exploring the data - Githubissues

cognoma / cancer-data

TCGA data acquisition and processing for Project Cognoma

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exploring the data #11

Open ypar opened 7 years ago

ypar commented 7 years ago

An issue has been raised in the meeting today regarding visualizations of the clinical data. Other data viz are also considered. However, more immediately, we need viz schemes of the clinical data for assessments and covariate selection.

ypar commented 7 years ago

@Inquisitive-Geek is interested in resolving this issue

clairemcleod commented 7 years ago

Approach: seaborn/matplotlib in jupyter notebook

Potential visualizations:

Clinical:

Prevalence of tumor sites amongst samples
'Time to event' distribution
Other variables of interest?

Sequencing (HiSeqV2):

Examine for batch effects? (potentially link to clinical matrix contributing variables)

Mutation:

Prevalence of mutation types
Number of mutations/sample ID
Most and least mutated genes

Feel free to add your own suggestions below!

ypar commented 7 years ago

my only worry with seaborn is that it is very memory heavy. However, for the scale of data, I suppose it will be ok.