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V2.0 (#1) #211

Merged
merged 1 commit into from
Aug 7, 2024
Merged

V2.0 (#1) #211

merged 1 commit into from
Aug 7, 2024

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rvitancol
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  • Test with matching gene sets

  • Parallelize calls to lldist by profile

  • Determine number of cores for mclapply

  • saving flightpath plot to /tmp/NBClust-Plots/

  • better file naming with time formatting

  • file name without spaces

  • fixing 7X7 in for save size

  • typo fix for units

  • delete detritus in rescaleProfiles

  • iss161 update refineClusters

  • tidy vignettes

  • pass check()

  • make default settings more robust

and use lower max_iters in phase 1

  • update docs

  • partial progress

  • remove geosketch redundancy

and speed up subsampling

  • remove dependency on rcolorbrewer

  • delete comments

  • add colorCellTypes function

Function copied from ptolemy, for choosing a good initial set of colors for cell types

  • document colorcelltypes

  • add color info to vignettes

  • add colorCellTypes function to vignettes

  • fix iss165

  • vignette bugfix

  • copy test script for colorCellTypes from ptolemy

  • Updated the temp folder creation logic

  • updated package version

  • Hardcode isRelease to true and comment out to deploy to all envs

  • New include

  • add specs and remove @exports

  • add missing @params

  • R CMD check fixes

  • new documentation

  • Remove exports

  • Fix imports

  • Update to MIT license

  • Add to .Rbuildignore

  • complete docs

  • Fix documentation

  • Reference global variable for R CMD check

  • doc update

  • Change package name to InSituType

  • Change package name in Rcpp files

  • Linting style changes

  • Update documentation

  • Unify names for vignettes

  • delete settings file

  • Remove writing plot to file

  • Keep as one row matrix

  • Render latest vignettes

  • BiocCheck items

  • Revert "Remove writing plot to file"

  • Specify package for dataset

  • Specify package for data

  • Update vignettes with reference to CosMx

  • Bump version

  • SingleCellExperiment option for core functions

  • Add dependency

  • Use one core for building vignettes

  • Add documentation

  • keep supercluster consister when subclustering

subclustered cells are now required to fall within their original supercluster, even if another supercluster has a greater loglik

  • Bump to version 0.99.3

  • add link to manuscript and citation

  • update README

  • correct dependencies flowchart in readme

  • remove dependency on lsa package in DESCRIPTION; faster way to calculate cell-level cosine similarity with celltype profiles in get_anchor_stats function

  • Don't track RStudio project file

  • Remove set.seed usage

  • Bump version

  • Change maintainer

  • Add examples

  • Merged PR 15109: Update azure-pipelines.yml for Azure Pipelines

Related work items: #175413

  • Update azure-pipelines.yml for Azure Pipelines

  • Updated trigger

  • Removed 1.0 environments from main branch

  • Added QA 1.1 environment

  • Updated local path for copying

  • Fixed variable

  • Update azure-pipelines.yml for Azure Pipelines

  • Fixed globExpression

  • message help wip

  • sync with main

  • explicit convert to dgCMatrix for ensuring access to counts2@x in next line

  • Re-add writing plot to disk.

  • Implement OpenMP parallelization for lldist

  • Don't save plot

  • Added license

  • Fix merge error

  • Restore saving plot

  • Use 64 bit integers

  • filter anchor, platform adjustment

  • fix umap in flightpath

  • add utilities func

  • Bump version to 1.1.0

  • I add the updateReferenceProfiles function to estimate gene-level platform effect and rescale raw reference profile

  • update function name

  • replace the estimatePlatformEffects function with updated version

  • auto anchor selection & reference update

  • update estimatePlatformEffects function

  • update the name of output list

  • rename the output list name

  • anchor threshold, lost genes

  • anchor threshold

  • fix testthat

  • update mans

  • outlier beta range

  • lostgenes vs. blacklist

  • sparse array compatibility

  • net expr

  • default mc.cores option

  • handle glm error

  • fastglm method

  • remove warning_genes

  • fix 0 bg in Poisson start

  • fix zero bg in estimateBackground()

  • Remove unneeded dependency

  • Updated 13 files under /R

  • Updated 7 files under /src

  • Updated 32 files under /man

  • added protein insituType clustering

  • update InsituType.R

  • updated all files

  • testing folder updated

  • testing folder updated

  • InsituType function updated

  • Deleted rescale_reference.R

  • Updated gen_profiles_protein.R

  • Added gen_profiles_protein_old.R

  • Added 2 files to /data

  • Renamed default_signature_matrix.csv to human_signature_matrix.csv

  • Fix S4 method

  • Remove build outputs

  • Update docs

  • Deleted gen_profiles_protein_old.R

  • Updated nbclust.R

  • insitutype function updated for protein

  • gen_profiles_protein function updated

  • Add lsa as dependency

  • Add dependencies

  • update insitutypeML

  • update Rcpp functions

  • update lldist function

  • rcpp change

  • updated all files

  • Update pipeline for devnext.

