Merge pull request #185 from immunomind/dev

Release 0.6.7

Author: Alexander230

.Rbuildignore

@@ -9,6 +9,8 @@
 ^fixVis$
 ^experiment data$
 ^docker$
+^Dockerfile$
+^.dockerignore$
 ^private$
 ^.gitlab-ci.yml$
 ^CONTRIBUTION.md$
@@ -18,3 +20,5 @@
 ^LICENSE$
 ^immunarch-citation.xml$
 ^.github$
+^.RDataFiles$
+^.idea$

.dockerignore

@@ -0,0 +1,4 @@
+.git*
+.RDataFiles
+.idea
+*.Rproj

.github/workflows/dockerhub.yml

@@ -0,0 +1,45 @@
+name: DockerHub Image
+
+on:
+  push:
+    branches:
+      - master
+      - dev
+    tags:
+      - "*"
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Get Image Tag
+        shell: bash
+        run: echo "##[set-output name=tag;]$([ "${GITHUB_REF}" == "refs/heads/master" ] && echo base || echo ${GITHUB_REF##*/})"
+        id: get_tag
+
+      - name: Check Out Repo
+        uses: actions/checkout@v2
+
+      - name: Login to Docker Hub
+        uses: docker/login-action@v1
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Set up Docker Buildx
+        id: buildx
+        uses: docker/setup-buildx-action@v1
+
+      - name: Build and push
+        id: docker_build
+        uses: docker/build-push-action@v2
+        with:
+          context: ./
+          file: ./Dockerfile
+          builder: ${{ steps.buildx.outputs.name }}
+          push: true
+          tags: ${{ secrets.DOCKERHUB_USERNAME }}/immunarch-docker:${{ steps.get_tag.outputs.tag }}
+
+      - name: Image digest
+        run: echo ${{ steps.docker_build.outputs.digest }}

.gitignore

@@ -2,9 +2,10 @@
 .Rhistory
 .RData
 .Ruserdata
+.RDataFiles/*
 src/*.o
 src/*.so
 src/*.dll
 *.DS_Store
 docs/*
-
+.idea/*

DESCRIPTION

@@ -1,23 +1,25 @@
 Package: immunarch
 Type: Package
 Title: Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires
-Version: 0.6.5
+Version: 0.6.7
 Authors@R: c(
-    person("Vadim I.", "Nazarov", , "[email protected]", c("aut", "cre")),
+    person("Vadim I.", "Nazarov", , "[email protected]", c("aut", "cre")),
     person("Vasily O.", "Tsvetkov", , role = "aut"),
     person("Eugene", "Rumynskiy", , role = "aut"),
+    person("Aleksandr A.", "Popov", , role = "aut"),
+    person("Ivan", "Balashov", , 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 exploratory analysis of bulk and single-cell 
-    T-cell receptor and antibody repertoires. It provides seamless data loading, analysis and 
+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, 
-    such as: clonality analysis, estimation of repertoire similarities in distribution of clonotypes 
-    and gene segments, repertoire diversity analysis, annotation of clonotypes using external immune receptor 
+    and single-cell sequencing (scRNAseq). It implements most of the widely used AIRR analysis methods,
+    such as: clonality analysis, estimation of repertoire similarities in distribution of clonotypes
+    and gene segments, repertoire diversity analysis, annotation of clonotypes using external immune receptor
     databases and clonotype tracking in vaccination and cancer studies. A successor to our
     previously published 'tcR' immunoinformatics package (Nazarov 2015) <doi:10.1186/s12859-015-0613-1>.
 License: AGPL-3
@@ -33,25 +35,28 @@ Imports:
     circlize,
     MASS (>= 7.3),
     Rtsne (>= 0.15),
-    readr (>= 1.3.1),
     readxl (>= 1.3.1),
     shiny (>= 1.4.0),
     shinythemes,
     airr,
     ggseqlogo,
-    stringr (>= 1.4.0),
     ggalluvial (>= 0.10.0),
     Rcpp (>= 1.0),
     magrittr,
-    tibble (>= 2.0),
     methods,
     scales,
     ggpubr (>= 0.2),
     rlang (>= 0.4),
     plyr,
-    dbplyr (>= 1.4.0)
+    dbplyr (>= 1.4.0),
+    jsonlite,
+    readr,
+    stringr,
+    tibble,
+    tidyselect,
+    purrr
 Depends:
-    R (>= 3.5.0),
+    R (>= 4.0.0),
     ggplot2 (>= 3.1.0),
     dplyr (>= 0.8.0),
     dtplyr (>= 1.0.0),
@@ -63,8 +68,9 @@ Suggests:
     roxygen2 (>= 3.0.0),
     testthat (>= 2.1.0),
     pkgdown (>= 0.1.0),
-    assertthat
+    assertthat,
+    rmarkdown
 VignetteBuilder: knitr
 Encoding: UTF-8
-RoxygenNote: 7.1.0
+RoxygenNote: 7.1.2
 LazyData: true

