and a separate matrix is used

_pkgdown.yml

@@ -14,8 +14,12 @@ navbar:
       href: index.html
     tutorial:
       icon: fa-graduation-cap
-      href: articles/CHOIR.html
-      text: Quick Tutorial
+      text: Tutorials
+      menu:
+        - text: Quick start
+          href: articles/CHOIR.html
+        - text: Atlas-scale data
+          href: articles/atlas_scale_data.html
     functions:
       icon: fa-code
       href: reference/index.html
@@ -27,3 +31,4 @@ navbar:
 
 toc:
   depth: 4
+