Describe the bug
When running in pre-computed mode, the method errors, but works with a numeric matrix.
To Reproduce
Run phate function with parameter: knn.dist.method = "precomputed"
Expected behavior
Phate embedding computed from affinity matrix
Actual behavior
Verbose Output
Calculating PHATE...
Running PHATE on precomputed affinity matrix with 6900 observations.
Calculating graph and diffusion operator...
Error in py_call_impl(callable, dots$args, dots$keywords) :
ValueError: assignment destination is read-only
System information:
Please run phate.__version__ and paste the results here.
1.0.8
Please run pd.show_versions() and paste the results here.
INSTALLED VERSIONS
------------------
commit : e8093ba372f9adfe79439d90fe74b0b5b6dea9d6
python : 3.10.5.final.0
python-bits : 64
OS : Darwin
OS-release : 21.5.0
Version : Darwin Kernel Version 21.5.0: Tue Apr 26 21:08:22 PDT 2022; root:xnu-8020.121.3~4/RELEASE_X86_64
machine : x86_64
processor : i386
byteorder : little
LC_ALL : None
LANG : en_GB.UTF-8
LOCALE : en_GB.UTF-8
pandas : 1.4.3
numpy : 1.23.1
pytz : 2022.1
dateutil : 2.8.2
setuptools : 64.0.0
pip : 22.2.2
Cython : None
pytest : None
hypothesis : None
sphinx : None
blosc : None
feather : None
xlsxwriter : None
lxml.etree : None
html5lib : None
pymysql : None
psycopg2 : None
jinja2 : None
IPython : None
pandas_datareader: None
bs4 : None
bottleneck : None
brotli : None
fastparquet : None
fsspec : None
gcsfs : None
markupsafe : None
matplotlib : 3.5.2
numba : None
numexpr : None
odfpy : None
openpyxl : None
pandas_gbq : None
pyarrow : None
pyreadstat : None
pyxlsb : None
s3fs : None
scipy : 1.9.0
snappy : None
sqlalchemy : None
tables : None
tabulate : None
xarray : None
xlrd : None
xlwt : None
zstandard : None
Output of sessionInfo():
> sessionInfo()
R version 4.2.1 (2022-06-23)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.4
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] SoupX_1.6.1 BUSpaRse_1.10.0 DropletUtils_1.16.0
[4] SingleCellExperiment_1.18.0 scDblFinder_1.10.0 annotables_0.1.91
[7] SingleR_1.10.0 phateR_1.0.7 Matrix_1.4-1
[10] patchwork_1.1.1 DESeq2_1.36.0 SummarizedExperiment_1.26.1
[13] Biobase_2.56.0 MatrixGenerics_1.8.1 matrixStats_0.62.0
[16] GenomicRanges_1.48.0 GenomeInfoDb_1.32.2 IRanges_2.30.0
[19] S4Vectors_0.34.0 BiocGenerics_0.42.0 edgeR_3.38.1
[22] limma_3.52.2 harmony_0.1.0 Rcpp_1.0.9
[25] sp_1.5-0 SeuratObject_4.1.0 Seurat_4.1.1
[28] forcats_0.5.1 stringr_1.4.0 dplyr_1.0.9
[31] purrr_0.3.4 readr_2.1.2 tidyr_1.2.0
[34] tibble_3.1.8 ggplot2_3.3.6 tidyverse_1.3.2
[37] reticulate_1.25
loaded via a namespace (and not attached):
