diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 7e2072c78..34e4c6170 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -1,16 +1,18 @@ -# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag. -# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions +# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples +# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help +# +# NOTE: This workflow is overkill for most R packages and +# check-standard.yaml is likely a better choice. +# usethis::use_github_action("check-standard") will install it. on: push: - branches: - - main - - master + branches: [main, master, Update_2024Sep] pull_request: - branches: - - main - - master + branches: [main, master, Update_2024Sep] -name: R-CMD-check +name: R-CMD-check.yaml + +permissions: read-all jobs: R-CMD-check: @@ -22,66 +24,39 @@ jobs: fail-fast: false matrix: config: + - {os: macos-latest, r: 'release'} + - {os: windows-latest, r: 'release'} - - {os: macOS-latest, r: 'release'} - - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} - - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} + # use 4.0 or 4.1 to check with rtools40's older compiler + - {os: windows-latest, r: 'oldrel-3'} + + - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'} + - {os: ubuntu-latest, r: 'release'} + - {os: ubuntu-latest, r: 'oldrel-1'} + - {os: ubuntu-latest, r: 'oldrel-2'} + - {os: ubuntu-latest, r: 'oldrel-3'} env: - R_REMOTES_NO_ERRORS_FROM_WARNINGS: true - RSPM: ${{ matrix.config.rspm }} GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} + R_KEEP_PKG_SOURCE: yes steps: - - uses: actions/checkout@v2 + - uses: actions/checkout@v4 - - uses: r-lib/actions/setup-r@v1 + - uses: r-lib/actions/setup-pandoc@v2 + + - uses: r-lib/actions/setup-r@v2 with: r-version: ${{ matrix.config.r }} + http-user-agent: ${{ matrix.config.http-user-agent }} + use-public-rspm: true - - uses: r-lib/actions/setup-pandoc@v1 - - - name: Query dependencies - run: | - install.packages('remotes') - saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) - writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version") - shell: Rscript {0} - - - name: Cache R packages - if: runner.os != 'Windows' - uses: actions/cache@v2 + - uses: r-lib/actions/setup-r-dependencies@v2 with: - path: ${{ env.R_LIBS_USER }} - key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} - restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1- - - - name: Install system dependencies - if: runner.os == 'Linux' - run: | - while read -r cmd - do - eval sudo $cmd - done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))') - - - name: Install dependencies - run: | - remotes::install_deps(dependencies = TRUE) - remotes::install_cran("rcmdcheck") - shell: Rscript {0} - - - name: Check - env: - _R_CHECK_CRAN_INCOMING_REMOTE_: false - _R_CHECK_FORCE_SUGGESTS_: false - run: | - options(crayon.enabled = TRUE) - rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check") - shell: Rscript {0} + extra-packages: any::rcmdcheck + needs: check - - name: Upload check results - if: failure() - uses: actions/upload-artifact@main + - uses: r-lib/actions/check-r-package@v2 with: - name: ${{ runner.os }}-r${{ matrix.config.r }}-results - path: check + upload-snapshots: true + build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")' diff --git a/DESCRIPTION b/DESCRIPTION index 9f0da0ee6..ceaa4810e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: CALANGO Type: Package Title: Comparative Analysis with Annotation-Based Genomic Components -Version: 1.0.16 -Date: 2023-04-26 +Version: 1.0.20 +Date: 2024-09-03 Language: en-US Authors@R: c(person("Francisco", "Lobo", email = "franciscolobo@gmail.com", @@ -35,7 +35,6 @@ Imports: assertthat (>= 0.2.1), rmarkdown (>= 2.1.0), nlme (>= 3.1.0), BiocManager (>= 1.30.10), - taxize (>= 0.9.92), dendextend (>= 1.15.2), heatmaply (>= 1.1.0), ggplot2 (>= 2.3.2), @@ -49,7 +48,7 @@ Suggests: AnnotationDbi, KEGGREST, GO.db Encoding: UTF-8 -RoxygenNote: 7.2.3 +RoxygenNote: 7.3.2 URL: https://labpackages.github.io/CALANGO/ BugReports: https://github.com/fcampelo/CALANGO/issues/ VignetteBuilder: knitr diff --git a/Meta/vignette.rds b/Meta/vignette.rds index d1393b65c..7520bd7ee 100644 Binary files a/Meta/vignette.rds and b/Meta/vignette.rds differ diff --git a/NEWS.md b/NEWS.md index c68d5edbd..05b51ab81 100644 --- a/NEWS.md +++ b/NEWS.md @@ -3,6 +3,9 @@ - Regular maintenance update: - Minor bug fix that resulted in occasional errors on Windows machines - Minor updates to documentation + - Minor tweak to dependencies + - Fixed problem that resulted in `retrieve_calanguize_genomes()` wiping out + the target folder # CALANGO 1.0.14 diff --git a/R/GenerateTree.R b/R/GenerateTree.R index 8bdedb08d..791356781 100644 --- a/R/GenerateTree.R +++ b/R/GenerateTree.R @@ -1,7 +1,11 @@ +# Function removed since it's not being used anywhere else in the package +# by: F. Campelo, 3 Sept 2024 + + # Function to generate and plot a taxonomic tree -GenerateTree <- function(taxonIds, db = "ncbi") { - taxize_class <- taxize::classification(taxonIds, db = db) - taxize_tree <- taxize::class2tree(taxize_class, check = TRUE) - # taxize::plot.classtree(taxize_tree) - invisible(taxize_tree) -} +# GenerateTree <- function(taxonIds, db = "ncbi") { +# taxize_class <- taxize::classification(taxonIds, db = db) +# taxize_tree <- class2tree(taxize_class, check = TRUE) +# # taxize::plot.classtree(taxize_tree) +# invisible(taxize_tree) +# } diff --git a/R/retrieve_calanguize_genomes.R b/R/retrieve_calanguize_genomes.R index 78d6a8bf6..9c6a1fdd3 100644 --- a/R/retrieve_calanguize_genomes.R +++ b/R/retrieve_calanguize_genomes.R @@ -17,6 +17,9 @@ #' documentation of \code{utils::download.file()}. #' @param unzip The unzip method to be used. See the documentation of #' \code{utils::unzip()} for details. +#' @param overwrite If TRUE, overwrite existing files in target the folder +#' (the equivalent of unzip -o), otherwise ignore such files (the equivalent of +#' unzip -n). #' #' @export #' @@ -29,7 +32,8 @@ retrieve_calanguize_genomes <- function(target.dir, method = "auto", - unzip = getOption("unzip")){ + unzip = getOption("unzip"), + overwrite = TRUE){ # ================== Sanity checks ================== assertthat::assert_that(is.character(target.dir), @@ -37,10 +41,7 @@ retrieve_calanguize_genomes <- function(target.dir, if(!dir.exists(target.dir)){ dir.create(target.dir, recursive = TRUE) - } else { - filelist <- dir(target.dir, full.names = TRUE) - unlink(filelist, recursive = TRUE, force = TRUE) - } + } url <- "https://github.com/fcampelo/CALANGO/raw/master/inst/extdata/calanguize_genomes.zip" @@ -53,8 +54,9 @@ retrieve_calanguize_genomes <- function(target.dir, utils::unzip(paste0(target.dir, "/tmpdata.zip"), unzip = unzip, - exdir = target.dir) - unlink(paste0(target.dir, "/__MACOSX"), recursive = TRUE, force = TRUE) + exdir = target.dir, + overwrite = overwrite) + #unlink(paste0(target.dir, "/__MACOSX"), recursive = TRUE, force = TRUE) file.remove(paste0(target.dir, "/tmpdata.zip")) diff --git a/R/utils_taxize_functions.R b/R/utils_taxize_functions.R new file mode 100644 index 000000000..f63fd7dce --- /dev/null +++ b/R/utils_taxize_functions.R @@ -0,0 +1,475 @@ +#' # functions borrowed/adapted from package taxize +#' # https://CRAN.R-project.org/package=taxize +#' # which was orphaned in CRAN as of 3 Sep 2024 +#' +#' dt2df <- function(x, idcol = TRUE) +#' { +#' data.table::setDF(data.table::rbindlist(x, +#' use.names = TRUE, +#' fill = TRUE, +#' idcol = idcol)) +#' } +#' +#' +#' #' List of available NCBI taxonomy ranks +#' #' @noRd +#' #' @author Vinh Tran {tran@bio.uni-frankfurt.de} +#' #' Added by Felipe Campelo {f.campelo@bristol.ac.uk} on 3 Sep 2024 in package +#' #' CALANGO. +#' mainTaxonomyRank <- function() { +#' return( +#' c( +#' "isolate","strain","pathogroup","serotype","serogroup", +#' "forma","formaspecialis","varietas", +#' "genotype","morph","subvariety","biotype", +#' "subspecies","species","speciessubgroup", +#' "speciesgroup","series","section","subgenus","genus", +#' "subtribe","tribe", "subfamily","family","superfamily", +#' "parvorder","infraorder","suborder","order","superorder", +#' "subcohort","cohort","infraclass","subclass","class","superclass", +#' "subphylum","phylum","superphylum", +#' "subkingdom","kingdom","superkingdom" +#' ) +#' ) +#' } +#' +#' +#' #' Indexing all available ranks (including norank) +#' #' @noRd +#' #' @param rankList dataframe, whose each row is a rank list of a taxon +#' #' @return A dataframe containing a list of all possible ranks and their indexed +#' #' values. +#' #' @author Vinh Tran {tran@bio.uni-frankfurt.de} +#' #' Edited by Felipe Campelo {f.campelo@bristol.ac.uk} on 3 Sep 2024 for package +#' #' CALANGO. +#' rank_indexing <- function (rankList) { +#' ### get all available ranks from input rankList +#' uList <- unlist(rankList[seq(2, length(rankList))]) +#' +#' # get final list of available ranks (remove NA items) +#' allInputRank <- as.character(unique(uList)) +#' allInputRank <- allInputRank[!is.na(allInputRank)] +#' +#' ### initial index for main ranks +#' mainRank <- mainTaxonomyRank() +#' rank2index <- new.env(hash = TRUE) +#' getHash <- Vectorize(get, vectorize.args = "x") +#' assignHash <- Vectorize(assign, vectorize.args = c("x", "value")) +#' for (i in seq_len(length(mainRank))) rank2index[[mainRank[i]]] <- i +#' +#' ### the magic happens here +#' for (k in seq_len(nrow(rankList))) { +#' ## get rank list for current taxon containing only ranks in allInputRank +#' subList <- rankList[k,][!is.na(rankList[k,])] +#' filter <- vapply( +#' subList, function(x) x %in% allInputRank, FUN.VALUE = logical(1)) +#' subList <- subList[filter] +#' +#' ## indexing +#' tmpEnv <- new.env(hash = TRUE) +#' flag <- 0 +#' for (i in seq_len(length(subList))) { +#' iRank <- subList[i] +#' if (is.null(rank2index[[iRank]])) { +#' for (j in seq_len(length(subList))) { +#' if (j < i) { +#' if (!is.null(tmpEnv[[subList[i - j]]])) { +#' tmpEnv[[iRank]] <- tmpEnv[[subList[i - j]]] + 1 +#' break +#' } +#' } else j = j - 1 +#' } +#' } else { +#' # for old rank +#' if (i > 1) { +#' if (flag == 0) { +#' if (!(iRank %in% ls(rank2index))) stop(paste(iRank,"not found!")) +#' currentIndex <- rank2index[[iRank]] +#' } else { +#' if (!(iRank %in% ls(tmpEnv))) { +#' tmpEnv[[iRank]] <- tmpEnv[[subList[i-1]]] +#' } +#' currentIndex <- tmpEnv[[iRank]] +#' } +#' +#' if (currentIndex <= tmpEnv[[subList[i-1]]]) { +#' if (flag == 0) { +#' tmpEnv[[iRank]] <- tmpEnv[[subList[i-1]]] + 1 +#' # list of current ranks whose index should be increased +#' candidateList <- unlist( +#' mget( +#' ls(rank2index)[!