Hi,

I was wondering if opt-SNE also supports FIt-SNE besides BH-SNE implementation?
Which other methods are possible besides method = "barnes_hut"?

Thank you,
Kind regards
Jo

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I used seurat3 object as input and got the following error:

> tmp <- PAGA(s1)
Error in py_call_impl(callable, dots$args, dots$keywords) : 
  Evaluation error: ValueError: Length mismatch: Expected axis has 0 elements, new values have 25339 elements

Detailed traceback: 
  File "/Users/xinli/miniconda3/lib/python3.7/site-packages/pandas/core/generic.py", line 5287, in __setattr__
    return object.__setattr__(self, name, value)
  File "pandas/_libs/properties.pyx", line 67, in pandas._libs.properties.AxisProperty.__set__
  File "/Users/xinli/miniconda3/lib/python3.7/site-packages/pandas/core/generic.py", line 661, in _set_axis
    self._data.set_axis(axis, labels)
  File "/Users/xinli/miniconda3/lib/python3.7/site-packages/pandas/core/internals/managers.py", line 178, in set_axis
    f"Length mismatch: Expected axis has {old_len} elements, new "
.
Called from: py_call_impl(callable, dots$args, dots$keywords)

Hello, do you know how to solve this?

remotes::install_github("milescsmith/dim.reduction.wrappers")
Downloading GitHub repo milescsmith/dim.reduction.wrappers@HEAD
Error: Failed to install 'ReductionWrappers' from GitHub:
Git does not seem to be installed on your system.

thanks!

Hi!

Thanks for making these wrappers available in R!
I have a problem running DoForceAtlas2. It spills out a matrix (below showing top 4 rows only) and through an error about converting R objects to Python.

library(Seurat)
pbmc <- ReductionWrappers::DoForceAtlas2(SeuratObject::pbmc_small)

80 x 80 Matrix of class "dgeMatrix"
               ATGCCAGAACGACT CATGGCCTGTGCAT GAACCTGATGAACC TGACTGGATTCTCA
ATGCCAGAACGACT      1.0000000      0.6666667      0.5789474      0.7142857
CATGGCCTGTGCAT      0.6666667      1.0000000      0.6216216      0.5000000
GAACCTGATGAACC      0.5789474      0.6216216      1.0000000      0.5000000
TGACTGGATTCTCA      0.7142857      0.5000000      0.5000000      1.0000000

Error in py_call_impl(callable, dots$args, dots$keywords) :
  Evaluation error: Unable to convert R object to Python type.

I would appreciate it if you could help with that.
Best,
Mohamed

Hello,

The pacmap wrapper needs to map n_dims to n_components now.

Hi!
I just installed the package and am trying to run PAGA() on a Seurat object. However, I am encountering the error:

> a = PAGA(sobj)

Error in py_module_import(module, convert = convert): 
ModuleNotFoundError: No module named 's2a'

Any idea what the issue may be?

Thanks in advance!

Cheers,
Marta

Thank you for sharing the script.

I ran in some errors when using PAGA function. Here is the output (cdS is a Seurat (3.0) object:
cdS <- PAGA(cdS)
[1] "pca"
Error in py_call_impl(callable, dots$args, dots$keywords) :
ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
[1] "tsne"
[1] "umap"
Error in alpha$uns$paga$connectivities$todense() %>% rownames<-(levels(alpha$obs[[alpha$uns$paga$groups]])) %>% :
could not find function "%>%"

Any suggestions?
Thank you,
J