Can you show us a much more detailful vignette from 10X datasets?

[pangxueyu233]

It's really an impressive study!!! And I really want to use this powerful weapen in my study. Firstly, in your reconstruct_tissue.py scripts. I cannot make sure the dge.txt meaning that a count table including cells expression information with hvgs as rownames or a count table including cells expressing information with top markers in each cell subtypes as rownames.

Secondly, in your packages there is no 'novosparc.rc.construct_target_grid' formula because I got the error like that:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
AttributeError: module 'novosparc.reconstruction' has no attribute 'construct_target_grid'

Could you help me work it out? Thanks

[pangxueyu233]

I Find your construct_target_grid formula, it's in novosparc.geometry, and I tried to move on by using the counts table including cells expression information with hvgs as rownames. Unfortunately, I find the gwa.gromov_wasserstein_adjusted_norm() didn't exist, but I replaced the formula by novosparc.rc.gromov_wasserstein_adjusted_norm.

[Eddylyf]

Hi Pangxueyu233, I also got the same error "AttributeError: module 'novosparc.reconstruction' has no attribute 'construct_target_grid'" I saw your answer but still do not clear how to make it work, may I ask you what should I do with the could you please help me resolve this issue? Thanks so much! Best, Yanfang

[pangxueyu233]

@Eddylyf Hi, I find the formula in 'novosparc.geometry' module. And you just tried codes as following:

locations = novosparc.geometry.construct_target_grid(num_cells)

And that will help you to fix it up. But I still meet so many errors in the later processing, I think maybe developers need to give us a much more detail vignette and that will finally help. And if you have worked it out, please show me what the results you have got.

[Eddylyf]

Hi @pangxueyu233 , Thanks so much for your great help! I will try it again with my dataset, indeed I also think author should give us a more detail code. Thanks again! Best, Yanfang

[nukappa]

We're working on updating the vignettes and also on facilitating the construction of the tissue grids, in a couple of days we'll push those to the repo

[pangxueyu233]

@nukappa
That would be very nice. Appreciated for your working, and we are waiting for your new version.

[matq007]

Hey @nukappa, any update on the reconstruct_tissue.py?

[nukappa]

@matq007 @pangxueyu233 I just pushed a tutorial on reconstructing the Drosophila embryo.