(ls(rank2index) %in% ls(tmpEnv))], rank2index +#' ) +#' ) +#' candidateList <- candidateList[order(unlist(candidateList))] +#' for (cl in seq_len(length(candidateList))) { +#' r <- names(candidateList)[cl] +#' fromIndex <- rank2index[[iRank]] +#' if(subList[i-1] %in% ls(rank2index)) { +#' fromIndex <- rank2index[[subList[i-1]]] +#' } +#' +#' if (rank2index[[r]] > fromIndex) { +#' tmpEnv[[r]] <- +#' rank2index[[r]] + (tmpEnv[[iRank]] - rank2index[[iRank]]) +#' flag <- 1 +#' } +#' } +#' } else { +#' step <- tmpEnv[[subList[i-1]]] - rank2index[[iRank]] + 1 +#' tmpEnv[[iRank]] <- tmpEnv[[subList[i-1]]] + 1 +#' for (tmpRank in ls(tmpEnv)) { +#' if (tmpEnv[[tmpRank]] >= tmpEnv[[subList[i-1]]]){ +#' if (!(tmpRank == iRank) && !(tmpRank == subList[i-1])){ +#' tmpEnv[[tmpRank]] <- tmpEnv[[tmpRank]] + step +#' } +#' } +#' } +#' } +#' assignHash(ls(tmpEnv), getHash(ls(tmpEnv), tmpEnv), rank2index) +#' } else { +#' if (is.null(tmpEnv[[iRank]])) { +#' tmpEnv[[iRank]] <- rank2index[[iRank]] +#' } +#' } +#' } else { +#' tmpEnv[[iRank]] <- rank2index[[iRank]] +#' } +#' } +#' } +#' assignHash(ls(tmpEnv), getHash(ls(tmpEnv), tmpEnv), rank2index) +#' } +#' +#' # convert env into dataframe and return +#' index2RankList <- lapply( +#' seq_len(length(allInputRank)), function (x) { +#' data.frame( +#' index = rank2index[[allInputRank[x]]], +#' rank = allInputRank[x], stringsAsFactors = FALSE +#' ) +#' } +#' ) +#' index2RankDf <- do.call(rbind, index2RankList) +#' index2RankDf <- index2RankDf[with(index2RankDf, order(index2RankDf$index)),] +#' return(index2RankDf) +#' } +#' +#' +#' +#' +#' +#' #' Align NCBI taxonomy IDs of list of taxa into a sorted rank list +#' #' @noRd +#' #' @param nameList a dataframe whose each row is a rank+ID list of a taxon +#' #' @param rankList a dataframe whose each row is a rank list of a taxon +#' #' @return An aligned taxonomy dataframe which contains all the available +#' #' taxonomy ranks from the id list and rank list +#' #' @author Vinh Tran {tran@bio.uni-frankfurt.de} +#' #' Edited by Felipe Campelo {f.campelo@bristol.ac.uk} on 3 Sep 2024 for package +#' #' CALANGO. +#' #' @importFrom data.table rbindlist setDF transpose melt dcast as.data.table +#' taxonomy_table_creator <- function (nameList, rankList) { +#' colnames(nameList)[1] <- "tip" +#' # get indexed rank list +#' index2RankDf <- rank_indexing(rankList) +#' # get ordered rank list +#' orderedRank <- factor(index2RankDf$rank, levels = index2RankDf$rank) +#' # create a dataframe containing ordered ranks +#' full_rank_name_df <- data.frame( +#' "rank"= matrix(unlist(orderedRank), nrow = length(orderedRank), byrow=TRUE), +#' stringsAsFactors = FALSE +#' ) +#' full_rank_name_df$index <- as.numeric(rownames(full_rank_name_df)) +#' +#' fullRankIDdf <- data.frame( +#' rank = matrix( +#' unlist(orderedRank), nrow = length(orderedRank), byrow = TRUE +#' ), stringsAsFactors = FALSE) +#' fullRankIDdf$index <- as.numeric(rownames(fullRankIDdf)) +#' +#' for (i in 1:nrow(nameList)) { +#' ### get list of all IDs for this taxon +#' taxonDf <- data.frame(nameList[i,]) +#' taxonName <- unlist( +#' strsplit(as.character(nameList[i,]$tip), "##", fixed = TRUE) +#' ) +#' +#' ### convert into long format +#' mTaxonDf <- data.table::setDF( +#' suppressWarnings( +#' data.table::melt(data.table::as.data.table(taxonDf), id = "tip") +#' ) +#' ) +#' +#' ### get rank names and corresponding IDs +#' splitCol <- data.frame( +#' do.call( +#' 'rbind', strsplit(as.character(mTaxonDf$value), "##", fixed=TRUE) +#' ) +#' ) +#' mTaxonDf <- cbind(mTaxonDf,splitCol) +#' +#' ### remove NA cases +#' mTaxonDf <- mTaxonDf[complete.cases(mTaxonDf),] +#' +#' ### subselect mTaxonDf to keep only 2 column rank id and rank name +#' mTaxonDf <- mTaxonDf[, c("X1", "X2")] +#' if(mTaxonDf$X2[1] != index2RankDf$rank[1] && +#' !index2RankDf$rank[1] %in% mTaxonDf$X2){ +#' mTaxonDf <- rbind( +#' data.frame("X1" = mTaxonDf$X1[1], "X2" = index2RankDf$rank[1]), mTaxonDf +#' ) +#' } +#' +#' ### rename columns +#' colnames(mTaxonDf) <- c(taxonName[1],"rank") +#' +#' ### merge with index2RankDf (Df contains all available ranks of input data) +#' full_rank_name_df <- merge( +#' full_rank_name_df,mTaxonDf, by=c("rank"), all.x = TRUE +#' ) +#' +#' ### reorder ranks +#' full_rank_name_df <- full_rank_name_df[order(full_rank_name_df$index),] +#' +#' ### replace NA id by id of previous rank +#' full_rank_name_df <- zoo::na.locf(full_rank_name_df) +#' } +#' +#' ### remove index column +#' full_rank_name_df <- subset(full_rank_name_df, select = -c(index)) +#' +#' ### transpose into wide format +#' t_full_rank_name_df <- data.table::transpose(full_rank_name_df) +#' +#' ### set first row to column names +#' colnames(t_full_rank_name_df) = as.character(unlist(t_full_rank_name_df[1,])) +#' t_full_rank_name_df <- t_full_rank_name_df[-1,] +#' +#' ### replace NA values in the dataframe t_full_rank_name_df +#' if(nrow(t_full_rank_name_df[is.na(t_full_rank_name_df),]) > 0){ +#' t_full_rank_name_dfTMP <- +#' t_full_rank_name_df[complete.cases(t_full_rank_name_df),] +#' t_full_rank_name_dfEdit <- t_full_rank_name_df[is.na(t_full_rank_name_df),] +#' +#' for(i in 1:nrow(t_full_rank_name_dfEdit)){ +#' for(j in 1:(ncol(t_full_rank_name_df)-1)){ +#' if(is.na(t_full_rank_name_dfEdit[i,j])){ +#' t_full_rank_name_dfEdit[i,j] <- t_full_rank_name_dfEdit[i,j+1] +#' } +#' } +#' if(is.na(t_full_rank_name_dfEdit[i,ncol(t_full_rank_name_df)])){ +#' t_full_rank_name_dfEdit[i,ncol(t_full_rank_name_df)] <- +#' t_full_rank_name_dfEdit[i,ncol(t_full_rank_name_df)-1] +#' } +#' } +#' t_full_rank_name_df <- rbind(t_full_rank_name_dfEdit,t_full_rank_name_dfTMP) +#' } +#' +#' ### add fullName column into t_full_rank_name_df +#' fullName <- colnames(full_rank_name_df)[-c(1)] +#' full_rank_name_df <- cbind(fullName,t_full_rank_name_df) +#' +#' ### return +#' return(full_rank_name_df) +#' } +#' +#' +#' # Function from the vegan package +#' # CRAN: http://cran.rstudio.com/web/packages/vegan/ +#' # License: GPL-2 +#' # Maintainer: Jari Oksanen +#' #' Edited by Felipe Campelo {f.campelo@bristol.ac.uk} on 3 Sep 2024 for package +#' #' CALANGO. +#' taxa2dist <- function(x, varstep = FALSE, check = TRUE, labels) { +#' rich <- apply(x, 2, function(taxa) length(unique(taxa))) +#' S <- nrow(x) +#' +#' if (check) { +#' keep <- (rich < S) & (rich > 1) +#' rich <- rich[keep] +#' x <- x[, keep] +#' } +#' i <- rev(order(rich)) +#' x <- x[, i] +#' rich <- rich[i] +#' +#' if (varstep) { +#' add <- -diff(c(nrow(x), rich, 1)) +#' add <- add / c(S, rich) +#' add <- add / sum(add) * 100 +#' } +#' else { +#' add <- rep(100 / (ncol(x) + check), ncol(x) + check) +#' } +#' +#' if (!is.null(names(add))) +#' names(add) <- c("Base", names(add)[-length(add)]) +#' +#' if (!check) +#' add <- c(0, add) +#' +#' out <- matrix(add[1], nrow(x), nrow(x)) +#' for (i in 1:ncol(x)) { +#' out <- out + add[i + 1] * outer(x[, i], x[, i], "!=") +#' } +#' +#' out <- as.dist(out) +#' attr(out, "method") <- "taxa2dist" +#' attr(out, "steps") <- add +#' if (missing(labels)) { +#' attr(out, "Labels") <- rownames(x) +#' } +#' else { +#' if (length(labels) != nrow(x)) +#' warning("Labels are wrong: needed ", nrow(x), " got ", +#' length(labels)) +#' attr(out, "Labels") <- as.character(labels) +#' } +#' +#' if (!check && any(out <= 0)) +#' warning("you used 'check=FALSE' and some distances are zero -- was this intended?") +#' +#' return(out) +#' } +#' +#' +#' +#' #' Convert a list of classifications to a tree. +#' #' +#' #' This function converts a list of hierarchies for individual species into +#' #' a single species by taxonomic level matrix, then calculates a distance +#' #' matrix based on taxonomy alone, and outputs either a phylo or dist object. +#' #' See details for more information. +#' #' +#' #' @noRd +#' #' @param input List of classification data.frame's from the function +#' #' [classification()] +#' #' @param varstep Vary step lengths between successive levels relative to +#' #' proportional loss of the number of distinct classes. +#' #' @param check If TRUE, remove all redundant levels which are different for +#' #' all rows or constant for all rows and regard each row as a different basal +#' #' taxon (species). If FALSE all levels are retained and basal taxa (species) +#' #' also must be coded as variables (columns). You will get a warning if +#' #' species are not coded, but you can ignore this if that was your intention. +#' #' @param ... Further arguments passed on to hclust. +#' #' @param x Input object to print or plot - output from class2tree function. +#' #' @return An object of class "classtree" with slots: +#' #' +#' #' * phylo - The resulting object, a phylo object +#' #' * classification - The classification data.frame, with taxa as rows, +#' #' and different classification levels as columns +#' #' * distmat - Distance matrix +#' #' * names - The names of the tips of the phylogeny +#' #' +#' #' Note that when you execute the resulting object, you only get the phylo +#' #' object. You can get to the other 3 slots by calling them directly, like +#' #' output$names, etc. +#' #' @details See [vegan::taxa2dist()]. Thanks to Jari Oksanen for +#' #' making the taxa2dist function and pointing it out, and Clarke & Warwick +#' #' (1998, 2001), which taxa2dist was based on. +#' #' The taxonomy tree created is not only based on the clustering of the +#' #' taxonomy ranks (e.g. strain, species, genus, ...), but it also utilizes the +#' #' actual taxon clades (e.g. mammals, plants or reptiles, etc.). The process of +#' #' this function is as following: First, all possible taxonomy ranks and their +#' #' corresponding IDs for each given taxon will be collected from the input. +#' #' Then, the rank vectors of all taxa will be aligned, so that they together +#' #' will become a matrix where columns are ordered taxonomy ranks of all taxa and +#' #' rows are the rank vectors of those taxa. After that, the rank matrix will be +#' #' converted into taxonomy ID matrix, any missing rank will have a pseudo +#' #' ID from the previous rank. Finally, this taxonomy ID matrix will be used to +#' #' cluster taxa that have similar taxonomy hierarchy together. +#' #' @examples \dontrun{ +#' #' spnames <- c('Quercus robur', 'Iris oratoria', 'Arachis paraguariensis', +#' #' 'Helianthus annuus','Madia