Scraping Github organization for personal BPG functions

[lydiayliu]

Before this repo, many users of BPG don't have anywhere to submit issues and thus must take it to their own hands to fix bugs encountered or implement features required for their projects. This ship-it day project (Nov 2022) aims to find these custom definitions of bpg plotting functions, and discovery what they were trying to implement.

Limitations

• Github web search does not apply the use of wildcard and symbols

You can't use the following wildcard characters as part of your search query: . , : ; / \ ` ' " = * ! ? # $ & + ^ | ~ < > ( ) { } [ ] @. The search will simply ignore these symbols

• Github web search only happens for the recently indexed version of repositories
• Only works for direct user copies of BPG functions and thus last-resort bug fixes and feature additions, not "creative hacks" of input data to achieve specific desired outputs, or not

Workflow

• search on github web
• copy user-defined BPG function
• Compare Side-By-Side to latest BPG script
• note large sections of user-changed lines

create.barplot

org:uclahs-cds "create.barplot <- function(formula" NOT repo:uclahs-cds/public-R-BoutrosLab-plotting-general NOT path:Resources/code/R/BoutrosLab.plotting.general/

Hits: 3
Relevant: 1

Raag Agrawal project-CPC-GENE-MethyBiomarker

"create barplot with error bar"
Fixes problem with barplot error bar placement when there are groups, added to existing issue #33

create.boxplot

org:uclahs-cds "create.boxplot <- function(formula" NOT repo:uclahs-cds/public-R-BoutrosLab-plotting-general NOT path:Resources/code/R/BoutrosLab.plotting.general/

Hits: 8
Relevant: 0

create.densityplot

org:uclahs-cds "create.densityplot <- function" NOT repo:uclahs-cds/public-R-BoutrosLab-plotting-general NOT path:Resources/code/R/BoutrosLab.plotting.general/

create.dotmap

org:uclahs-cds "create.dotmap <- function(x" NOT repo:uclahs-cds/public-R-BoutrosLab-plotting-general NOT path:Resources/code/R/BoutrosLab.plotting.general/

Hits: 15
Relevant: 2 (1)

Natalie Fox project-disease-ProstateTumor-PRAD-000050-666PG

Commented out the lines that fill in the pch vector for is.na(x). The replacement is erroneous in the code because it causes misalignment between x and pch.
Created issue #56

create.heatmap

org:uclahs-cds "create.heatmap <- function(x" NOT repo:uclahs-cds/public-R-BoutrosLab-plotting-general NOT path:Resources/code/R/BoutrosLab.plotting.general/

Hits: 39
Relevant: 1

Natalie Fox BoutrosLab-Biomarkers-BreastCancer-hypoxia_preprocessing_sensitivity

"allows control of the height of the xaxis covariates"
Added size control for xaxis covariates.
Created issue #57

create.hexbinplot

org:uclahs-cds "create.hexbinplot <- function(formula" NOT repo:uclahs-cds/public-R-BoutrosLab-plotting-general NOT path:Resources/code/R/BoutrosLab.plotting.general/

create.histogram

org:uclahs-cds "create.histogram <- function(x" NOT repo:uclahs-cds/public-R-BoutrosLab-plotting-general NOT path:Resources/code/R/BoutrosLab.plotting.general/

Hits: 8

create.lollipopplot

org:uclahs-cds "create.lollipopplot" NOT repo:uclahs-cds/public-R-BoutrosLab-plotting-general NOT path:Resources/code/R/BoutrosLab.plotting.general/

create.manhattanplot

org:uclahs-cds "create.manhattanplot" NOT repo:uclahs-cds/public-R-BoutrosLab-plotting-general NOT path:Resources/code/R/BoutrosLab.plotting.general/

create.multipanelplot

org:uclahs-cds "create.multipanelplot <- function(plot.objects" NOT repo:uclahs-cds/public-R-BoutrosLab-plotting-general NOT path:Resources/code/R/BoutrosLab.plotting.general/

create.multiplot

org:uclahs-cds "create.multiplot <- function(plot.objects" NOT repo:uclahs-cds/public-R-BoutrosLab-plotting-general NOT path:Resources/code/R/BoutrosLab.plotting.general/

create.polygonplot

org:uclahs-cds "create.polygonplot <- function(formula" NOT repo:uclahs-cds/public-R-BoutrosLab-plotting-general NOT path:Resources/code/R/BoutrosLab.plotting.general/

create.scatterplot

org:uclahs-cds "create.scatterplot <- function(formula" NOT repo:uclahs-cds/public-R-BoutrosLab-plotting-general NOT path:Resources/code/R/BoutrosLab.plotting.general/

Hits: 5
Relevant: 1 (not part of 5)

Lydia Liu project-ExerciseOncology-PRESTO1

Grouped scatterplot error bar groups need to be explicitly made "factor". Already in issue #22

create.segplot

org:uclahs-cds "create.segplot <- function(formula" NOT repo:uclahs-cds/public-R-BoutrosLab-plotting-general NOT path:Resources/code/R/BoutrosLab.plotting.general/

create.stripplot

org:uclahs-cds "create.stripplot <- function(formula" NOT repo:uclahs-cds/public-R-BoutrosLab-plotting-general NOT path:Resources/code/R/BoutrosLab.plotting.general/

create.violinplot

org:uclahs-cds "create.violinplot <- function(formula" NOT repo:uclahs-cds/public-R-BoutrosLab-plotting-general NOT path:Resources/code/R/BoutrosLab.plotting.general/