mattssca commented 1 year ago

Pull Request Checklists

Important: When opening a pull request, keep only the applicable checklist and delete all other sections.

Checklist for all PRs

Required

[ ] I tested the new code for my use case (please provide a reproducible example of how you tested the new functionality)
[ ] I ensured all dplyr functions that commonly conflict with other packages are fully qualified.

This can be checked and addressed by running check_functions.pl and responding to the prompts. Test your code after you do this.

[ ] I generated the documentation and checked for errors relating to the new function (e.g. devtools::document()) and added NAMESPACE and all other modified files in the root directory and under man.

Optional but preferred with PRs

[ ] I updated and/or successfully knitted a vignette that relies on the modified code (which ones?)

Checklist for New Functions

Required

[ ] I documented my function using ROxygen style.)
[ ] All parameters for the function are described in the documentation and the function has a decriptive title.

Example:

#' Use GISTIC2.0 scores output to reproduce maftools::chromoplot with more flexibility
#'
#' @param scores output file scores.gistic from the run of GISTIC2.0
#' @param genes_to_label optional. Provide a data frame of genes to label (if mutated). The first 3 columns must contain chromosome, start, and end coordinates. Another required column must contain gene names and be named `gene`. (truncated for example)
#' @param cutoff optional. Used to determine which regions to color as aberrant. Must be float in the range [0-1]. (truncated for example)

[ ] My function uses a library that isn't already a dependency of GAMBLR and I made the package aware of this dependency using the function documentation import statment.

Example:

#' @return nothing
#' @export
#' @import tidyverse ggrepel

Checklist for changes to existing code

[ ] I added/removed arguments to a function and updated documentation for all changed/new arguments
[ ] I tested the new code for compatability with existing functionality in the Master branch (please provide a reprex of how you tested the original functionality)

mattssca commented 1 year ago

To the reviewer (or anyone interested in contributing)

Let's have a discussion on how to categorize the different GAMBLR functions best. This relates to how the functions will be organized on the reference page. This is specified in the _pkgdown.yml file.

This is how the functions are currently being grouped:

Annotations

Functions used to annotate GAMBL data.

[x] - annotate_driver_ssm
[x] - annotate_hotspots
[x] - annotate_igh_breakpoints
[x] - annotate_recurrent_cnv
[x] - annotate_ssm_blacklist
[x] - annotate_sv

Bundled Data

This is the bundled data used by GAMBLR.

[x] - chromosome_arms_grch37
[x] - chromosome_arms_hg38
[x] - dhitsig_genes_with_weights
[x] - gene_blacklist
[x] - grande_maf
[x] - grch37_all_gene_coordinates
[x] - grch37_ashm_regions
[x] - grch37_gene_coordinates
[x] - grch37_lymphoma_genes_bed
[x] - grch37_oncogene
[x] - grch37_partners
[x] - hg38_ashm_regions
[x] - hg38_gene_coordinates
[x] - hg38_lymphoma_genes_bed
[x] - hg38_oncogene
[x] - hg38_partners
[x] - hotspot_regions_grch37
[x] - hotspot_regions_hg38
[x] - lymphoma_genes
[x] - lymphoma_genes_comprehensive
[x] - reddy_genes
[x] - target_regions_grch37
[x] - target_regions_hg38
[x] - wright_genes_with_weights

cBioPortal

Functions tailored to setting up a new study or updating an existing cBioPortal instance.

[x] - cbioportal_create
[x] - custom_caselist
[x] - finalize_study
[x] - get_study_info
[x] - setup_expreession_data
[x] - setup_fusions
[x] - setup_study
[x] - study_check

Checks

GAMBLR functions fall under the check category.

[x] - check_gambl_metadata
[x] - check_gamblr_config
[x] - check_host
[x] - check_remote_configuration
[x] - fread_maf

Get Data

A collection of functions used to retrieve data of different types.