elegans','Lupinus albicaulis', +#' #' 'Pinus lambertiana') +#' #' out <- classification(spnames, db='itis') +#' #' tr <- class2tree(out) +#' #' plot(tr) +#' #' +#' #' spnames <- c('Klattia flava', 'Trollius sibiricus', +#' #' 'Arachis paraguariensis', +#' #' 'Tanacetum boreale', 'Gentiana yakushimensis','Sesamum schinzianum', +#' #' 'Pilea verrucosa','Tibouchina striphnocalyx','Lycium dasystemum', +#' #' 'Berkheya echinacea','Androcymbium villosum', +#' #' 'Helianthus annuus','Madia elegans','Lupinus albicaulis', +#' #' 'Pinus lambertiana') +#' #' out <- classification(spnames, db='ncbi') +#' #' tr <- class2tree(out) +#' #' plot(tr) +#' #' } +#' #' +#' #' Edited by Felipe Campelo {f.campelo@bristol.ac.uk} on 3 Sep 2024 for package +#' #' CALANGO. +#' +#' class2tree <- function(input, varstep = TRUE, check = TRUE, ...) { +#' if (any(is.na(input))) { +#' message('Removed species without classification') +#' input <- input[!is.na(input)] +#' } +#' +#' # Check that there is more than 2 taxon +#' if (length(input) < 3) +#' stop("Your input list of classifications must be 3 or longer.") +#' +#' if (length(unique(names(input))) < length(names(input))) +#' stop("Input list of classifications contains duplicates") +#' +#' # Get rank and ID list +#' message('Get all ranks and their taxIDs') +#' rankList <- dt2df(lapply(input, get_rank), idcol = FALSE) +#' nameList <- dt2df(lapply(input, get_name), idcol = FALSE) +#' strainIndex <- grep("norank", rankList$X1) +#' rankList$X1[strainIndex] <- "strain" +#' nameList$X1[strainIndex] <- +#' gsub("norank_[[:digit:]]+", "strain", nameList$X1[strainIndex]) +#' +#' # Create taxonomy matrix +#' message('Align taxonomy hierarchies...') +#' df <- taxonomy_table_creator(nameList, rankList) +#' +#' if (!inherits(df, "data.frame")) { +#' stop("no taxon ranks in common - try different inputs") +#' } +#' message('Taxonomy alignment done!') +#' +#' row.names(df) <- df[,1] +#' df <- df[,-1] +#' +#' # calculate distance matrix +#' taxdis <- tryCatch(taxa2dist(df, varstep = varstep, check = check), +#' error = function(e) e) +#' +#' tdf <- t(df) +#' for (i in 1:ncol(tdf)){ +#' tdf[,i][duplicated(tdf[,i])] <- NA +#' } +#' +#' # check for incorrect dimensions error +#' if (is(taxdis, 'simpleError')) +#' stop("Try check=FALSE, but see docs for taxa2dist function in the vegan package for details.") +#' +#' message('Calculate distance matrix') +#' out <- ape::as.phylo.hclust(stats::hclust(taxdis, ...)) +#' out <- ape::di2multi(out) +#' # Add node labels +#' message('Add node labels') +#' node_ids <- sort(unique(out$edge[,1])) +#' node_labels <- sapply(phangorn::Descendants(out, node_ids), function(x) { +#' sub_df <- df[out$tip.label[x],] +#' node_col_i <- which(sapply(1:ncol(sub_df), function(i) { +#' length(unique(sub_df[,i]))==1 +#' }))[1] +#' if (is.na(node_col_i)) { +#' NA_character_ +#' } else { +#' unique(sub_df[,node_col_i]) +#' } +#' }) +#' out$node.label <- node_labels +#' +#' res <- list(phylo = out, classification = as.data.frame(t(tdf)), +#' distmat = taxdis, names = names(input)) +#' class(res) <- 'classtree' +#' return( res ) +#' } diff --git a/README.md b/README.md index 15b72283d..289b6509f 100644 --- a/README.md +++ b/README.md @@ -3,6 +3,7 @@ [![R-CMD-check](https://github.com/fcampelo/CALANGO/workflows/R-CMD-check/badge.svg)](https://github.com/fcampelo/CALANGO/actions) [![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/CALANGO)](https://CRAN.R-project.org/package=CALANGO) [![CRAN Downloads](https://cranlogs.r-pkg.org/badges/CALANGO)](https://CRAN.R-project.org/package=CALANGO) +[![R-CMD-check](https://github.com/fcampelo/CALANGO/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/fcampelo/CALANGO/actions/workflows/R-CMD-check.yaml) [![DOI](https://zenodo.org/badge/446743427.svg)](https://zenodo.org/badge/latestdoi/446743427) diff --git a/cran-comments.md b/cran-comments.md index 27737782c..1a454ae8e 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,20 +1,16 @@ ## Changes and notes * Regular maintenance update: - * Updated documentation. - * Added links to published paper and updated citation() + * Removed dependency on orphaned package 'taxize'. + * Fixed minor bug that resulted in occasional errors in Windows. + * Minor updates to documentation + * Fixed malfunction in retrieve_calanguize_genomes() that let to it wiping + out existing files in the target directory. ## R CMD check results -* Duration: 42.5s +* Duration: 28.7s * 0 errors | 0 warnings | 0 notes ; R CMD check succeeded -## Test environments -* macOS: - * macOS 11.6.4 (R 4.1.3): - * macOS 10.16 (R 4.1.0): using `devtools::check()` - -* Linux: - * Ubuntu 20.04.4 (R 4.1.3 and devel): - -* Windows: - * Microsoft Windows Server 2022 - 10.0.20348 (R 4.1.3): - * Microsoft Windows Windows 10 Enterprise v.20H2 (R 4.2.0): using `devtools::check()` +## Test environments (via Github actions) +* macOS 14.6.1 (R 4.4.1) +* Linux Ubuntu 20.04.4 (R 4.1.3, 4.2.3, 4.3.3, 4.4.1 and devel) +* Microsoft Windows Server 2022 - 10.0.20348 (R 4.2.3 and 4.4.1) diff --git a/doc/CALANGO_Parameters.html b/doc/CALANGO_Parameters.html index 839a513c0..f10c5c09a 100644 --- a/doc/CALANGO_Parameters.html +++ b/doc/CALANGO_Parameters.html @@ -239,7 +239,22701 @@

CALANGO Parameters

-

CALANGO logo. Drawn by Brazilian artist Berze - https://www.facebook.com/berzearte

+

+ + + + image/svg+xml + + + + + + + + + +

This document lists the input parameters expected / accepted in the CALANGO definition files (or, alternatively, in the defs list).

diff --git a/docs/404.html b/docs/404.html index 48c458d98..0d8df34b0 100644 --- a/docs/404.html +++ b/docs/404.html @@ -12,7 +12,7 @@ - + @@ -25,7 +25,7 @@ - +
@@ -51,15 +51,15 @@
    • @@ -71,7 +71,7 @@
  • - +
    • @@ -82,7 +82,7 @@
    - +
    @@ -110,16 +110,16 @@

    Page not found (404)

    -

    Site built with pkgdown 2.0.6.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index ee95e8509..804e8494f 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -1,9 +1,9 @@ -License • CALANGOLicense • CALANGO - +
    @@ -28,14 +28,14 @@
  • @@ -44,14 +44,14 @@
    • - +
    @@ -415,15 +415,15 @@

    License

    -

    Site built with pkgdown 2.0.6.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/articles/CALANGO_Parameters.html b/docs/articles/CALANGO_Parameters.html index 5319ac3a8..e0d63d91f 100644 --- a/docs/articles/CALANGO_Parameters.html +++ b/docs/articles/CALANGO_Parameters.html @@ -12,21 +12,19 @@ - + - - - +
    @@ -52,15 +50,15 @@
    • @@ -72,7 +70,7 @@
  • - +
    • @@ -83,7 +81,7 @@
    - +
    @@ -414,9 +412,7 @@

    raw_data_sd_filter - -

    +
    @@ -429,16 +425,16 @@

    raw_data_sd_filter

    -

    Site built with pkgdown 2.0.6.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/articles/CALANGO_examples.html b/docs/articles/CALANGO_examples.html index 7d5d9b006..ce9662da9 100644 --- a/docs/articles/CALANGO_examples.html +++ b/docs/articles/CALANGO_examples.html @@ -12,21 +12,19 @@ - + - - - +
    @@ -52,15 +50,15 @@
    • @@ -72,7 +70,7 @@
  • - +
    • @@ -83,7 +81,7 @@
    - +
    @@ -185,16 +183,16 @@

    CALANGO Examples

    -

    Site built with pkgdown 2.0.6.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/articles/index.html b/docs/articles/index.html index 845d61687..3fb35c90f 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -1,9 +1,9 @@ -Articles • CALANGOArticles • CALANGO - +
    @@ -28,14 +28,14 @@
  • @@ -44,14 +44,14 @@
    • - +
    @@ -63,9 +63,9 @@

    Articles

    All vignettes

    -
    CALANGO Parameters
    +
    CALANGO Examples
    -
    CALANGO Examples
    +
    CALANGO Parameters
    @@ -77,15 +77,15 @@

    All vignettes

    -

    Site built with pkgdown 2.0.6.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/authors.html b/docs/authors.html index f4aca1b4b..1499e7dcd 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -1,9 +1,9 @@ -Authors and Citation • CALANGOAuthors and Citation • CALANGO - +
    @@ -28,14 +28,14 @@
  • @@ -44,41 +44,41 @@
    • - +
    -

    Authors

    +

    Authors and Citation

    - +
    • -

      Francisco Lobo. Author. +

      Francisco Lobo. Author.

