Open shermas opened 2 years ago
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
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
Hi Shachar and Lilia,
thanks for the comments! We will implement the 3D visualisation in the following months (as soon as possible)
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
@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
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