[ ] - assign_cn_to_ssm
[ ] - consolidate_lymphgen
[x] - get_ashm_count_matrix
[x] - get_bams
[x] - get_cn_segments
[x] - get_cn_states
[x] - get_coding_ssm
[x] - get_coding_ssm_status
[x] - get_combined_sv
[x] - get_excluded_samples
[x] - get_gambl_colours
[x] - get_gambl_metadata
[x] - get_gene_cn_and_expression
[x] - get_gene_expression
[x] - get_lymphgen
[x] - get_manta_sv
[x] - get_manta_sv_by_sample
[x] - get_manta_sv_by_samples
[x] - get_mutation_frequency_bin_matrix
[x] - get_sample_cn_segments
[x] - get_sample_wildcards
[x] - get_samples_md5_hash
[x] - get_ssh_session
[x] - get_ssm_by_patients
[x] - get_ssm_by_sample
[x] - get_ssm_by_samples
[x] - get_ssm_by_region
[x] - get_ssm_by_regions

I/O

Functions used to write or read GAMBL data.

[ ] - fetch_output_files
[ ] - maf_to_custom_track
[ ] - sv_to_bedpe_file
[ ] - sv_to_custom_track

Plotting

Functions used for visualizing GAMBL data.

[x] - ashm_multi_rainbow_plot
[x] - ashm_rainbow_plot
[x] - comp_report
[x] - copy_number_vaf_plot
[x] - fancy_alignment_plot
[x] - fancy_circos_plot
[x] - fancy_cnbar
[x] - fancy_ideogram
[x] - fancy_multisamp_ideogram
[x] - fancy_propcov_plot
[x] - fancy_proportions_plot
[x] - fancy_qc_plot
[x] - fancy_snv_chrdistplot
[x] - fancy_sv_sizedens
[x] - fancy_v_chrcount
[x] - fancy_v_count
[x] - fancy_v_sizedis
[x] - focal_cn_plot
[x] - plot_sample_circos
[x] - prettyChromoplot
[x] - prettyCoOncoplot
[ ] - prettyForestPlot
[x] - prettyGeneCloud
[x] - prettyOncoplot
[x] - prettyRainfallPlot
[x] - pretty_lollipop_plot
[x] - splendidHeatmap

Statistical Testing and Computing

Functions used for executing statistical and other calculations on incoming GAMBL data.

[ ] - FtestCNV
[ ] - calc_mutation_frequency_sliding_windows
[x] - calculate_pga
[ ] - cnvKompare
[x] - count_ssm_by_region
[x] - estimate_purity

Utilities

A collection of functions that fall under the utility category.

[x] - adjust_ploidy
[x] - assemble_file_details
[x] - cleanup_maf
[x] - collate_lymphgen
[x] - collate_results
[x] - find_expected_outputs
[x] - find_files_extract_wildcards
[x] - gene_to_region
[x] - genome_to_exome
[x] - intersect_maf
[x] - liftover_bedpe
[x] - make_igv_snapshot
[x] - populate_each_tool_result
[x] - populate_tool_results
[x] - region_to_bins
[x] - region_to_gene
[x] - review_hotspots
[x] - sanitize_maf_data
[x] - supplement_maf
[ ] - theme_Morons
[x] - tidy_gene_expression
[x] - tidy_lymphgen
[x] - write_sample_set_hash

Besides updates relating to GAMBLR website, this PR also includes an update to finalize_study. This update allows for additional sample-level summary fields to be added to the clinical metadata file. The function now internally calls collate_results and joins with the full metadata. This allows us to pick any columns available in the collated results output (and the standard metadata). If no such columns are specified, the function will run in the same way it did prior to this update.