    • -

      Felipe Campelo. Author, maintainer. +

      Felipe Campelo. Author, maintainer.

    • -

      Jorge Augusto Hongo. Author. +

      Jorge Augusto Hongo. Author.

    • -

      Giovanni Marques de Castro. Author. +

      Giovanni Marques de Castro. Author.

    • -

      Gabriel Almeida. Scientific advisor, dancer. +

      Gabriel Almeida. Scientific advisor, dancer.

    @@ -93,7 +93,7 @@

    Citation

    Hongo JA, de Castro GM, Menezes AP, Picorelli AC, da Silva TT, Imada EL, Marchionni L, Del-Bem LE, Chaves AV, Almeida GM, Campelo F, Lobo FP (2023). “CALANGO: A phylogeny-aware comparative genomics tool for discovering quantitative genotype-phenotype associations across species.” Patterns. -doi:10.1016/j.patter.2023.100728. +doi:10.1016/j.patter.2023.100728. 

    @Article{,
   title = {CALANGO: A phylogeny-aware comparative genomics tool for discovering quantitative genotype-phenotype associations across species},
@@ -114,15 +114,15 @@ 
    Citation
    -

    Site built with pkgdown 2.0.6.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/index.html b/docs/index.html index 2ac757ce1..80dc7ed42 100644 --- a/docs/index.html +++ b/docs/index.html @@ -12,19 +12,13 @@ - + - + - +
    @@ -58,15 +52,15 @@
    • @@ -78,7 +72,7 @@
  • - +
    • @@ -89,7 +83,7 @@
    - +
    @@ -158,10 +152,10 @@

    PREPARING YOUR INPUT FILES

    genome annotation file

    A text file for each species describing their set of biologically meaningful genomic elements and their respective annotation IDs (e.g. non redundant proteomes annotated to GO terms, or non-redundant protein domains annotated to protein domain IDs). An example of such file, where gene products are annotated using Gene Ontology (GO) terms and Kegg Orthology (KO) identifiers would be as follows:

    -
    Entry   GO_IDs   KEGG_Orthology_ID
-Q7L8J4  GO:0017124;GO:0005737;GO:0035556;GO:1904030;GO:0061099;GO:0004860
-Q8WW27  GO:0016814;GO:0006397;GO:0008270  K18773
-Q96P50  GO:0005096;GO:0046872   K12489
    +
    Entry   GO_IDs   KEGG_Orthology_ID
+Q7L8J4  GO:0017124;GO:0005737;GO:0035556;GO:1904030;GO:0061099;GO:0004860
+Q8WW27  GO:0016814;GO:0006397;GO:0008270  K18773
+Q96P50  GO:0005096;GO:0046872   K12489

    And is specified as:

    In a more abstract representation, files representing genome annotations for a single annotation schema would have two columns and the following general structure:

    -
    genomic_element_name/ID_1     annotation_ID_1;(...);annotation_ID_N
-genomic_element_name/ID_2     annotation_ID_12
    +
    genomic_element_name/ID_1     annotation_ID_1;(...);annotation_ID_N
+genomic_element_name/ID_2     annotation_ID_12

    phylogenetic tree file

    newick or PHYLIP format, containing at least:

    @@ -182,7 +176,7 @@

    PREPARING YOUR INPUT FILES

    no polytomies (if there are such cases, CALANGO will resolve star branches using multi2di method as implemented in ape package.

    A tree in newick format (however, with no branch lengths), would be:

    -
    (genome_ID_1,(genome_ID_2,genome_ID_3))
    +
    (genome_ID_1,(genome_ID_2,genome_ID_3))

    A metadata file

    Containing species-specific information:

    @@ -192,9 +186,9 @@

    PREPARING YOUR INPUT FILES

    A normalizing factor (e.g. proteome size or length; number of annotation terms) to correct for potential biases in datasets (e.g. organisms with different annotation levels or with highly discrepant proteome sizes) If users are using GO as annotation schema, CALANGO can compute a normalizing factor that takes into account all GO counts, including internal nodes, and therefore may not provide any normalizing factor for this case.

    The tabular format for the correlation analysis where column 1 contains the genome IDs, column 2 contains the variable to rank genomes and column 3 contains the normalizing factor could be as follows:

    -
    ../projects/my_project/genome_ID_1  1.7  2537
-../projects/my_project/genome_ID_2  1.2  10212
-../projects/my_project/genome_ID_3  0.9  1534
    +
    ../projects/my_project/genome_ID_1  1.7  2537
+../projects/my_project/genome_ID_2  1.2  10212
+../projects/my_project/genome_ID_3  0.9  1534

    Metadada files are specified as follows:

    -
    Annotation_ID     Annotation_definition
-annotation_ID_1   All alpha proteins
-annotation_ID_2   Globin-like
-annotation_ID_3   Globin-like
-annotation_ID_4   Truncated hemoglobin
-(...)
-annotation_ID_N   annotation_ID_description
    +
    Annotation_ID     Annotation_definition
+annotation_ID_1   All alpha proteins
+annotation_ID_2   Globin-like
+annotation_ID_3   Globin-like
+annotation_ID_4   Truncated hemoglobin
+(...)
+annotation_ID_N   annotation_ID_description

    CALANGO can treat each identifier as its own description, preventing the need to prepare an ontology that isn’t natively supported. For that, do not specify any ontology file and set the ontology = "other".

