anndataToGiotto only support scr_matrix format anndata object

[wwang-chcn]

Description

anndataToGiotto function only support scr_matrix format anndata object.

There are four types (ndarray, spmatrix, DataFrame, None) of expression matrix format support in anndata. However, anndataToGiotto function only support spmatrix for now.

---

Reproducible code

## load libs
library(Giotto)
library(reticulate)

use_condaenv("giotto_env", required = TRUE)

## create h5ad
### import Python libs
sc <- import("scanpy", convert = FALSE)
ad <- import("anndata", convert = FALSE)
scipy <- import("scipy", convert = FALSE)
pd <- import("pandas", convert = FALSE)
np <- import("numpy", convert = FALSE)

### create various types of gene expression
npArrayCounts <- np$random$poisson(1, size=c(10L,20L)) # numpy.array
cellNames <- paste0("Cell_", rep(1:10)) # cell names
geneNames <- paste0("Gene_", rep(1:20)) # gene names
csrMatrixCounts <- scipy$sparse$csr_matrix(npArrayCounts,
                                           dtype=np$float32) # csr matrix
dataFrameCounts <- pd$DataFrame(npArrayCounts,
                                columns = geneNames,
                                index = cellNames) # pandas.DataFrame

### adata with numpy.array
adataNpArray <- ad$AnnData(npArrayCounts)
adataNpArray$obs$index <- cellNames
adataNpArray$var$index <- geneNames
adataNpArray$write("adataNpArray.h5ad")

### adata with csr matrix
adataSpMatrix <- ad$AnnData(csrMatrixCounts)
adataSpMatrix$obs$index <- cellNames
adataSpMatrix$var$index <- geneNames
adataSpMatrix$write("adataSpMatrix.h5ad")

### adata with pandas.DataFrame
adataPdDF <- ad$AnnData(dataFrameCounts)
adataPdDF$write("adataPdDF.h5ad")

## convert into giotto
### csr matrix: success
giottoFromAdSpMatrix <- anndataToGiotto(anndata_path =  "adataSpMatrix.h5ad")
### pandas.DataFrame: fail
giottoFromPdDataFrame <- anndataToGiotto(anndata_path =  "adataPdDF.h5ad")
### numpy.array: fail
giottoFromNpArray <- anndataToGiotto(anndata_path =  "adataNpArray.h5ad")

---

Session info

R version 4.4.0 (2024-04-24)
Platform: aarch64-apple-darwin20
Running under: macOS Ventura 13.6.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/New_York
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] reticulate_1.38.0 Giotto_4.1.0      GiottoClass_0.3.3

loaded via a namespace (and not attached):
 [1] tidyr_1.3.1         plotly_4.10.4       utf8_1.2.4          generics_0.1.3     
 [5] gtools_3.9.5        stringi_1.8.4       lattice_0.22-6      digest_0.6.35      
 [9] magrittr_2.0.3      grid_4.4.0          RColorBrewer_1.1-3  fastmap_1.2.0      
[13] plyr_1.8.9          jsonlite_1.8.8      Matrix_1.7-0        ggrepel_0.9.5      
[17] backports_1.5.0     scattermore_1.2     httr_1.4.7          purrr_1.0.2        
[21] fansi_1.0.6         viridisLite_0.4.2   scales_1.3.0        lazyeval_0.2.2     
[25] codetools_0.2-20    cli_3.6.3           rlang_1.1.4         cowplot_1.1.3      
[29] munsell_0.5.1       withr_3.0.1         colorRamp2_0.1.0    parallel_4.4.0     
[33] tools_4.4.0         reshape2_1.4.4      deldir_2.0-4        GiottoUtils_0.1.10 
[37] checkmate_2.3.2     dplyr_1.1.4         colorspace_2.1-0    ggplot2_3.5.1      
[41] vctrs_0.6.5         R6_2.5.1            png_0.1-8           matrixStats_1.3.0  
[45] lifecycle_1.0.4     magick_2.8.4        stringr_1.5.1       htmlwidgets_1.6.4  
[49] GiottoVisuals_0.2.4 dbscan_1.2-0        pkgconfig_2.0.3     terra_1.7-78       
[53] pillar_1.9.0        gtable_0.3.5        data.table_1.15.4   glue_1.7.0         
[57] Rcpp_1.0.13         xfun_0.44           tibble_3.2.1        tidyselect_1.2.1   
[61] rstudioapi_0.16.0   knitr_1.47          htmltools_0.5.8.1   igraph_2.0.3       
[65] compiler_4.4.0      sp_2.1-4