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iSEE extension for panels related to pathway analysis

Home Page: https://isee.github.io/iSEEpathways/

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iseepathways's Introduction

iSEEpathways

The goal of iSEEpathways is to provide panels to facilitate the interactive visualisation of pathway analysis results in iSEE applications.

Installation instructions

Get the latest stable R release from CRAN. Then install iSEEpathways from Bioconductor using the following code:

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}

BiocManager::install("iSEEpathways")

And the development version from GitHub with:

BiocManager::install("iSEE/iSEEpathways")

Example

This is a basic example which shows you how to load the package:

library("iSEEpathways")
library("fgsea")
library("iSEE")

# Example data ----

simulated_data <- simulateExampleData()

pathways_list <- simulated_data[["pathwaysList"]]
features_stat <- simulated_data[["featuresStat"]]
se <- simulated_data[["summarizedexperiment"]]

# fgsea ----

set.seed(42)
fgseaRes <- fgsea(pathways = pathways_list, 
                  stats    = features_stat,
                  minSize  = 15,
                  maxSize  = 500)
fgseaRes <- fgseaRes[order(pval), ]
head(fgseaRes)
#>         pathway         pval      padj   log2err         ES       NES size
#> 1: pathway_1350 0.0004373110 0.5905978 0.4984931  0.2858201  1.503211  299
#> 2: pathway_4907 0.0005947840 0.5905978 0.4772708  0.3250965  1.599638  178
#> 3: pathway_3983 0.0007509197 0.5905978 0.4772708  0.2558001  1.398213  451
#> 4:  pathway_398 0.0008716489 0.5905978 0.4772708  0.2799932  1.477849  305
#> 5: pathway_3359 0.0009809867 0.5905978 0.4550599 -0.3724340 -1.674911  106
#> 6: pathway_1289 0.0009835850 0.5905978 0.4550599  0.3479133  1.638048  124
#>                                                                            leadingEdge
#> 1:  feature_6060,feature_9203,feature_1852,feature_1883,feature_12903,feature_2143,...
#> 2: feature_9265,feature_6286,feature_14879,feature_9600,feature_5335,feature_12205,...
#> 3:  feature_495,feature_12466,feature_13128,feature_3069,feature_5278,feature_4248,...
#> 4:    feature_6478,feature_2164,feature_922,feature_4298,feature_6585,feature_1633,...
#> 5:    feature_3879,feature_2726,feature_6870,feature_6787,feature_9700,feature_693,...
#> 6: feature_6376,feature_12953,feature_8391,feature_3147,feature_7330,feature_11551,...

# iSEE ---

se <- embedPathwaysResults(fgseaRes, se, name = "fgsea", class = "fgsea", pathwayType = "simulated",
                           pathwaysList = pathways_list, featuresStats = features_stat)

app <- iSEE(se, initial = list(
  PathwaysTable(ResultName="fgsea", Selected = "pathway_3363 ", PanelWidth = 6L),
  FgseaEnrichmentPlot(ResultName="fgsea", PathwayId = "pathway_3363", PanelWidth = 6L)
))

if (interactive()) {
  shiny::runApp(app)
}

Citation

Below is the citation output from using citation('iSEEpathways') in R. Please run this yourself to check for any updates on how to cite iSEEpathways.

print(citation('iSEEpathways'), bibtex = TRUE)
#> To cite package 'iSEEpathways' in publications use:
#> 
#>   Rue-Albrecht K (2023). _iSEEpathways: iSEE extension for panels
#>   related to pathway analysis_. R package version 0.99.0,
#>   <https://github.com/iSEE/iSEEpathways>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Manual{,
#>     title = {iSEEpathways: iSEE extension for panels related to pathway analysis},
#>     author = {Kevin Rue-Albrecht},
#>     year = {2023},
#>     note = {R package version 0.99.0},
#>     url = {https://github.com/iSEE/iSEEpathways},
#>   }

Please note that the iSEEpathways was only made possible thanks to many other R and bioinformatics software authors, which are cited either in the vignettes and/or the paper(s) describing this package.

Code of Conduct

Please note that the iSEEpathways project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

Development tools

Continuous code testing is possible thanks to GitHub actions through usethis, remotes, and rcmdcheck customized to use Bioconductor’s docker containers and BiocCheck.
Code coverage assessment is possible thanks to codecov and covr.
The documentation website is automatically updated thanks to pkgdown.
The code is styled automatically thanks to styler.
The documentation is formatted thanks to devtools and roxygen2.

For more details, check the dev directory.

This package was developed using biocthis.

Code of Conduct

Please note that the iSEEpathways project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

iseepathways's People

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iseepathways's Issues

[FEATURE] Create getter function to complement embedPathwaysResults()

See TODO note in https://isee.github.io/iSEEpathways/reference/iSEEfgseaResults-class.html

Users should not be taught to retrieve those results manually from the metadata slot, or even where in there the results are stored.

Instead, write an getter function similar to iSEEde::contrastResults(), see https://isee.github.io/iSEEde/reference/contrastResults.html

[BUG] rcmdcheck warnings and notes

Fix the various warnings and notes below.

❯ checking whether package ‘iSEEpathways’ can be installed ... WARNING
  See below...

❯ checking for missing documentation entries ... WARNING
  Undocumented code objects:
    ‘featuresStats’ ‘pathways’
  Undocumented S4 methods:
    generic '.defineInterface' and siglist 'FgseaEnrichmentPlot'
    generic '.defineInterface' and siglist 'PathwaysTable'
    generic '.defineOutput' and siglist 'FgseaEnrichmentPlot'
    generic '.generateOutput' and siglist 'FgseaEnrichmentPlot'
    generic '.renderOutput' and siglist 'FgseaEnrichmentPlot'
    generic 'featuresStats' and siglist 'iSEEfgseaResults'
    generic 'pathways' and siglist 'iSEEfgseaResults'
  All user-level objects in a package (including S4 classes and methods)
  should have documentation entries.
  See chapter ‘Writing R documentation files’ in the ‘Writing R
  Extensions’ manual.

