Merge pull request #70 from immunomind/dev

0.6.5 CRAN release

Author: vadimnazarov

.Rbuildignore

@@ -13,6 +13,7 @@
 ^.gitlab-ci.yml$
 ^CONTRIBUTION.md$
 ^_pkgdown.yml$
+^pkgdown$
 ^code-of-conduct.md$
 ^LICENSE$
 ^immunarch-citation.xml$

CONTRIBUTION.md

@@ -1,14 +1,19 @@
 # Contributing to immunarch
 
-This outlines how to propose a change to immunarch.
+This document outlines how to propose a change to immunarch.
 
-### Fixing typos
 
-Small typos or grammatical errors in documentation may be edited directly using
-the GitLab web IDE functionality / GitHub web interface, so long as the changes are made in the _source_ file.
+## How to contribute?
 
-*  YES: you edit a roxygen comment in a `.R` file below `R/`.
-*  NO: you edit an `.Rd` file below `man/`.
+There are three general ways to contribute to the package.
+
+1. Code contribution via pull requests. Helps us improve the codebase of the package, add new features or fix bugs and typos in the documentation.
+
+2. Bug reports and feature requests via GitHub issues. Helps us notice important issues and improvements to address.
+
+3. Helping others by answering tickets in GitHub issues. Greatly helps build the community and accelerates the immune repertoire research progress.
+
+## Code contribution via pull requests
 
 ### Prerequisites
 
@@ -20,23 +25,79 @@ that via GitHub, please note it in the issue.
 
 ### Pull request process
 
+*  Always start by forking the `dev` branch [from here](https://github.com/immunomind/immunarch/tree/dev) to make sure you have the latest pre-release version of `immunarch`. Name it accordingly to your contributions. `repClonality refactor` or `fix-issue-12` would work.
 *  We recommend that you create a Git branch for each pull request (PR).  
-*  Look at the CI (Continuous Integration) build status before and after making changes.
-The `README` should contain badges for any continuous integration services used
-by the package.  
-*  New code should follow our style guide that is the tidyverse [style guide](http://style.tidyverse.org)
-with a very minor addition of using `=` instead of `<-` in variable assignment.
-You can use the [styler](https://CRAN.R-project.org/package=styler) package to
+*  We follow the [following guidelines for commit naming](https://medium.com/@kevinkreuzer/the-way-to-fully-automated-releases-in-open-source-projects-44c015f38fd6).
+*  New code should follow our style guide that is the tidyverse [style guide](http://style.tidyverse.org) You can use the [styler](https://CRAN.R-project.org/package=styler) package to
 apply these styles, but please don't restyle code that has nothing to do with 
 your PR.  
 *  We use [roxygen2](https://cran.r-project.org/package=roxygen2) for documentation.  
 *  We use [testthat](https://cran.r-project.org/package=testthat). Contributions
-with test cases included are easier to accept.  
-*  For user-facing changes, add a bullet to the top of `NEWS.md` below the current
-development version header describing the changes made followed by your GitHub
-username, and links to relevant issue(s)/PR(s).
+with test cases included are easier to accept.
+*  Look at the CI (Continuous Integration) build status before and after making changes.
+The `README` should contain badges for any continuous integration services used
+by the package.
+
+### Fixing typos
+
+Small typos or grammatical errors in documentation may be edited directly using
+the GitLab web IDE functionality / GitHub web interface, so long as the changes are made in the _source_ file. Please make sure to create a Pull Request instead of commiting directly to the `master` branch.
+
+*  YES: you edit a roxygen comment in a `.R` file below `R/`.
+*  NO: you edit an `.Rd` file below `man/`.
+
+### Version naming
+
+We employ Major.Minor.Patch. E.g., 0.4.0.
+
+Hotfixes: Major.Minor.Patch → Major.Minor.(Patch + 1)
+
+Guidelines: [http://r-pkgs.had.co.nz/release.html](http://r-pkgs.had.co.nz/release.html)
+
+### Commit naming
+
+We follow the [following guidelines for commit naming](https://medium.com/@kevinkreuzer/the-way-to-fully-automated-releases-in-open-source-projects-44c015f38fd6).
+
+#### Commit types
+
+There are eight types of commits: `chore`, `docs`, `feat`, `fix`, `refactor`, `test`, `perf`, `style`. Most used are `feat` for implementation of a new feauture, `docs` for updating the documentation, `fix` for fixing a bug.
+
+Commit name examples: `feat(diversity): added the Chao1 method for diversity estimations`, `fix(clonality): fixed a bug in clonality computations #12`, where `#12` is a link to the issue on the immunarch issue page.
+
+#### Commit scopes
+
+- Changes in analysis- and visualisation-specific functions: `diversity`, `overlap`, `pub-rep`, `clonality`, `gene-usage`, `explore`, `kmers`, `spectratype`, `dynamics`, `tools`, `single-cell`.
+
+- General changes in visualisation functions (e.g., replace one package with another, or change a non-specific visualisation function such as `vis_bar`): `vis`
+
+- Changes in parsing: `io`
+
+- Changes in databases support: `db`
+
+- Changes in additional functions such as general statistics functions: `utility`
+
+- Changes in data: `data`
+
+- Changes in NAMESPACE, DESCRIPTION, citations, ISSUE_TEMPLATE.md, etc., without README: `upkeep`
+
+- Changes in README and vignettes: `vignette`
+
+- Changes in Continuous Integration: `ci`
+
+- Changes in Shiny applications: `shiny`
+
+
+## Bug reports and feature requests
+
+### How to create an Issue
+
+We have a rich list of templates for Issues [here](https://github.com/immunomind/immunarch/tree/master/.github/ISSUE_TEMPLATE). Go to the [GitHub Issues page](https://github.com/immunomind/immunarch/issues) for `immunarch` and create a new Issue ticket from there.
+
+## Helping others by answering tickets
+
+Got to [GitHub Issues page](https://github.com/immunomind/immunarch/issues) and find Issues that you are familiar with to answer.
 