See function documentation and examples for more info.

mattssca commented 1 year ago

This is the updated groups and contents (based on the discussion in Slack) of the reference page;

Annotations

Functions used to annotate GAMBL data.

annotate_driver_ssm
annotate_hotspots
annotate_igh_breakpoints
annotate_recurrent_cnv
annotate_ssm_blacklist
annotate_sv

Bundled Data

This is the bundled data used by GAMBLR.

chromosome_arms_grch37
chromosome_arms_hg38
dhitsig_genes_with_weights
gene_blacklist
grande_maf
grch37_all_gene_coordinates
grch37_ashm_regions
grch37_gene_coordinates
grch37_lymphoma_genes_bed
grch37_oncogene
grch37_partners
hg38_ashm_regions
hg38_gene_coordinates
hg38_lymphoma_genes_bed
hg38_oncogene
hg38_partners
hotspot_regions_grch37
hotspot_regions_hg38
lymphoma_genes
lymphoma_genes_comprehensive
reddy_genes
target_regions_grch37
target_regions_hg38
wright_genes_with_weights

cBioPortal

Functions tailored to setting up a new study or updating an existing cBioPortal instance.

cbioportal_create
custom_caselist
finalize_study
get_study_info
setup_expreession_data
setup_fusions
setup_study
study_check

Checks

GAMBLR functions that fall under the check category.

check_gambl_metadata
check_gamblr_config
check_host
check_remote_configuration
fread_maf

Get Data

A collection of functions used to retrieve data of different types.

get_ashm_count_matrix
get_bams
get_cn_segments
get_cn_states
get_coding_ssm
get_coding_ssm_status
get_combined_sv
get_excluded_samples
get_gambl_colours
get_gambl_metadata
get_gene_cn_and_expression
get_gene_expression
get_lymphgen
get_manta_sv
get_manta_sv_by_sample
get_manta_sv_by_samples
get_mutation_frequency_bin_matrix
get_sample_cn_segments
get_sample_wildcards
get_samples_md5_hash
get_ssh_session
get_ssm_by_patients
get_ssm_by_sample
get_ssm_by_samples
get_ssm_by_region
get_ssm_by_regions

Plotting

Functions used for visualizing GAMBL data.

ashm_multi_rainbow_plot
ashm_rainbow_plot
calc_mutation_frequency_sliding_windows
cnvKompare
comp_report
copy_number_vaf_plot
fancy_alignment_plot
fancy_circos_plot
fancy_cnbar
fancy_ideogram
fancy_multisamp_ideogram
fancy_propcov_plot
fancy_proportions_plot
fancy_qc_plot
fancy_snv_chrdistplot
fancy_sv_sizedens
fancy_v_chrcount
fancy_v_count
fancy_v_sizedis
focal_cn_plot
FtestCNV
plot_sample_circos
prettyChromoplot
prettyCoOncoplot
prettyForestPlot
prettyGeneCloud
prettyOncoplot
prettyRainfallPlot
pretty_lollipop_plot
splendidHeatmap
theme_Morons

Statistical tests and Computing

Functions used for executing statistical and other calculations on incoming GAMBL data.

FtestCNV
calc_mutation_frequency_sliding_windows
calculate_pga
cnvKompare
count_ssm_by_region
estimate_purity
prettyForestPlot

Utilities

A collection of functions that fall under the utility category.

adjust_ploidy
assemble_file_details
assign_cn_to_ssm
cleanup_maf
consolidate_lymphgen
collate_lymphgen
collate_results
fetch_output_files
find_expected_outputs
find_files_extract_wildcards
gene_to_region
genome_to_exome
intersect_maf
liftover_bedpe
maf_to_custom_track
make_igv_snapshot
populate_each_tool_result
populate_tool_results
region_to_bins
region_to_gene
review_hotspots
sanitize_maf_data
sv_to_bedpe_file
sv_to_custom_track
supplement_maf
tidy_gene_expression
tidy_lymphgen
write_sample_set_hash

morinlab / GAMBLR

GAMBLR Website and cBioPortal #192

Pull Request Checklists

Checklist for all PRs

Required

Optional but preferred with PRs

Checklist for New Functions

Required

Checklist for changes to existing code

To the reviewer (or anyone interested in contributing)

Annotations

Bundled Data

cBioPortal

Checks

Get Data

I/O

Plotting

Statistical Testing and Computing

Utilities

Annotations

Bundled Data

cBioPortal

Checks

Get Data

Plotting

Statistical tests and Computing

Utilities