Hello,
I was using the liana_tensor_c2c function for my dataset, which worked when selecting "inner" or "outer" for the how parameter. However, "outer_lr" doesn't work for me.
Here is the command I used:
liana_tensor_c2c(sce = sce, score_col = 'LRscore', init = "random", runs = 10, rank = NULL, ='outer_lr', conda_env = NULL, use_available = FALSE)
And below is the error I get:
Building the tensor using LRscore... Error in py_call_impl(callable, call_args$unnamed, call_args$named) : ValueError: Not a valid input for parameter 'how' Run reticulate::py_last_error()` for details.
reticulate::py_last_error()
── Python Exception Message ─────────────────────────────────────────────────────────
Traceback (most recent call last):
File "/Users/jamesjaraddollar/Library/Caches/org.R-project.R/R/basilisk/1.18.0/liana/0.1.14/liana_cell2cell/lib/python3.8/site-packages/cell2cell/tensor/external_scores.py", line 171, in dataframes_to_tensor
raise ValueError("Not a valid input for parameter 'how'")
ValueError: Not a valid input for parameter 'how'
── R Traceback ──────────────────────────────────────────────────────────────────────
▆
- └─liana::liana_tensor_c2c(...)
- └─c2c$tensor$dataframes_to_tensor(...)
-
└─reticulate:::py_call_impl(callable, call_args$unnamed, call_args$named)
See reticulate::py_last_error()$r_trace$full_call for more details.
`
SessionInfo:
R version 4.4.2 (2024-10-31)
Platform: aarch64-apple-darwin20
Running under: macOS Sequoia 15.0.1
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] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] Seurat_5.2.1 SeuratObject_5.0.2
[3] sp_2.2-0 patchwork_1.3.0
[5] ExperimentHub_2.14.0 AnnotationHub_3.14.0
[7] BiocFileCache_2.14.0 dbplyr_2.5.0
[9] liana_0.1.14 magrittr_2.0.3
[11] reticulate_1.41.0 SingleCellExperiment_1.28.1
[13] SummarizedExperiment_1.36.0 Biobase_2.66.0
[15] GenomicRanges_1.58.0 GenomeInfoDb_1.42.3
[17] IRanges_2.40.1 S4Vectors_0.44.0
[19] BiocGenerics_0.52.0 MatrixGenerics_1.18.1
[21] matrixStats_1.5.0 lubridate_1.9.4
[23] forcats_1.0.0 stringr_1.5.1
[25] dplyr_1.1.4 purrr_1.0.4
[27] readr_2.1.5 tidyr_1.3.1
[29] tibble_3.2.1 ggplot2_3.5.1
[31] tidyverse_2.0.0
Hello,
I was using the
liana_tensor_c2cfunction for my dataset, which worked when selecting "inner" or "outer" for thehowparameter. However, "outer_lr" doesn't work for me.Here is the command I used:
liana_tensor_c2c(sce = sce, score_col = 'LRscore', init = "random", runs = 10, rank = NULL, ='outer_lr', conda_env = NULL, use_available = FALSE)And below is the error I get:
Building the tensor using LRscore... Error in py_call_impl(callable, call_args$unnamed, call_args$named) : ValueError: Not a valid input for parameter 'how' Runreticulate::py_last_error()` for details.── Python Exception Message ─────────────────────────────────────────────────────────
Traceback (most recent call last):
File "/Users/jamesjaraddollar/Library/Caches/org.R-project.R/R/basilisk/1.18.0/liana/0.1.14/liana_cell2cell/lib/python3.8/site-packages/cell2cell/tensor/external_scores.py", line 171, in dataframes_to_tensor
raise ValueError("Not a valid input for parameter 'how'")
ValueError: Not a valid input for parameter 'how'
── R Traceback ──────────────────────────────────────────────────────────────────────
▆
See
reticulate::py_last_error()$r_trace$full_callfor more details.`
SessionInfo:
R version 4.4.2 (2024-10-31)
Platform: aarch64-apple-darwin20
Running under: macOS Sequoia 15.0.1
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] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] Seurat_5.2.1 SeuratObject_5.0.2
[3] sp_2.2-0 patchwork_1.3.0
[5] ExperimentHub_2.14.0 AnnotationHub_3.14.0
[7] BiocFileCache_2.14.0 dbplyr_2.5.0
[9] liana_0.1.14 magrittr_2.0.3
[11] reticulate_1.41.0 SingleCellExperiment_1.28.1
[13] SummarizedExperiment_1.36.0 Biobase_2.66.0
[15] GenomicRanges_1.58.0 GenomeInfoDb_1.42.3
[17] IRanges_2.40.1 S4Vectors_0.44.0
[19] BiocGenerics_0.52.0 MatrixGenerics_1.18.1
[21] matrixStats_1.5.0 lubridate_1.9.4
[23] forcats_1.0.0 stringr_1.5.1
[25] dplyr_1.1.4 purrr_1.0.4
[27] readr_2.1.5 tidyr_1.3.1
[29] tibble_3.2.1 ggplot2_3.5.1
[31] tidyverse_2.0.0