Closed Jiayi-Zheng closed 1 year ago
Hi!! The function read_h5ad
is added from v0.13.0b1, you need to explicitly specify the version when you install stereopy because it is just a beta build.
You can run the command: pip install --use-pep517 stereopy==0.13.0b1
@tanliwei-coder Thank you so much for your reply! Could you maybe help me out on my two other questions as well? I didn't seem to find a function annotation of all the available functions in sterepy package... Not sure if it's I didn't look into the right place?
About your second question, you can get the cells infomation by running data.cells.to_df()
.
About the first, i need more investigation and will reply to you as soon as possible.
Hello, I installed stereopy in a newly created env with python3.8 with
conda create --name st python=3.8
thenpip install --use-pep517 stereopy
and then doimport stereo as st
followed bydata = st.io.read_h5ad('/usersdata/user/BGI_Stereo/E16.5_E2S6.MOSTA.h5ad')
I tried to read in h5ad file from
https://db.cngb.org/stomics/mosta/download/
but it tells memodule 'stereo.io' has no attribute 'read_h5ad'
Further check in my stereopy package indicated:
Checking the init.py file I read:
I then tried
data = st.io.read_stereo_h5ad('/usersdata/user/BGI_Stereo/E16.5_E2S6.MOSTA.h5ad')
which gives me the following:For reference:
One more question... The manual tutorial talked about how to get result from the gef file. I'm trying to visualize the E16.5 E1S3 whole embryo data. Could kindly point me to any tutorial or instruction on how to assemble datasets regarding E1S3 in
https://db.cngb.org/stomics/mosta/download/
? For example, how to embed the tiff image file into the h5ad file. I didn't seem to find relevant instruction from the stereopy tutorial.Sorry another really simple question... How do I extract cells information? I have a StereoExpData object called data. If I do
data.cells
it tells me<stereo.core.cell.Cell at 0x7f756fd85970>
. But how do I visualize it or convert it to a pandas dataframe? my data object looks like: