Merge pull request #233 from immunomind/dev

Author: Aleksandr Popov

.gitignore

@@ -9,3 +9,4 @@ src/*.dll
 *.DS_Store
 docs/*
 .idea/*
+vignettes/web_only/*.html

DESCRIPTION

@@ -1,13 +1,14 @@
 Package: immunarch
 Type: Package
 Title: Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires
-Version: 0.6.7
+Version: 0.6.8
 Authors@R: c(
     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("Maria", "Volobueva", , role = "aut"),
     person("Anna", "Lorenc", , role = "ctb"),
     person("Daniel J.", "Moore", , role = "ctb"),
     person("Victor", "Greiff", , role = "ctb"),
@@ -48,13 +49,23 @@ Imports:
     ggpubr (>= 0.2),
     rlang (>= 0.4),
     plyr,
-    dbplyr (>= 1.4.0),
+    purrr,
+    stringdist,
     jsonlite,
     readr,
     stringr,
     tibble,
     tidyselect,
-    purrr
+    tidyr,
+    igraph,
+    ape,
+    doParallel,
+    rlist,
+    utils,
+    glue,
+    phangorn,
+    uuid,
+    stringi
 Depends:
     R (>= 4.0.0),
     ggplot2 (>= 3.1.0),
@@ -74,3 +85,4 @@ VignetteBuilder: knitr
 Encoding: UTF-8
 RoxygenNote: 7.1.2
 LazyData: true
+LazyDataCompression: xz

Dockerfile

@@ -4,6 +4,7 @@ FROM r-base
 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 \
+    libnlopt-dev muscle phylip \
     && rm -rf /var/lib/apt/lists/*
 
 # Install R dependencies
@@ -17,3 +18,6 @@ RUN R -e "remotes::install_local('/immunarch-src', dependencies=TRUE)"
 
 # Delete Immunarch source from the image
 RUN rm -rf /immunarch-src
+
+# Check the image for Immunarch existence; fail if Immunarch not found
+RUN R -e 'library("immunarch")'

NAMESPACE

@@ -75,17 +75,22 @@ export(publicRepertoire)
 export(publicRepertoireApply)
 export(publicRepertoireFilter)
 export(public_matrix)
+export(repAlignLineage)
+export(repClonalFamily)
 export(repClonality)
 export(repDiversity)
 export(repExplore)
 export(repFilter)
+export(repGermline)
 export(repLoad)
 export(repOverlap)
 export(repOverlapAnalysis)
 export(repSample)
 export(repSave)
 export(select_barcodes)
 export(select_clusters)
+export(seqCluster)
+export(seqDist)
 export(spectratype)
 export(split_to_kmers)
 export(top)
@@ -105,32 +110,43 @@ importFrom(Rcpp,cppFunction)
 importFrom(Rcpp,sourceCpp)
 importFrom(UpSetR,fromExpression)
 importFrom(UpSetR,upset)
+importFrom(ape,as.DNAbin)
+importFrom(ape,muscle)
+importFrom(ape,read.tree)
 importFrom(circlize,chordDiagram)
 importFrom(data.table,":=")
 importFrom(data.table,as.data.table)
 importFrom(data.table,data.table)
+importFrom(data.table,fread)
 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)
+importFrom(doParallel,registerDoParallel)
 importFrom(dplyr,arrange)
 importFrom(dplyr,as_tibble)
 importFrom(dplyr,collect)
 importFrom(dplyr,contains)
+importFrom(dplyr,cur_group_id)
 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)
+importFrom(dplyr,group_keys)
+importFrom(dplyr,group_map)
+importFrom(dplyr,left_join)
 importFrom(dplyr,mutate)
 importFrom(dplyr,n)
 importFrom(dplyr,pull)
 importFrom(dplyr,rename)
+importFrom(dplyr,rowwise)
 importFrom(dplyr,select)
+importFrom(dplyr,select_if)
 importFrom(dplyr,summarise)
 importFrom(dplyr,tally)
 importFrom(dplyr,top_n)
@@ -152,19 +168,38 @@ importFrom(ggpubr,stat_compare_means)
 importFrom(ggpubr,theme_pubr)
 importFrom(ggseqlogo,geom_logo)
 importFrom(ggseqlogo,theme_logo)
+importFrom(glue,glue)
 importFrom(grDevices,colorRampPalette)
 importFrom(graphics,plot)
 importFrom(grid,gpar)
 importFrom(grid,rectGrob)
+importFrom(igraph,clusters)
+importFrom(igraph,graph_from_data_frame)
 importFrom(jsonlite,read_json)
 importFrom(magrittr,"%<>%")
 importFrom(magrittr,"%>%")
+importFrom(magrittr,extract2)
+importFrom(magrittr,set_attr)
 importFrom(methods,as)
+importFrom(parallel,detectCores)
+importFrom(parallel,mclapply)
 importFrom(patchwork,plot_annotation)
 importFrom(patchwork,wrap_plots)
+importFrom(phangorn,write.phyDat)
 importFrom(pheatmap,pheatmap)
+importFrom(plyr,.)
+importFrom(plyr,dlply)
 importFrom(plyr,mapvalues)
+importFrom(purrr,imap)
 importFrom(purrr,map)
+importFrom(purrr,map2)
+importFrom(purrr,map2_chr)
+importFrom(purrr,map2_lgl)
+importFrom(purrr,map_chr)
+importFrom(purrr,map_df)
+importFrom(purrr,map_dfr)
+importFrom(purrr,map_lgl)
+importFrom(purrr,pmap)
 importFrom(readr,col_character)
 importFrom(readr,col_double)
 importFrom(readr,col_guess)
@@ -178,6 +213,7 @@ importFrom(readr,write_lines)
 importFrom(readxl,read_xlsx)
 importFrom(reshape2,melt)
 importFrom(rlang,sym)
+importFrom(rlist,list.remove)
 importFrom(scales,percent)
 importFrom(shiny,actionButton)
 importFrom(shiny,br)
@@ -216,18 +252,32 @@ importFrom(stats,na.omit)
 importFrom(stats,prcomp)
 importFrom(stats,qnorm)
 importFrom(stats,rmultinom)
+importFrom(stringdist,stringdistmatrix)
+importFrom(stringi,stri_replace_all_fixed)
+importFrom(stringr,boundary)
+importFrom(stringr,fixed)
 importFrom(stringr,str_count)
 importFrom(stringr,str_detect)
+importFrom(stringr,str_extract_all)
+importFrom(stringr,str_length)
+importFrom(stringr,str_match)
 importFrom(stringr,str_order)
+importFrom(stringr,str_replace)
 importFrom(stringr,str_replace_all)
 importFrom(stringr,str_sort)
 importFrom(stringr,str_split)
+importFrom(stringr,str_sub)
 importFrom(stringr,str_trim)
+importFrom(tibble,rownames_to_column)
 importFrom(tibble,tibble)
+importFrom(tidyr,unite)
 importFrom(tidyselect,starts_with)
+importFrom(utils,capture.output)
 importFrom(utils,packageVersion)
 importFrom(utils,read.table)
 importFrom(utils,setTxtProgressBar)
+importFrom(utils,str)
 importFrom(utils,tail)
 importFrom(utils,txtProgressBar)
+importFrom(uuid,UUIDgenerate)
 useDynLib(immunarch, .registration = TRUE)