Dockerfile

@@ -0,0 +1,19 @@
+FROM r-base
+
+# Install apt dependencies
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    build-essential file libcurl4-openssl-dev libcairo2-dev libxml2-dev libssl-dev \
+    libharfbuzz-dev libfribidi-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev \
+    && rm -rf /var/lib/apt/lists/*
+
+# Install R dependencies
+RUN R -e "install.packages(c('remotes', 'svglite'))"
+
+# Copy source files to the image
+COPY . /immunarch-src/
+
+# Install Immunarch from source
+RUN R -e "remotes::install_local('/immunarch-src', dependencies=TRUE)"
+
+# Delete Immunarch source from the image
+RUN rm -rf /immunarch-src

NAMESPACE

@@ -43,6 +43,7 @@ export(cross_entropy)
 export(dbAnnotate)
 export(dbLoad)
 export(entropy)
+export(exclude)
 export(fixVis)
 export(geneUsage)
 export(geneUsageAnalysis)
@@ -56,10 +57,14 @@ export(immunr_mds)
 export(immunr_pca)
 export(immunr_tsne)
 export(inc_overlap)
+export(include)
 export(inframes)
+export(interval)
 export(js_div)
 export(kl_div)
 export(kmer_profile)
+export(lessthan)
+export(morethan)
 export(noncoding)
 export(outofframes)
 export(pubRep)
@@ -73,6 +78,7 @@ export(public_matrix)
 export(repClonality)
 export(repDiversity)
 export(repExplore)
+export(repFilter)
 export(repLoad)
 export(repOverlap)
 export(repOverlapAnalysis)
@@ -127,7 +133,6 @@ importFrom(dplyr,rename)
 importFrom(dplyr,select)
 importFrom(dplyr,summarise)
 importFrom(dplyr,tally)
-importFrom(dplyr,tbl_df)
 importFrom(dplyr,top_n)
 importFrom(dplyr,ungroup)
 importFrom(dtplyr,lazy_dt)
@@ -151,12 +156,15 @@ importFrom(grDevices,colorRampPalette)
 importFrom(graphics,plot)
 importFrom(grid,gpar)
 importFrom(grid,rectGrob)
+importFrom(jsonlite,read_json)
+importFrom(magrittr,"%<>%")
 importFrom(magrittr,"%>%")
 importFrom(methods,as)
 importFrom(patchwork,plot_annotation)
 importFrom(patchwork,wrap_plots)
 importFrom(pheatmap,pheatmap)
 importFrom(plyr,mapvalues)
+importFrom(purrr,map)
 importFrom(readr,col_character)
 importFrom(readr,col_double)
 importFrom(readr,col_guess)
@@ -214,7 +222,9 @@ importFrom(stringr,str_order)
 importFrom(stringr,str_replace_all)
 importFrom(stringr,str_sort)
 importFrom(stringr,str_split)
+importFrom(stringr,str_trim)
 importFrom(tibble,tibble)
+importFrom(tidyselect,starts_with)
 importFrom(utils,packageVersion)
 importFrom(utils,read.table)
 importFrom(utils,setTxtProgressBar)