-### Code of Conduct
+## Code of Conduct
 
 Please note that this project is released with a [Contributor Code of
 Conduct](code-of-conduct.md). By participating in this project you agree to

DESCRIPTION

@@ -1,18 +1,18 @@
 Package: immunarch
 Type: Package
 Title: Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires
-Version: 0.6.4
+Version: 0.6.5
 Authors@R: c(
     person("Vadim I.", "Nazarov", , "[email protected]", c("aut", "cre")),
     person("Vasily O.", "Tsvetkov", , role = "aut"),
     person("Eugene", "Rumynskiy", , role = "aut"),
-    person("Anna", "Lorenc", , role = "aut"),
-    person("Daniel J.", "Moore", , role = "aut"),
-    person("Victor", "Greiff", , role = "aut"),
+    person("Anna", "Lorenc", , role = "ctb"),
+    person("Daniel J.", "Moore", , role = "ctb"),
+    person("Victor", "Greiff", , role = "ctb"),
     person("ImmunoMind", role = c("cph", "fnd"))
     )
 Contact: [email protected]
-Description: A comprehensive framework for bioinformatics analysis of bulk and single-cell 
+Description: A comprehensive framework for bioinformatics exploratory analysis of bulk and single-cell 
     T-cell receptor and antibody repertoires. It provides seamless data loading, analysis and 
     visualisation for AIRR (Adaptive Immune Receptor Repertoire) data, both bulk immunosequencing (RepSeq)
     and single-cell sequencing (scRNAseq). It implements most of the widely used AIRR analysis methods, 
@@ -24,22 +24,21 @@ License: AGPL-3
 URL: https://immunarch.com/, https://github.com/immunomind/immunarch
 BugReports: https://github.com/immunomind/immunarch/issues
 Imports:
+    factoextra (>= 1.0.4),
+    fpc,
+    UpSetR (>= 1.4.0),
     pheatmap (>= 1.0.12),
     ggrepel (>= 0.8.0),
     reshape2 (>= 1.4.2),
-    factoextra (>= 1.0.4),
-    fpc,
     circlize,
     MASS (>= 7.3),
     Rtsne (>= 0.15),
     readr (>= 1.3.1),
     readxl (>= 1.3.1),
     shiny (>= 1.4.0),
     shinythemes,
-    treemap,
     airr,
     ggseqlogo,
-    UpSetR (>= 1.4.0),
     stringr (>= 1.4.0),
     ggalluvial (>= 0.10.0),
     Rcpp (>= 1.0),
@@ -57,7 +56,7 @@ Depends:
     dplyr (>= 0.8.0),
     dtplyr (>= 1.0.0),
     data.table (>= 1.12.6),
-    gridExtra (>= 2.2.1)
+    patchwork
 LinkingTo: Rcpp
 Suggests:
     knitr (>= 1.8),

