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oncoprint update PR 2/n replace display group with cancer_group #1147
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- update gene lists (add a few C19MC key genes for ETMRs to embryonal, add ALK and ROS to hgat, move ependymal genes to other list, remove ependymal list) - move ependymal tumor to CNS other oncoprint since there were so few genes in the plot - to enable better panel set up for a main figure - convert relative paths to point to the data directory - updated README
- remove 7316 IDs (TSB) - remove row bar
…BTA-analysis into onco-updated-display-group
…BTA-analysis into onco-updated-display-group
…BTA-analysis into onco-updated-display-group
Co-authored-by: Jo Lynne Rokita <jharenza@gmail.com>
Co-authored-by: Jo Lynne Rokita <jharenza@gmail.com>
Co-authored-by: Jo Lynne Rokita <jharenza@gmail.com>
Co-authored-by: Jo Lynne Rokita <jharenza@gmail.com>
…BTA-analysis into onco-updated-display-group
jharenza
approved these changes
Aug 21, 2021
added 7 commits
August 25, 2021 18:38
…BTA-analysis into onco-updated-display-group
…kar6/OpenPBTA-analysis into onco-updated-display-group
Co-authored-by: Jo Lynne Rokita <jharenza@gmail.com>
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🚨 merge #1142 and #1143 before this PR
Purpose/implementation Section
What scientific question is your analysis addressing?
Rerunning oncoprint with cancer_group color codes
What was your approach?
I've created this branch from #1143 and pulled the latest branch from #1142 and updated code to use cancer_group instead of display_group along with the required hex_codes for cancer_group.
What GitHub issue does your pull request address?
#1141
Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.
Which areas should receive a particularly close look?
Do the plots look as expected?
Is there anything that you want to discuss further?
Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are ready for review?
Results
What types of results are included (e.g., table, figure)?
figure
What is your summary of the results?
Reproducibility Checklist
Documentation Checklist
READMEand it is up to date.analyses/README.mdand the entry is up to date.