R/RcppExports.R

@@ -2,10 +2,9 @@
 # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 
 fill_vec <- function(read_vec, read_indices) {
-    .Call(`_immunarch_fill_vec`, read_vec, read_indices)
+  .Call(`_immunarch_fill_vec`, read_vec, read_indices)
 }
 
 fill_reads <- function(new_reads, new_counts) {
-    .Call(`_immunarch_fill_reads`, new_reads, new_counts)
+  .Call(`_immunarch_fill_reads`, new_reads, new_counts)
 }
-

R/diversity.R

@@ -184,8 +184,7 @@ repDiversity <- function(.data, .method = "chao1", .col = "aa", .max.q = 6, .min
 
     res <- add_class(res, new_class)
     return(res)
-  }
-  else if (.method == "raref") {
+  } else if (.method == "raref") {
     if (!has_class(.data, "list")) {
       .data <- list(Sample = .data)
     }
@@ -203,8 +202,7 @@ repDiversity <- function(.data, .method = "chao1", .col = "aa", .max.q = 6, .min
         summarise(Div.count = sum(!!sym(IMMCOL$count))) %>%
         pull(Div.count)
     })
-  }
-  else {
+  } else {
     .col <- process_col_argument(.col)
 
     if (has_class(.data, "data.table")) {
@@ -406,7 +404,7 @@ rarefaction <- function(.data, .step = NA, .quantile = c(.025, .975),
         lo <- Sind
         hi <- Sind
       }
-      res <- c(sz, Sind, lo, hi)
+      res <- c(sz, lo, Sind, hi)
       names(res) <- c("Size", paste0("Q", .quantile[1]), "Mean", paste0("Q", .quantile[2]))
       if (.verbose) add_pb(pb)
       res

R/dynamics.R

@@ -97,9 +97,7 @@
 #' vis(tc, .order = sample_order)
 #' @export trackClonotypes
 trackClonotypes <- function(.data, .which = list(1, 15), .col = "aa", .norm = TRUE) {
-  if (!has_class(.data, "list")) {
-    stop("Error: please pass a list with immune repertoires to track clonotypes.")
-  }
+  .validate_repertoires_data(.data)
   if (length(.data) < 2) {
     stop("Error: please pass a list with 2 or more immune repertoires to track clonotypes.")
   }
@@ -147,8 +145,8 @@ trackClonotypes <- function(.data, .which = list(1, 15), .col = "aa", .norm = TR
   result_df <- NULL
   for (i_df in 1:length(.data)) {
     temp_df <- .data[[i_df]] %>%
-      select(.col, Count = count_col)
-    setDT(temp_df)
+      select(.col, Count = count_col) %>%
+      as.data.table()
 
     if (.norm) {
       temp_df$Count <- temp_df$Count / sum(temp_df$Count)

R/explore.R

@@ -101,7 +101,11 @@ repExplore <- function(.data, .method = c("volume", "count", "len", "clones"), .
     res <- do.call(rbind, res)
     res <- add_class(res, "immunr_exp_count")
   } else if (.method[1] %in% c("len", "lens", "length")) {
-    seq_col <- switch(.col[1], nt = IMMCOL$cdr3nt, aa = IMMCOL$cdr3aa, stop("Unknown sequence column: ", .col, ". Please provide either 'nt' or 'aa'"))
+    seq_col <- switch(.col[1],
+      nt = IMMCOL$cdr3nt,
+      aa = IMMCOL$cdr3aa,
+      stop("Unknown sequence column: ", .col, ". Please provide either 'nt' or 'aa'")
+    )
     res <- lapply(.data, function(df) {
       if (has_class(df, "data.table")) {
         df <- df %>% lazy_dt()