h5Seurat format

[wajm]

Hi,
is it possible to use h5Seurat format converted by SeuratDisk in STREAM?
https://mojaveazure.github.io/seurat-disk/articles/convert-anndata.html

My data is integrated seurat object.

[wajm]

for using seurat object, STREAM had suggested loomR conversion in seurat.
however now loomR using seurat-disk, all setting is change.

[wajm]

Okay, I've tried this. and working like previous #100 setting.
but I'm not sure this is correct or not.
Please check this.

patient object is subset of original my data and performed "FindVariableFeatures", "ScaleData" after subsetting.

library(Seurat)
library(SeuratDisk)
SaveH5Seurat(patient, filename = "patient.h5Seurat")
Convert("patient.h5Seurat", dest = "h5ad")

in STREAM:

adata = ad.read_h5ad("patient.h5ad")
st.set_workdir(adata,'result')
st.add_metadata(adata,file_name='metadata.txt')

adata.obsm['top_pcs'] = adata.obsm['X_pca']
adata.obsm['X_dr'] = adata.obsm['X_umap']
adata.obsm['X_vis_umap'] = adata.obsm['X_umap']

then I can either learn graphical structure directly on UMAP from seurat:

st.plot_visualization_2D(adata,method='umap',n_neighbors=50,color=['label'],use_precomputed=True,fig_size=[11,9])
st.seed_elastic_principal_graph(adata,n_clusters=100,use_vis=True)
st.elastic_principal_graph(adata,epg_alpha=0.01,epg_mu=0.2,epg_lambda=0.01,n_jobs=4)

[huidongchen]

Sorry about the delay. Thanks very much for the feedback and solution. This looks all right to me. I would suggest lowering n_clusters though (a reasonable range would be 5~20 for it)

We are currently working on STREAM2 and making STREAM compatible with other single-cell analysis is one big part of it. Hope that our STREAM2 will facilitate the conversion between different file formats. Stay tuned!

[wajm]

I'm realized an issue.

in STREAM:
adata = ad.read_h5ad("patient.h5ad")
st.set_workdir(adata,'result')
st.add_metadata(adata,file_name='metadata.txt')

adata.obsm['top_pcs'] = adata.obsm['X_pca']
adata.obsm['X_dr'] = adata.obsm['X_umap']
adata.obsm['X_vis_umap'] = adata.obsm['X_umap']

For my integration Seurat object, upper code in STREAM was used.
but I've got partial data from seurat object.

Please check whether the upper setting is correct.

[huidongchen]

Hi, the setting looks all right to me. It seems the same as the code you shared previously though. I am not sure what the problem here is.

[wajm]

Hi, the setting looks all right to me. It seems the same as the code you shared previously though. I am not sure what the problem here is.

hmmm. My integrated Seruat object lost many cells in subway plot and flat tree plot.
Thanks.

[wajm]

AnnData object with n_obs × n_vars = 11826 × 2000
obs: 'label', 'label_color'
var: 'features'
uns: 'workdir', 'label_color'
obsm: 'X_pca', 'X_umap', 'top_pcs', 'X_dr', 'X_vis_umap'
varm: 'PCs'

in my data, n_vars is only 2000. I think that is problem.

[huidongchen]

I don't think the number of features should be a problem.

I am not sure why cells are missing in those plots, which is something new to me. It would be helpful if you can share with me a notebook to reproduce the issue. Give such information, unfortunately i can not help much.