ismms-himc / clustergrammer2-notebooks Goto Github PK

We're working on Saturn Cloud and MyBinder examples:

We want to test whether Saturn Cloud can handle normal sized (~100-200MB) user uploaded datasets (larger than toy datasets). We would like to do the following:

MyBinder and Saturn Cloud

• Run Jupyter Notebook from Gallery (preferably Jupyter-Lab)
• Have user upload their data
• Save HTML-snapshot of their results
• Upload notebook to a new public GitHub repo and share through NBVIewer
• Run Jupyter Notebook from Saturn Cloud Gallery (preferably Jupyter-Lab) link
• Add links to documentation under case studies (MaayanLab/clustergrammer-docs#4)
• Publish examples on Code Ocean

bqplot/bqplot#884

Make a MNIST (and fashion MNIST) example with a heatmap and a bqplot widget that shows selected digits or selected pixels as images. We will have the bqplot widget observe the selected rows/columns of the Clustergrammer2 widget. This will be a nice way of showing the linked views we can generate using widgets. We can also make the example in Jupyter Lab and position the two views next to each other.

There are additional data types available for the 1,037 cancer cell lines from the CCLE. Try adding another data type to the example to show how we can work with multi-modal data. And to show the similarity between bulk and single cell workflows.

http://software.broadinstitute.org/gsea/msigdb/supplementary_genesets.jsp

10X released a dataset of ~100K CD8 T Cells, we should make an example notebook working with this data. We need to be careful to not add too much data to this repo however. Make a branch for this.

Dataset link: https://www.10xgenomics.com/extra/#whats-new?utm_source=Twitter&utm_medium=&utm_content=&utm_campaign=2019-Social-Twitter

https://support.10xgenomics.com/single-cell-vdj/datasets/3.0.2/vdj_v1_hs_aggregated_donor1

I was following the notebook:

net.load_df(df)
net.widget()
Error displaying widget: model not found

Any ideas?

Section: # Predict Cell Types using CIBERSORT Signatures
Error: AttributeError: 'Series' object has no attribute 'get_values'

Following error when I try to run the PBMC-scRNA notebook:

/clustergrammer_fun/categories.py in dict_cat(net, define_cat_colors)
    131             for inst_full_name in inst_dict:
    132 
--> 133                 inst_name = inst_full_name.split(': ')[1]
    134                 inst_color = inst_dict[inst_full_name]
    135 

IndexError: list index out of range

I solved this issue by changing the dict iteration in categories.py

to:

for k, v in inst_dict.items():
      inst_name = k
      inst_color = v
      global_cat_colors[inst_name] = inst_color