NAMESPACE

@@ -43,7 +43,6 @@ export(cross_entropy)
 export(dbAnnotate)
 export(dbLoad)
 export(entropy)
-export(filter_barcodes)
 export(fixVis)
 export(geneUsage)
 export(geneUsageAnalysis)
@@ -79,6 +78,8 @@ export(repOverlap)
 export(repOverlapAnalysis)
 export(repSample)
 export(repSave)
+export(select_barcodes)
+export(select_clusters)
 export(spectratype)
 export(split_to_kmers)
 export(top)
@@ -93,7 +94,6 @@ export(vis_hist)
 export(vis_immunr_kmer_profile_main)
 export(vis_seqlogo)
 export(vis_textlogo)
-export(vis_treemap)
 import(ggplot2)
 importFrom(Rcpp,cppFunction)
 importFrom(Rcpp,sourceCpp)
@@ -105,6 +105,7 @@ importFrom(data.table,as.data.table)
 importFrom(data.table,data.table)
 importFrom(data.table,melt.data.table)
 importFrom(data.table,set)
+importFrom(data.table,setDF)
 importFrom(data.table,setDT)
 importFrom(data.table,setcolorder)
 importFrom(data.table,setnames)
@@ -115,6 +116,7 @@ importFrom(dplyr,contains)
 importFrom(dplyr,desc)
 importFrom(dplyr,distinct)
 importFrom(dplyr,filter)
+importFrom(dplyr,first)
 importFrom(dplyr,full_join)
 importFrom(dplyr,group_by)
 importFrom(dplyr,group_by_at)
@@ -149,10 +151,10 @@ importFrom(grDevices,colorRampPalette)
 importFrom(graphics,plot)
 importFrom(grid,gpar)
 importFrom(grid,rectGrob)
-importFrom(gridExtra,arrangeGrob)
-importFrom(gridExtra,grid.arrange)
 importFrom(magrittr,"%>%")
 importFrom(methods,as)
+importFrom(patchwork,plot_annotation)
+importFrom(patchwork,wrap_plots)
 importFrom(pheatmap,pheatmap)
 importFrom(plyr,mapvalues)
 importFrom(readr,col_character)
@@ -213,7 +215,6 @@ importFrom(stringr,str_replace_all)
 importFrom(stringr,str_sort)
 importFrom(stringr,str_split)
 importFrom(tibble,tibble)
-importFrom(treemap,treemap)
 importFrom(utils,packageVersion)
 importFrom(utils,read.table)
 importFrom(utils,setTxtProgressBar)

R/search.R R/annotation.R

@@ -60,3 +60,38 @@ AA_TABLE_REVERSED <- sapply(unique(AA_TABLE), function(aa) {
   names(AA_TABLE)[AA_TABLE == aa]
 })
 AA_TABLE_REVERSED <- AA_TABLE_REVERSED[order(names(AA_TABLE_REVERSED))]
+
+
+#' Single chain immune repertoire dataset
+#'
+#' @concept data
+#'
+#' @description A dataset with single chain TCR data for testing and examplatory purposes.
+#'
+#' @format A list of two elements. First element ("data") is a list with data frames with clonotype tables.
+#' Second element ("meta") is a metadata table.
+#' \describe{
+#'   \item{data}{List of immune repertoire data frames.}
+#'   \item{meta}{Metadata}
+#'   ...
+#' }
+"immdata"
+
+
+#' Paired chain immune repertoire dataset
+#'
+#' @concept data
+#'
+#' @description A dataset with paired chain IG data for testing and examplatory purposes.
+#'
+#' @format A list of four elements.
+#' "data" is a list with data frames with clonotype tables.
+#' "meta" is a metadata table.
+#' "bc_patients" is a list of barcodes corresponding to specific patients.
+#' "bc_clusters" is a list of barcodes corresponding to specific cell clusters.
+#' \describe{
+#'   \item{data}{List of immune repertoire data frames.}
+#'   \item{meta}{Metadata}
+#'   ...
+#' }
+"scdata"

R/data.R

@@ -169,7 +169,7 @@ repDiversity <- function(.data, .method = "chao1", .col = "aa", .max.q = 6, .min
       .extrapolation = .extrapolation, .perc = .perc,
       .verbose = .verbose, .do.norm = .do.norm, .laplace = .laplace
     )
-    new_class <- tail(class(res[[1]]), 1)
+    new_class <- head(class(res[[1]]), 1)
     res <- do.call(rbind, res)
     if (.method == "hill") {
       res <- reshape2::melt(res)

R/data_docs.R

@@ -73,4 +73,9 @@ IMMCOL$type <- c(
   "integer", "integer", "integer", "character"
 )
 
+# Additional information
+IMMCOL_ADD <- new.env()
+# separator for paired chain data
+IMMCOL_ADD$scsep <- ";"
+
 IMMUNR_ERROR_NOT_IMPL <- "ERROR: not implemented yet. Please contact us via [email protected] if you need it in your research."