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Chromosomal Instability (PR 3 of 3): The notebook with plots#419

Merged

jaclyn-taroni merged 71 commits intoAlexsLemonade:masterfrom cansavvy:cin_setup

Jan 18, 2020

+4,399-103

Commits on Jan 3, 2020

It's a start of a notebook
Candace Savonen
committed
Got some of the code converted and working
Candace Savonen
committed
Percent genome change plot added
Candace Savonen
committed

Commits on Jan 6, 2020

Have overlap of CNV and SV
Candace Savonen
committed
Breakpoint summary df
Candace Savonen
committed
Got things mostly organized and the wrangling functions are formed up more
Candace Savonen
committed
Load my functions as they are so far. TileGenome setting up
Candace Savonen
committed

Commits on Jan 7, 2020

Made a plotting function that probably won't work yet
Candace Savonen
committed
Things are here, just need to test things, reorg and add more doc
Candace Savonen
committed
Plotting function works
Candace Savonen
committed
Merge remote-tracking branch 'upstream/master' into cin_setup
Candace Savonen
committed
Merge remote-tracking branch 'upstream/master' into cin_setup
Candace Savonen
committed
It's working!
Candace Savonen
committed
Plots are working just need more doc
Candace Savonen
committed
Add a README and change the function file name
Candace Savonen
committed

Commits on Jan 8, 2020

Some reorganization and adding the plots
Candace Savonen
committed
lintered and neatened up some things
Candace Savonen
committed
Few more touches to the README
Candace Savonen
committed
Add the functions
Candace Savonen
committed
Edited a messed up comment
Candace Savonen
committed
Merge branch 'master' into cin_functions
cansavvy
authored
Fixed some issues with the functions
cansavvy
authored
Add tumor type plots
Candace Savonen
committed
Rearrange and fix some things with the group calculations
Candace Savonen
committed
Smoothing out some metadata handling of GenomicRanges
Candace Savonen
committed
Functions handle multiple samples
Candace Savonen
committed
The functions handle grouped data
Candace Savonen
committed
Got rid of a development remnant I found
Candace Savonen
committed
minor typo fixes
Candace Savonen
committed
Apply percentage filter to CNV data
Candace Savonen
committed

Commits on Jan 9, 2020

Minor edits
Candace Savonen
committed
Changes to logic and plot names
Candace Savonen
committed
Incorporate @sjspielman suggestions
Candace Savonen
committed
Missed a paranthesis
Candace Savonen
committed
re-linter
Candace Savonen
committed
Merge branch 'cin_functions' into cin_setup
Candace Savonen
committed
Reorganize the plots
Candace Savonen
committed
Add tumor type plots
Candace Savonen
committed
Add to CircleCI
Candace Savonen
committed
Merge branch 'master' into cin_setup
cansavvy
authored
Get rid of development remnant
Candace Savonen
committed
Merge remote-tracking branch 'origin/cin_setup' into cin_setup
Candace Savonen
committed
Delete sample PNGs and zip up tumor type PNGs
Candace Savonen
committed
some svcnvplus files snuck in.
Candace Savonen
committed
Fix tumor-type plots and add automatic zip
Candace Savonen
committed
Get rid of 01-process-sv-file.R source step. Use straight file.
Candace Savonen
committed
Had to change sample name getter step
Candace Savonen
committed
Fix a missing dplyr::
Candace Savonen
committed

Commits on Jan 10, 2020

Add chromosomal instability to main README table
Candace Savonen
committed
Add a sample number check to avoid the error
Candace Savonen
committed
See if suppressing the warning for the bin overlap helps.
Candace Savonen
committed
Fix logic statement for sample check.
Candace Savonen
committed
Remove histology groups if they don't have at least 2 samples
Candace Savonen
committed
Merge remote-tracking branch 'upstream/master' into cin_setup
Candace Savonen
committed
Merge branch 'master' into cin_setup
cansavvy
authored
update notebook
Candace Savonen
committed
Merge branch 'master' into cin_setup
cansavvy
authored

Commits on Jan 13, 2020

Fix plot zipping to overwrite current zip files
Candace Savonen
committed
The easy changes suggested by @jashapiro have been implemented
Candace Savonen
committed

Commits on Jan 14, 2020

Heatmap is mostly there.
Candace Savonen
committed
Merge branch 'master' into cin_setup
cansavvy
authored
Upload the heatmaps and fixed stuff
Candace Savonen
committed
Merge remote-tracking branch 'origin/cin_setup' into cin_setup
Candace Savonen
committed
Merge branch 'master' into cin_setup
cansavvy
authored

Commits on Jan 16, 2020

Commits on Jan 18, 2020