  • updated chooseclusternumber for protein

  • Deleted NBClust-Plots

  • Deleted NBClust-Plots

  • added examples and commented lines

  • Add back ARMA fix

  • testing examples and tests files

  • Fix example and vignettes

  • Fix roxygen for Rcpp

  • Add dependencies

  • Deleted NBClust-Plots

  • Re-add dependencies

  • Fix errors in unit tests and examples

  • Fix example

  • Remove duplicates

  • calling signature matrix from the package

  • calling signature matrix from the package

  • updated vignette

  • updated the namespace

  • Deleted NBClust-Plots

  • Update version to 1.2.0

  • Update ado pipeline.

  • Merged PR 20275: Create "undefined" profile for cells with zero counts

Change behavior of InSituType in all modes--supervised, unsupervised, semi-supervised--to no longer error when there are cells with zero counts but instead set their cell type to "undefined".

For the other error in linked work item generate a more informative message indicating that the profiles do not have sufficient shared genes with panel.

Related work items: #201286

  • Bump version for dev branch

  • fix compatability with platform correction

  • add default and limit choices for assay_type

  • Bump dev version to v1.2.2

  • PD updates

  • update docs

  • update tests

  • update version and NEWS and README

  • code review updates

  • update news

  • delete duplicated functions

  • new docs

  • 2nd code review updates

  • update FAQ - new qc recommendation

  • Merged PR 21765: handle collinearity issues with fastCohorting

handle collinearity issues with fastCohorting:

  1. Reduce to 2 PC's.
  2. If this fails, then try successively smaller # of cohorts with the 2 pc's.

Related work items: #211163

  • Bump version for dev to 1.2.3

  • bugfix

rownames(sds) was creating an error in rna mode.

  • Merged PR 21963: Update pipeline for dev branch.

Update pipeline for dev branch.

Related work items: #211130

  • faqs update

  • updates per LW code review

  • vignette finessing

  • r cmd check updates

  • faq updates

  • remove vestigial plots


* Test with matching gene sets

* Parallelize calls to lldist by profile

* Determine number of cores for mclapply

* saving flightpath plot to /tmp/NBClust-Plots/

* better file naming with time formatting

* file name without spaces

* fixing 7X7 in for save size

* typo fix for units

* delete detritus in rescaleProfiles

* iss161 update refineClusters

* tidy vignettes

* pass check()

* make default settings more robust

and use lower max_iters in phase 1

* update docs

* partial progress

* remove geosketch redundancy

and speed up subsampling

* remove dependency on rcolorbrewer

* delete comments

* add colorCellTypes function

Function copied from ptolemy, for choosing a good initial set of colors for cell types

* document colorcelltypes

* add color info to vignettes

* add colorCellTypes function to vignettes

* fix iss165

* vignette bugfix

* copy test script for colorCellTypes from ptolemy

* Updated the temp folder creation logic

* updated package version

* Hardcode isRelease to true and comment out to deploy to all envs

* New include

* add specs and remove @exports

* add missing @params

* R CMD check fixes

* new documentation

* Remove exports

* Fix imports

* Update to MIT license

* Add to .Rbuildignore

* complete docs

* Fix documentation

* Reference global variable for R CMD check

* doc update

* Change package name to InSituType

* Change package name in Rcpp files

* Linting style changes

* Update documentation

* Unify names for vignettes

* delete settings file

* Remove writing plot to file

* Keep as one row matrix

* Render latest vignettes

* BiocCheck items

* Revert "Remove writing plot to file"

* Specify package for dataset

* Specify package for data

* Update vignettes with reference to CosMx

* Bump version

* SingleCellExperiment option for core functions

* Add dependency

* Use one core for building vignettes

* Add documentation

* keep supercluster consister when subclustering

subclustered cells are now required to fall within their original supercluster, even if another supercluster has a greater loglik

* Bump to version 0.99.3

* add link to manuscript and citation

* update README

* correct dependencies flowchart in readme

* remove dependency on lsa package in DESCRIPTION; faster way to calculate cell-level cosine similarity with celltype profiles in get_anchor_stats function

* Don't track RStudio project file

* Remove set.seed usage

* Bump version

* Change maintainer

* Add examples

* Merged PR 15109: Update azure-pipelines.yml for Azure Pipelines

Related work items: #175413

* Update azure-pipelines.yml for Azure Pipelines

* Updated trigger

* Removed 1.0 environments from main branch

* Added QA 1.1 environment

* Updated local path for copying

* Fixed variable

* Update azure-pipelines.yml for Azure Pipelines

* Fixed globExpression

* message help wip

* sync with main

* explicit convert to dgCMatrix for ensuring access to counts2@x in next line

* Re-add writing plot to disk.

