Error saving the output figures in png or pdf format

[archanabhardwaj]

empty figures
Hi

I am runing NCEM code from the scratch for coupling and cell enrichment analysis. Meanwhile, I wanted to save all the imaging output in png (or pdf) format. But except for the sc.pl.umap output , I am getting empty png file for the remaining analysis. I tried different ways to save the "image output" but still its not working.

import ncem as nc
import numpy as np
import matplotlib.pyplot as plt
import scanpy as sc
import squidpy as sq

sc.settings.set_figure_params(dpi=100)

import warnings
warnings.filterwarnings("ignore")

from ncem.interpretation import InterpreterInteraction
from ncem.data import get_data_custom, customLoader

results_folder = 'test'
run_name = f'{results_folder}/anndata/'
import scanpy as sc

import anndata as an

adata_file = f"{run_name}/sp.h5ad" # sp_cluster
ad = an.read_h5ad(adata_file)
ncem = InterpreterInteraction()

adata_vis = ad

ncem.data = customLoader(
adata=adata_vis, cluster='region_cluster', patient='sampleid', library_id='sample', radius=150
)

get_data_custom(interpreter=ncem)

var_decomp = ncem.data.compute_variance_decomposition()

ncem.data.variance_decomposition(var_decomp, figsize=(5,3))

plt.savefig('test.png')

ncem.data = customLoader(
adata=adata_vis, cluster='region_cluster', patient='sample', library_id='sample', radius=52
)
get_data_custom(interpreter=ncem)

adata_img, adata_vis, log_pval, fold_change = ncem.data.compute_cluster_enrichment(
image_key=['S1_A1_Complete'],
target_cell_type='2',
clip_pvalues=-5,
n_neighbors=50,
n_pcs=None,
)

sc.pl.umap(adata_vis, color='2 substates', palette='tab10')

plt.savefig("subclust_test.png")
plt.show()

I would appreciate your help
Thanks

[AnnaChristina]

Hi @archanabhardwaj ,

thanks for opening this issue and your interest in using ncem.

all ncem plotting functions have a save argument that allow the user to specifiy the path where figures should be stored, e.g.

ncem/ncem/data.py

Lines 900 to 912 in 9b6d3fb

	def cluster_enrichment(
	self,
	pvalues,
	fold_change,
	figsize: Tuple[float, float] = (4.0, 10.0),
	fontsize: Optional[int] = None,
	pad: float = 0.15,
	pvalues_cmap=None,
	linspace: Optional[Tuple[float, float, int]] = None,
	save: Union[str, None] = None,
	suffix: str = "_cluster_enrichment.pdf",
	show: bool = True,
	):

I am closing this issue, but feel free to open it again in case of further questions.