From 03679528390cf5065fa4185029af39629dac0ebd Mon Sep 17 00:00:00 2001
From: Ilia Kats <ilia-kats@gmx.net>
Date: Wed, 11 Oct 2023 13:25:39 +0200
Subject: [PATCH] correctly handle R/HDF5 dense array storage order

---
 R/read_h5mu.R  |  4 ++--
 R/write_h5mu.R | 18 +++++++++++-------
 2 files changed, 13 insertions(+), 9 deletions(-)

diff --git a/R/read_h5mu.R b/R/read_h5mu.R
index bfbd374..818772d 100644
--- a/R/read_h5mu.R
+++ b/R/read_h5mu.R
@@ -222,6 +222,8 @@ read_array <- function(attr, encoding, strict=TRUE) {
     if (!is.null(encoding) && (endsWith(encoding, "-scalar") || encoding == "string")) {
         attr(ret, "encoding-scalar") <- TRUE
     }
+    if (length(dim(ret)) > 1)
+        ret <- t(ret)
     ret
 }
 
@@ -329,8 +331,6 @@ read_modality <- function(view, backed=FALSE) {
         obsmnames <- h5ls(h5autoclose(view & "obsm"), recursive=FALSE)$name
         obsm <- lapply(obsmnames, function(space) {
             elem <- read_attribute(h5autoclose(view & paste("obsm", space, sep="/")))
-            if (!is.data.frame(elem) && length(dim(elem)) > 1)
-                elem <- t(elem)
             rownames(elem) <- rownames(obs)
             elem
         })
diff --git a/R/write_h5mu.R b/R/write_h5mu.R
index e5af57b..851f2e5 100644
--- a/R/write_h5mu.R
+++ b/R/write_h5mu.R
@@ -47,14 +47,14 @@ writeH5AD <- function(object, file, overwrite) {
         if (length(obsm) > 0) {
             obsmgrp <- H5Gcreate(file, "obsm")
             mapply(function(name, data) {
-                if (is.data.frame(data)) {
+                if (is(data, "data.frame_OR_DataFrame")) {
                     rownames(data) <- rownames(colData(object))
                     write_data_frame(obsmgrp, name, data)
                 } else {
                     if (length(dim(data)) == 1)
                         data <- as.vector(data)
                     else
-                        data <- t(data)
+                        data <- data
                     write_matrix(obsmgrp, name, data)
                 }
             }, names(obsm), obsm)
@@ -82,11 +82,11 @@ writeH5AD <- function(object, file, overwrite) {
 
         assays <- assays(object)
         nassays <- length(assays)
-        write_matrix(file, "X", assays[[1]])
+        write_matrix(file, "X", t(assays[[1]]))
         if (nassays > 1) {
             layersgrp <- H5Gcreate(file, "layers")
             mapply(function(name, mat) {
-                write_matrix(layersgrp, name, mat)
+                write_matrix(layersgrp, name, t(mat))
             }, names(assays[2:nassays]), assays[2:nassays])
             H5Gclose(layersgrp)
         }
@@ -200,6 +200,10 @@ write_matrix <- function(parent, key, mat) {
     if (is.matrix(mat) || is.vector(mat) || is.array(mat) || is.numeric(mat) || is.integer(mat) || is.logical(mat) || is.character(mat)) { # is.vector returns false for vectors with attributes
         isscalar <- length(mat) == 1 & !is.null(attr(mat, "encoding-scalar"))
         hasna <- anyNA(mat)
+        if (is.matrix(mat))
+            mat <- t(mat)
+        else if (is.array(mat))
+            mat <- aperm(mat, length(dim(mat)):1)
         if (hasna && is.double(mat)) {
             # FIXME: extend anndata spec to handle double NAs?
             mat[is.na(mat)] <- NaN
@@ -240,14 +244,14 @@ write_matrix <- function(parent, key, mat) {
         grp <- H5Gcreate(parent, key)
         writeDataset(grp, "indptr", mat@p)
         writeDataset(grp, "data", mat@x)
-        writeAttribute(grp, "shape", rev(dim(mat)))
+        writeAttribute(grp, "shape", dim(mat))
         writeAttribute(grp, "encoding-version", "0.1.0")
         if (is(mat, "dgCMatrix")) {
             writeDataset(grp, "indices", mat@i)
-            writeAttribute(grp, "encoding-type", "csr_matrix")
+            writeAttribute(grp, "encoding-type", "csc_matrix")
         } else {
             writeDataset(grp, "indices", mat@j)
-            writeAttribute(grp, "encoding-type", "csc_matrix")
+            writeAttribute(grp, "encoding-type", "csr_matrix")
         }
         H5Gclose(grp)
     } else if (is(mat, "DelayedArray") && requireNamespace("HDF5Array", quietly=TRUE)) {