[1] rsvd_1.0.5 ica_1.0-3 Rsamtools_2.12.0
[4] lmtest_0.9-40 crayon_1.5.1 spatstat.core_2.4-4
[7] MASS_7.3-58 rhdf5filters_1.8.0 nlme_3.1-158
[10] backports_1.4.1 reprex_2.0.1 GOSemSim_2.22.0
[13] rlang_1.0.4 XVector_0.36.0 ROCR_1.0-11
[16] readxl_1.4.0 irlba_2.3.5 scater_1.24.0
[19] filelock_1.0.2 xgboost_1.6.0.1 plyranges_1.16.0
[22] BiocParallel_1.30.3 rjson_0.2.21 bit64_4.0.5
[25] glue_1.6.2 pheatmap_1.0.12 sctransform_0.3.3
[28] parallel_4.2.1 vipor_0.4.5 spatstat.sparse_2.1-1
[31] AnnotationDbi_1.58.0 DOSE_3.22.0 spatstat.geom_2.4-0
[34] haven_2.5.0 tidyselect_1.1.2 fitdistrplus_1.1-8
[37] XML_3.99-0.10 zoo_1.8-10 ggpubr_0.4.0
[40] GenomicAlignments_1.32.1 xtable_1.8-4 magrittr_2.0.3
[43] evaluate_0.15 scuttle_1.6.2 cli_3.3.0
[46] zlibbioc_1.42.0 rstudioapi_0.13 miniUI_0.1.1.1
[49] rpart_4.1.16 fastmatch_1.1-3 ensembldb_2.20.2
[52] shiny_1.7.2 BiocSingular_1.12.0 xfun_0.31
[55] cluster_2.1.3 KEGGREST_1.36.3 interactiveDisplayBase_1.34.0
[58] ggrepel_0.9.1 listenv_0.8.0 Biostrings_2.64.0
[61] png_0.1-7 future_1.27.0 zeallot_0.1.0
[64] withr_2.5.0 bitops_1.0-7 plyr_1.8.7
[67] cellranger_1.1.0 AnnotationFilter_1.20.0 dqrng_0.3.0
[70] pillar_1.8.0 GlobalOptions_0.1.2 cachem_1.0.6
[73] GenomicFeatures_1.48.3 fs_1.5.2 DelayedMatrixStats_1.18.0
[76] vctrs_0.4.1 ellipsis_0.3.2 generics_0.1.3
[79] tools_4.2.1 beeswarm_0.4.0 munsell_0.5.0
[82] fgsea_1.22.0 DelayedArray_0.22.0 fastmap_1.1.0
[85] compiler_4.2.1 abind_1.4-5 httpuv_1.6.5
[88] rtracklayer_1.56.1 ExperimentHub_2.4.0 plotly_4.10.0
[91] rgeos_0.5-9 GenomeInfoDbData_1.2.8 gridExtra_2.3
[94] lattice_0.20-45 deldir_1.0-6 utf8_1.2.2
[97] later_1.3.0 BiocFileCache_2.4.0 jsonlite_1.8.0
[100] scales_1.2.0 ScaledMatrix_1.4.0 pbapply_1.5-0
[103] carData_3.0-5 sparseMatrixStats_1.8.0 genefilter_1.78.0
[106] lazyeval_0.2.2 promises_1.2.0.1 car_3.1-0
[109] R.utils_2.12.0 goftest_1.2-3 spatstat.utils_2.3-1
[112] cowplot_1.1.1 statmod_1.4.36 Rtsne_0.16
[115] BSgenome_1.64.0 uwot_0.1.11 igraph_1.3.4
[118] HDF5Array_1.24.1 survival_3.3-1 yaml_2.3.5
[121] htmltools_0.5.3 memoise_2.0.1 BiocIO_1.6.0
[124] locfit_1.5-9.6 viridisLite_0.4.0 digest_0.6.29
[127] assertthat_0.2.1 mime_0.12 rappdirs_0.3.3
[130] RSQLite_2.2.15 future.apply_1.9.0 Rmisc_1.5.1
[133] data.table_1.14.2 blob_1.2.3 R.oo_1.25.0
[136] labeling_0.4.2 splines_4.2.1 ggsci_2.9
[139] Rhdf5lib_1.18.2 googledrive_2.0.0 AnnotationHub_3.4.0
[142] ProtGenerics_1.28.0 RCurl_1.98-1.7 broom_1.0.0
[145] hms_1.1.1 modelr_0.1.8 rhdf5_2.40.0
[148] colorspace_2.0-3 BiocManager_1.30.18 ggbeeswarm_0.6.0
[151] shape_1.4.6 GEOquery_2.64.2 RANN_2.6.1
