visualizing gene expression in multiple slices or 3D

[shermas]

Hey,

To visualize predicted gene expression, I run novosparc.pl.embedding(dataset_reconst, pl_genes) after defining a 3d target space
and finding the probability space for each cell. This, however, outputs only a single 2d image, which looks like a projection of the 3d space. How could I in this case get the 3d predicted expression?
Or, alternatively, specify in which z section I wish to see the predicted expression pattern?

Best,
Shachar

[liliay]

Hi,

Have the exact same issue here. The representations on the target space are only in 2D. Did you find a way to have a 3D representation (i am using the "no prior knowledge technique and mapping my gene expression on a sphere) ?

Thanks in advance for your help,
Best,
Lilia

[shermas]

Hey,

I had to work around it. In the case of a sphere, you could probably convert it to a 2D sheet.
For my 3D volume, I ended exporting the important data and visualizing the expression using the plotly package
in either R or python.

I hope this helps,
Best,
Shachar

[enessenel]

Hi Shachar and Lilia,

thanks for the comments! We will implement the 3D visualisation in the following months (as soon as possible)

[liliay]

Thank you Shachar, very helpful, I tried 3D plotting using plotly and it works well with very nice visualization options, and also by modifying the embedding function so that it takes into account the z axis. Works fine tboth ways !
Can't wait to see this new feature within novosparc.

Again thank you guys so much for your suggestions and help,

Lilia

[liliay]

@enessenel One last question :
I looked at the code of the construct_sphere() and from my understanding, you generate evenly spaced points ON the sphere, so the sphere is not "filled" with points ?

Best,
lilia