* Implement OpenMP parallelization for lldist

* Don't save plot

* Added license

* Fix merge error

* Restore saving plot

* Use 64 bit integers

* filter anchor, platform adjustment

* fix umap in flightpath

* add utilities func

* Bump version to 1.1.0

* I add the updateReferenceProfiles function to estimate gene-level platform effect and rescale raw reference profile

* update function name

* replace the estimatePlatformEffects function with updated version

* auto anchor selection & reference update

* update estimatePlatformEffects function

* update the name of output list

* rename the output list name

* anchor threshold, lost genes

* anchor threshold

* fix testthat

* update mans

* outlier beta range

* lostgenes vs. blacklist

* sparse array compatibility

* net expr

* default mc.cores option

* handle glm error

* fastglm method

* remove warning_genes

* fix 0 bg in Poisson start

* fix zero bg in estimateBackground()

* Remove unneeded dependency

* Updated 13 files under /R

* Updated 7 files under /src

* Updated 32 files under /man

* added protein insituType clustering

* update InsituType.R

* updated all files

* testing folder updated

* testing folder updated

* InsituType function updated

* Deleted rescale_reference.R

* Updated gen_profiles_protein.R

* Added gen_profiles_protein_old.R

* Added 2 files to /data

* Renamed default_signature_matrix.csv to human_signature_matrix.csv

* Fix S4 method

* Remove build outputs

* Update docs

* Deleted gen_profiles_protein_old.R

* Updated nbclust.R

* insitutype function updated for protein

* gen_profiles_protein function updated

* Add lsa as dependency

* Add dependencies

* update insitutypeML

* update Rcpp functions

* update lldist function

* rcpp change

* updated all files

* Update pipeline for devnext.

* updated chooseclusternumber for protein

* Deleted NBClust-Plots

* Deleted NBClust-Plots

* added examples and commented lines

* Add back ARMA fix

* testing examples and tests files

* Fix example and vignettes

* Fix roxygen for Rcpp

* Add dependencies

* Deleted NBClust-Plots

* Re-add dependencies

* Fix errors in unit tests and examples

* Fix example

* Remove duplicates

* calling signature matrix from the package

* calling signature matrix from the package

* updated vignette

* updated the namespace

* Deleted NBClust-Plots

* Update version to 1.2.0

* Update ado pipeline.

* Merged PR 20275: Create "undefined" profile for cells with zero counts

Change behavior of InSituType in all modes--supervised, unsupervised, semi-supervised--to no longer error when there are cells with zero counts but instead set their cell type to "undefined".

For the other error in linked work item generate a more informative message indicating that the profiles do not have sufficient shared genes with panel.

Related work items: #201286

* Bump version for dev branch

* fix compatability with platform correction

* add default and limit choices for assay_type

* Bump dev version to v1.2.2

* PD updates

* update docs

* update tests

* update version and NEWS and README

* code review updates

* update news

* delete duplicated functions

* new docs

* 2nd code review updates

* update FAQ - new qc recommendation

* Merged PR 21765: handle collinearity issues with fastCohorting

handle collinearity issues with fastCohorting:
1. Reduce to 2 PC's.
2. If this fails, then try successively smaller # of cohorts with the 2 pc's.

Related work items: #211163

* Bump version for dev to 1.2.3

* bugfix

rownames(sds) was creating an error in rna mode.

* Merged PR 21963: Update pipeline for dev branch.

Update pipeline for dev branch.

Related work items: #211130

* faqs update

* updates per LW code review

* vignette finessing

* r cmd check updates

* faq updates

* remove vestigial plots

---------

Co-authored-by: David Ross <dross@nanostring.com>
Co-authored-by: r2ds <r2ds@Siddharth-Bhatis-Macbook-Pro.local>
Co-authored-by: patrickjdanaher <patrickjdanaher@gmail.com>
Co-authored-by: Maddy Griswold <mgriswold@nanostring.com>
Co-authored-by: Augustine <augustine@procogia.com>
Co-authored-by: siddharth.bhatia <siddharth.bhatia@procogia.com>
Co-authored-by: Nikola <ndjokic@icefyresolutions.com>
Co-authored-by: Dave Ross <48140684+davidpross@users.noreply.github.com>
Co-authored-by: Patrick Danaher <pdanaher@nanostring.com>
Co-authored-by: dan11mcguire <dan11mcguire@gmail.com>
Co-authored-by: Maksim Gorelov <maksims.gorelovs@swdfactory.com>
Co-authored-by: David Ross <dave@davidpross.com>
Co-authored-by: Lidan Wu <lwu@nanostring.com>
Co-authored-by: Yongfang <ylu@nanostring.com>
Co-authored-by: lidanwu <lidanwu2016@gmail.com>
Co-authored-by: Sangsoon Woo <sawoo@nanostring.com>
Co-authored-by: Artyom Labin <artyom.labin@seattlebiosoftware.com>
Co-authored-by: Dan McGuire <dmcguire@nanostring.com>
@rvitancol rvitancol merged commit bad5181 into Nanostring-Biostats:main Aug 7, 2024
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