Questions about "Construct GEMs"

[wangzlgithub]

Hello, thanks for developing this fantastic tool.

I don't think the parameter layer_key play a role when the inputting data has been normailzed in Construct GEMs step:

fs.pp.construct_gems_using_pyliger(adata,
                                n_gems = 10,
                                layer_key = 'counts',
                                condition_key = condition_key)

Because I saw the source codes in flowsig/preprocessing/_gem_construction.py as below:

flowsig/flowsig/preprocessing/_gem_construction.py

Lines 20 to 31 in f86164d

	ad.X = csr_matrix(ad.layers[layer_key].copy())
	ad.obs.index.name = 'index'
	ad.var.index.name = 'index'
	# Create LIGER object
	adata_list = []
	for cond in conditions:
	adata_cond = adata[adata.obs[condition_key] == cond].copy()
	adata_cond.uns['sample_name'] = cond
	adata_list.append(adata_cond)
	adata_liger = pyliger.create_liger(adata_list, make_sparse=True)

[axelalmet]

Hello wangzlgithub,

Wow, good catch! This explains why a previous issue had noticed a discrepancy between the GEMs I generated for the original paper generated by the current version of FlowSig. Thank you so much!

I will update FlowSig ASAP. The simple fix should be to replace line 27 with:
adata_cond = ad[ad.obs[condition_key] == cond].copy()

[zhangyl686]

Hello wangzlgithub,
I've been trying to install this package for half a month, but all attempts have failed. Every time I try to import this package in Python, it prompts me to install other dependent packages. After I install them, it prompts me to install yet another dependent package. After installing some dependent packages, conflicts arise among them. I've tried dozens of times. Could you please teach me how to install the flowsig package successfully?
Thank you very much indeed！
My email address is [email protected].

[tenlives]

Hello wangzlgithub, I've been trying to install this package for half a month, but all attempts have failed. Every time I try to import this package in Python, it prompts me to install other dependent packages. After I install them, it prompts me to install yet another dependent package. After installing some dependent packages, conflicts arise among them. I've tried dozens of times. Could you please teach me how to install the flowsig package successfully? Thank you very much indeed！ My email address is [email protected].

I have also have trouble with installing this package according current install mehtods. Could you provide us a simple and successful way ? Thank you very much! @axelalmet