This repository has been archived by the owner on Oct 2, 2024. It is now read-only.

Create corplots-PR-v2#33

Merged

AntoniaChroni merged 98 commits intomainfrom tmb-vaf-longitudinal-create-corplots

Oct 6, 2023

+68,559-3

Commits on Aug 3, 2023

Upload all files to create corplots
antoniachroni
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Run create-corplots
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Clean code based on Lint
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Change color order for timepoints
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Upload plots with new colors
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Update
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Commits on Aug 5, 2023

results from corplots
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run corplots 2
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Edit summary in the README file
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Add Results section in README file
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Add Results section
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Commits on Aug 8, 2023

Merge branch 'create-pptc-pdx-corplots' into tmb-vaf-longitudinal-create-corplots
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Commits on Aug 9, 2023

Merge branch 'create-pptc-pdx-corplots' into tmb-vaf-longitudinal-create-corplots
antoniachroni
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Merge branch 'create-pptc-pdx-corplots' into tmb-vaf-longitudinal-create-corplots
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Adjust text size in plot.title
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Run Rmd in Docker and update plots and html
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Update README.md
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Update Results section in the README file
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Merge branch 'create-pptc-pdx-corplots' into tmb-vaf-longitudinal-create-corplots
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Commits on Aug 10, 2023

Replace colors in the function
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Add color_palette tsv files
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Add timepoint_color_palette file and run in Docker
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Insert Roxygen skeleton into the function
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Edit title size in ggplot
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Run updated script via Docker
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Commits on Aug 11, 2023

Remove palettes - this will be added after merging PR#21
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Commits on Aug 14, 2023

Update analyses/tmb-vaf-longitudinal/util/function-create-corplot.R

AntoniaChroni
and
rjcorb
authored
Update analyses/tmb-vaf-longitudinal/util/function-create-corplot.R

AntoniaChroni
and
rjcorb
authored
Add temp palette
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Bring back the code for renaming colnames(timepoint_df)
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Bring back code for renaming colnames(deceased_df)
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Use timepoints_other_plot to create label for timepoint
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Fix typo in function for creating df for timepoints_deceased_plot
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Remove temp palettes
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Commits on Aug 15, 2023

Make corplot reproducible by adding set.seed
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Merge branch 'create-pptc-pdx-corplots' into tmb-vaf-longitudinal-create-corplots
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Update README file about the documentation for the timepoint models
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Commits on Aug 16, 2023

Edit dir where theme.R lives
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Add cancer_group information in the plot as subtitle in the function
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Add max.overlaps=Inf to the function to avoid overlaps in the plots
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Update plots and html with cancer_group
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Commits on Aug 22, 2023

Merge branch 'create-pptc-pdx-corplots' into tmb-vaf-longitudinal-create-corplots
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Rename palette_df
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Rename palette_df in Rmd
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Run Rmd
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Update 02-create-corplots.nb.html
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Commits on Sep 6, 2023

Merge branch 'main' into tmb-vaf-longitudinal-create-corplots
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Commits on Sep 7, 2023

Run Rmd under Docker to investigate PT_3CHB9PK5 plot
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Merge branch 'main' into tmb-vaf-longitudinal-create-corplots
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Edit #patients with TMB info in README
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Commits on Sep 13, 2023

Increase xintercept and yintercept and add documentation
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Move gene labels and add segments
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Remove segments
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Add file path to results_dir and save maf_join table per pair
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Remove subtitle
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Commits on Sep 14, 2023

Edit documentation about set.seed
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Add code for Save plots by cancer_group
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Add subtitle
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Edit code for Save results by cancer_group
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Run code and save plots per cancer group
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Remove old plots
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Add new plots
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Edit code on creating df for cancer_group and sample
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Add cg_sum to identify samples with different diagnosis across timepoints
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Create df for cancer_group and samples
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Code for single vs multiple diagnosis samples deactivated
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Add cg_results_dir
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Remove gap
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Save df in the function adn add kids_id in df
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Fix minot typos
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Save df in the function and add kids_id in df
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Fix minor typos
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Merge remote-tracking branch 'origin/tmb-vaf-longitudinal-create-corplots' into tmb-vaf-longitudinal-create-corplots
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Add cg_sum and edit code to save plots and results based on this
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Remove code with deactivated if statement
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Remove old plots
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Clean code
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Replace x with names in the loop for cg_sum
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Revert "Replace x with names in the loop for cg_sum"
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Revert "Clean code"
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Clean code
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Commits on Sep 16, 2023

Add code to sort cg_names
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Commits on Sep 20, 2023

Add code chunk for Print df per pair in a list
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Add library(reshape2) to reshape df before save
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Edit order of print plots that caused error
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Fix extra idents
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Upload plots and html
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Rename tsv file with all df with common genes
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Delete 04-tmb-unpaired-samples-plot.Rmd
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plots and results run in ec2
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Remove not necessary files after run to ec2
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Remove not necessary files - there was conflict
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Remove print(m)
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New plots and stop run
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Add new plots
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Run in ec2, add new plots, results, and html
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Commits on Oct 2, 2023

Merge branch 'main' into tmb-vaf-longitudinal-create-corplots
antoniachroni
committed
Merge branch 'main' into tmb-vaf-longitudinal-create-corplots
antoniachroni
committed