❯ checking for code/documentation mismatches ... WARNING
  Warning in formals(fun) : argument is not a function
  Warning in formals(fun) : argument is not a function

❯ checking whether the namespace can be loaded with stated dependencies ... NOTE
  Warning: no function found corresponding to methods exports from ‘iSEEpathways’ for: ‘.defineInterface’
  
  A namespace must be able to be loaded with just the base namespace
  loaded: otherwise if the namespace gets loaded by a saved object, the
  session will be unable to start.
  
  Probably some imports need to be declared in the NAMESPACE file.

❯ checking dependencies in R code ... NOTE
  Namespace in Imports field not imported from: ‘BiocGenerics’
    All declared Imports should be used.
  ':::' call which should be '::': ‘iSEE:::.organizationHeight’
    See the note in ?`:::` about the use of this operator.

❯ checking R code for possible problems ... NOTE
  Warning in formals(fun) : argument is not a function
  Warning in body(fun) : argument is not a function
  Warning in formals(fun) : argument is not a function
  Warning in body(fun) : argument is not a function
  .createObservers,FgseaEnrichmentPlot: no visible global function
    definition for ‘slot<-’
  .createObservers,FgseaEnrichmentPlot: no visible global function
    definition for ‘updateSelectizeInput’
  .defineDataInterface,FgseaEnrichmentPlot: no visible global function
    definition for ‘.selectizeInput.iSEE’
  .defineOutput,FgseaEnrichmentPlot: no visible global function
    definition for ‘.getPanelColor’
  .defineOutput,FgseaEnrichmentPlot: no visible global function
    definition for ‘brushOpts’
  .defineOutput,FgseaEnrichmentPlot: no visible global function
    definition for ‘plotOutput’
  Undefined global functions or variables:
    .getPanelColor .selectizeInput.iSEE brushOpts plotOutput slot<-
    updateSelectizeInput
  Consider adding
    importFrom("methods", "slot<-")
  to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
  contains 'methods').

0 errors ✔ | 3 warnings ✖ | 3 notes ✖

[BUG] Fix GO mapping function in vignette integration

On branch fgsea-plot, update vignette to define a GO mapping function that uses the gene_id to perform accurate pathway analysis (do not use the hybrid uniquified feature name). The function should still return the uniquified feature name (because it is in rownames) but mapping to unique gene identifiers first is necessary to make sure that uniquified feature names are not missed during the mapping

Please briefly describe your problem and what output you expect. If you have a question, please don't use this form. Instead, ask on https://support.bioconductor.org/ using the appropriate tag(s) including one for this package.

Context

Provide some context for your bug report or feature request. This could be the:

link to raw code, example: https://github.com/lcolladotor/osca_LIIGH_UNAM_2020/blob/master/00-template.Rmd#L24-L28
link to a commit, example: lcolladotor/osca_LIIGH_UNAM_2020@6aa30b2
link to a line of code inside a commit, example: lcolladotor/osca_LIIGH_UNAM_2020@6aa30b2#diff-e265269fe4f17929940e81341b92b116R17
link to code from an R package, example: https://github.com/LieberInstitute/spatialLIBD/blob/master/R/run_app.R#L51-L55

Code

Include the code you ran and comments

## prompt an error
stop('hola')

## check the error trace
traceback()

Small reproducible example

If you copy the lines of code that lead to your error, you can then run reprex::reprex() which will create a small website with code you can then easily copy-paste here in a way that will be easy to work with later on.

## prompt an error
stop('hola')
#> Error in eval(expr, envir, enclos): hola

## check the error trace
traceback()
#> No traceback available

R session information

Remember to include your full R session information.

options(width = 120)
sessioninfo::session_info()

The output of sessioninfo::session_info() includes relevant GitHub installation information and other details that are missed by sessionInfo().

[BUG] implement remaining brush events

As this is a direct Panel derivative, it needs reimplementing of the same brush events as DotPlot derivatives.

Context

Provide some context for your bug report or feature request. This could be the:

link to raw code, example: https://github.com/lcolladotor/osca_LIIGH_UNAM_2020/blob/master/00-template.Rmd#L24-L28
link to a commit, example: lcolladotor/osca_LIIGH_UNAM_2020@6aa30b2
link to a line of code inside a commit, example: lcolladotor/osca_LIIGH_UNAM_2020@6aa30b2#diff-e265269fe4f17929940e81341b92b116R17
link to code from an R package, example: https://github.com/LieberInstitute/spatialLIBD/blob/master/R/run_app.R#L51-L55

Code

Include the code you ran and comments

## prompt an error
stop('hola')

## check the error trace
traceback()

Small reproducible example

## prompt an error
stop('hola')
#> Error in eval(expr, envir, enclos): hola

## check the error trace
traceback()
#> No traceback available

R session information

Remember to include your full R session information.

options(width = 120)
sessioninfo::session_info()

The output of sessioninfo::session_info() includes relevant GitHub installation information and other details that are missed by sessionInfo().

[FEATURE] Implement unit tests

Now that the package implementation has matured, add unit tests

isee / iseepathways Goto Github PK

iseepathways's Introduction

iSEEpathways

Installation instructions

Example

Citation

Code of Conduct

Development tools

Code of Conduct

iseepathways's People

Contributors

Stargazers

Watchers

iseepathways's Issues

Context

Code

Small reproducible example

R session information

Context

Code

Small reproducible example

R session information

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