[154] circlize_0.4.15 fansi_1.0.3 tzdb_0.3.0
[157] parallelly_1.32.1 R6_2.5.1 grid_4.2.1
[160] ggridges_0.5.3 lifecycle_1.0.1 bluster_1.6.0
[163] curl_4.3.2 ggsignif_0.6.3 googlesheets4_1.0.0
[166] leiden_0.4.2 DO.db_2.9 qvalue_2.28.0
[169] RcppAnnoy_0.0.19 RColorBrewer_1.1-3 htmlwidgets_1.5.4
[172] beachmat_2.12.0 polyclip_1.10-0 biomaRt_2.52.0
[175] rvest_1.0.2 mgcv_1.8-40 globals_0.15.1
[178] spatstat.random_2.2-0 progressr_0.10.1 codetools_0.2-18
[181] lubridate_1.8.0 GO.db_3.15.0 metapod_1.4.0
[184] prettyunits_1.1.1 dbplyr_2.2.1 RSpectra_0.16-1
[187] R.methodsS3_1.8.2 celldex_1.6.0 gtable_0.3.0
[190] DBI_1.1.3 tensor_1.5 httr_1.4.3
[193] KernSmooth_2.23-20 stringi_1.7.8 progress_1.2.2
[196] farver_2.1.1 reshape2_1.4.4 annotate_1.74.0
[199] viridis_0.6.2 DT_0.23 xml2_1.3.3
[202] BiocNeighbors_1.14.0 restfulr_0.0.15 geneplotter_1.74.0
[205] scattermore_0.8 BiocVersion_3.15.2 scran_1.24.0
[208] bit_4.0.4 spatstat.data_2.2-0 pkgconfig_2.0.3
[211] gargle_1.2.0 rstatix_0.7.0 knitr_1.39
Details
Please run sessionInfo() and paste the results here.
Output of reticulate::py_discover_config(required_module = "phate"):
python: /Users/andrewskelton/miniconda3/envs/PHATE/bin/python
libpython: /Users/andrewskelton/miniconda3/envs/PHATE/lib/libpython3.10.dylib
pythonhome: /Users/andrewskelton/miniconda3/envs/PHATE:/Users/andrewskelton/miniconda3/envs/PHATE
version: 3.10.5 | packaged by conda-forge | (main, Jun 14 2022, 07:09:13) [Clang 13.0.1 ]
numpy: /Users/andrewskelton/miniconda3/envs/PHATE/lib/python3.10/site-packages/numpy
numpy_version: 1.23.1
phate: /Users/andrewskelton/miniconda3/envs/PHATE/lib/python3.10/site-packages/phate
NOTE: Python version was forced by RETICULATE_PYTHON
Details
Please run `reticulate::py_discover_config(required_module = "phate")` and paste the results here.
Output of phateR::check_pyphate_version():
TRUE
Details
Please run `phateR::check_pyphate_version()` and paste the results here.
You can do this with `R -e 'phateR::check_pyphate_version()'`
Additional context
Add any other context about the problem here.
Describe the bug
When running in pre-computed mode, the method errors, but works with a numeric matrix.
To Reproduce
Run phate function with parameter:
knn.dist.method = "precomputed"Expected behavior
Phate embedding computed from affinity matrix
Actual behavior
Verbose Output
System information:
Output of
sessionInfo():Details
Output of
reticulate::py_discover_config(required_module = "phate"):Details
Output of
phateR::check_pyphate_version():TRUE
Details
Additional context
Add any other context about the problem here.