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YeoLab / flotilla

Reproducible machine learning analysis of gene expression and alternative splicing data
http://yeolab.github.io/flotilla/docs
BSD 3-Clause "New" or "Revised" License
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study.interactive_clustermap does not take custom list #215

Open yanssbu opened 9 years ago

yanssbu commented 9 years ago

The same custom list works for interactive_pca but not for interactive_clustermap.

Raise the following error: ValueError: This data subset is empty. Please double-check that the gene ids are for the correct species!

mlovci commented 9 years ago

are you accessing it by path on local or url?

yanssbu commented 9 years ago

path on local.

On Dec 6, 2014, at 5:54 PM, Michael Lovci notifications@github.com wrote:

are you accessing it by path on local or url?

— Reply to this email directly or view it on GitHub.

mlovci commented 9 years ago

hm, seems broken for me too.

On Sat, Dec 6, 2014 at 5:55 PM, yanssbu notifications@github.com wrote:

path on local.

On Dec 6, 2014, at 5:54 PM, Michael Lovci notifications@github.com wrote:

are you accessing it by path on local or url?

— Reply to this email directly or view it on GitHub.

— Reply to this email directly or view it on GitHub https://github.com/YeoLab/flotilla/issues/215#issuecomment-65923122.

olgabot commented 9 years ago

This won't fix the problem, but you can add custom lists to the data itself with:

study.expression.feature_data['new_list_name'] = study.expression.feature_data.index.isin(your_list_of_genes)

I'll get to this after the weekend.

On Sat Dec 06 2014 at 5:57:37 PM Michael Lovci notifications@github.com wrote:

hm, seems broken for me too.

On Sat, Dec 6, 2014 at 5:55 PM, yanssbu notifications@github.com wrote:

path on local.

On Dec 6, 2014, at 5:54 PM, Michael Lovci notifications@github.com wrote:

are you accessing it by path on local or url?

— Reply to this email directly or view it on GitHub.

— Reply to this email directly or view it on GitHub https://github.com/YeoLab/flotilla/issues/215#issuecomment-65923122.

— Reply to this email directly or view it on GitHub https://github.com/YeoLab/flotilla/issues/215#issuecomment-65923162.

yanssbu commented 9 years ago

OK, thanks. On Dec 6, 2014 7:08 PM, "Olga Botvinnik" notifications@github.com wrote:

This won't fix the problem, but you can add custom lists to the data itself with:

study.expression.feature_data['new_list_name'] = study.expression.feature_data.index.isin(your_list_of_genes)

I'll get to this after the weekend.

On Sat Dec 06 2014 at 5:57:37 PM Michael Lovci notifications@github.com wrote:

hm, seems broken for me too.

On Sat, Dec 6, 2014 at 5:55 PM, yanssbu notifications@github.com wrote:

path on local.

On Dec 6, 2014, at 5:54 PM, Michael Lovci notifications@github.com wrote:

are you accessing it by path on local or url?

— Reply to this email directly or view it on GitHub.

— Reply to this email directly or view it on GitHub https://github.com/YeoLab/flotilla/issues/215#issuecomment-65923122.

— Reply to this email directly or view it on GitHub https://github.com/YeoLab/flotilla/issues/215#issuecomment-65923162.

— Reply to this email directly or view it on GitHub https://github.com/YeoLab/flotilla/issues/215#issuecomment-65924589.