An error happend with “palantir.preprocess.log_transform ” function, and with error message "Adding a nonzero scalar to a sparse matrix is not supported

[zyb1984]

 I tried to follow the example of "Palantir analysis notebook", and an error message was reported with “palantir.preprocess.log_transform ” function,  and an error message with "Adding a nonzero scalar to a sparse matrix is not supported".
The original code  with  

import palantir import scanpy as sc import numpy as np import pandas as pd import os

Plotting

import matplotlib import matplotlib.pyplot as plt import seaborn as sns import warnings

Inline plotting

%matplotlib inline

sns.set_style('ticks') matplotlib.rcParams['figure.figsize'] = [4, 4] matplotlib.rcParams['figure.dpi'] = 100 matplotlib.rcParams['image.cmap'] = 'Spectral_r' warnings.filterwarnings(action="ignore", module="matplotlib", message="findfont")

Reset random seed

np.random.seed(5)

Load sample data

palantir_dir = os.path.expanduser('data/') ad = sc.read(palantir_dir + 'marrow_sample_scseq_counts.h5ad') ad sc.pp.normalize_per_cell(ad) palantir.preprocess.log_transform(ad) Error message

NotImplementedError Traceback (most recent call last) Input In [12], in <cell line: 1>() ----> 1 palantir.preprocess.log_transform(ad)

File C:\ProgramData\Anaconda3\envs\r-reticulate\lib\site-packages\palantir\preprocess.py:43, in log_transform(data, pseudo_count) 37 """Log transform the matrix 38 39 :param data: Counts matrix: Cells x Genes 40 :return: Log transformed matrix 41 """ 42 if type(data) is sc.AnnData: ---> 43 data.X = np.log2(data.X + pseudo_count) - np.log2(pseudo_count) 44 else: 45 return np.log2(data + pseudo_count)

File C:\ProgramData\Anaconda3\envs\r-reticulate\lib\site-packages\scipy\sparse\base.py:410, in spmatrix.add(self, other) 408 return self.copy() 409 # Now we would add this scalar to every element. --> 410 raise NotImplementedError('adding a nonzero scalar to a ' 411 'sparse matrix is not supported') 412 elif isspmatrix(other): 413 if other.shape != self.shape:

NotImplementedError: adding a nonzero scalar to a sparse matrix is not supported palantir/SciPy/NumPy/Python version information 1.0.1 1.9.0 1.22.3 sys.version_info(major=3, minor=9, micro=12, releaselevel='final', serial=0)

[ManuSetty]

Hello - very sorry for the delayed response.

You should be able to resolve this issues using

from spicy.sparse import csr_matrix
ad.X = csr_matrix(ad.X)

[mbuttner]

Hi @ManuSetty

I tried the same solution, but it does not seem to solve the issue described above. I took the liberty to inspect the log_transform function in palantir. My suggestion is to replace if type(ad) is sc.Anndata by if isinstance(ad, anndata.AnnData) and import anndata in your header.

I tested the adapted log_transform function in Google Colabs and it worked fine.

[ManuSetty]

Thank you!