    @@ -360,16 +354,16 @@

    Dev status

    -

    Site built with pkgdown 2.0.6.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/news/index.html b/docs/news/index.html index 1396a78c8..717408295 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -1,9 +1,9 @@ -Changelog • CALANGOChangelog • CALANGO - +
    @@ -28,14 +28,14 @@
  • @@ -44,14 +44,14 @@
    • - +
    @@ -60,6 +60,14 @@

    Changelog

    Source: NEWS.md
    +
    +

    CALANGO 1.0.20

    +
    • Regular maintenance update: +
      • Minor bug fix that resulted in occasional errors on Windows machines
        • +
      • Minor updates to documentation
        • +
      • Minor tweak to dependencies
        • +
      • +

    CALANGO 1.0.14

    • Regular maintenance update: @@ -128,15 +136,15 @@

      CALANGO 1.0.2
      -

      Site built with pkgdown 2.0.6.

      +

      Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 197f1cef7..6a7d9d015 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,8 +1,7 @@ -pandoc: 2.19.2 -pkgdown: 2.0.6 +pandoc: 3.1.11 +pkgdown: 2.1.0 pkgdown_sha: ~ articles: - CALANGO_Parameters: CALANGO_Parameters.html CALANGO_examples: CALANGO_examples.html -last_built: 2023-04-26T13:03Z - + CALANGO_Parameters: CALANGO_Parameters.html +last_built: 2024-09-03T11:38Z diff --git a/docs/reference/index.html b/docs/reference/index.html index 16324a068..3a85075fa 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -1,9 +1,9 @@ -Function reference • CALANGOPackage index • CALANGO - +
    @@ -28,14 +28,14 @@
  • @@ -44,14 +44,14 @@
    • - +
    @@ -96,15 +96,15 @@

    All functions
    -

    Site built with pkgdown 2.0.6.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/install_bioc_dependencies.html b/docs/reference/install_bioc_dependencies.html index fa6904771..eaffb3ab2 100644 --- a/docs/reference/install_bioc_dependencies.html +++ b/docs/reference/install_bioc_dependencies.html @@ -1,5 +1,5 @@ -Install Bioconductor dependencies — install_bioc_dependencies • CALANGOInstall Bioconductor dependencies — install_bioc_dependencies • CALANGO - +
    @@ -34,14 +34,14 @@
  • @@ -50,14 +50,14 @@
    • - +
    @@ -80,24 +80,24 @@

    Install Bioconductor dependencies

    Arguments

    -
    bioc.args
    + + +
    bioc.args

    list containing further arguments to be passed down to `BiocManager::install()`.

    -
    force
    +
    force

    logical: reinstall already-installed packages?

    Value

    - - -

    No return value, called for side effects.

    +

    No return value, called for side effects.

    Details

    -

    It is essential that +

    It is essential that these Bioconductor packages be installed for CALANGO to work properly. It uses `BiocManager::install()` for installing Bioconductor packages. Further arguments to this function are passed as a list.

    @@ -105,9 +105,9 @@

    Details

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
   install_bioc_dependencies()
-}
+} # }
    @@ -123,15 +123,15 @@

    Examples

    -

    Site built with pkgdown 2.0.6.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/make_report.html b/docs/reference/make_report.html index c379349b3..3c6529a35 100644 --- a/docs/reference/make_report.html +++ b/docs/reference/make_report.html @@ -1,10 +1,10 @@ -Prepare and render the HTML5 report — make_report • CALANGOPrepare and render the HTML5 report — make_report • CALANGO - +
    @@ -29,14 +29,14 @@
  • @@ -45,14 +45,14 @@
    • - +
    @@ -73,26 +73,26 @@

    Prepare and render the HTML5 report

    Arguments

    -
    defs
    + + +
    defs

    an enriched `CALANGO`-type list generated by `run_CALANGO()`

    -
    render.report
    +
    render.report

    logical: should the HTML5 report be generated (for internal use only)

    Value

    - - -

    Updated `defs` list, containing:

    • All input parameters originally passed (see [run_CALANGO()] for +

      Updated `defs` list, containing:

      • All input parameters originally passed (see [run_CALANGO()] for details).

        • -

      • Derived fields calculated for displaying the results, including - several statistical summaries of the data (including correlations, +

      • Derived fields calculated for displaying the results, including + several statistical summaries of the data (including correlations, contrasts, covariances, p-values).

        • -

      This function is mainly called for its side effect, namely the generation of -an HTML5 report of the analysis, which is saved to the folder indicated in +

    This function is mainly called for its side effect, namely the generation of +an HTML5 report of the analysis, which is saved to the folder indicated in `defs$output.dir`.

    @@ -108,15 +108,15 @@

    Value

    -

    Site built with pkgdown 2.0.6.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/retrieve_calanguize_genomes.html b/docs/reference/retrieve_calanguize_genomes.html index a10264d31..833bca53e 100644 --- a/docs/reference/retrieve_calanguize_genomes.html +++ b/docs/reference/retrieve_calanguize_genomes.html @@ -1,13 +1,13 @@ -Retrieve calanguize_genomes script from the Github repository — retrieve_calanguize_genomes • CALANGORetrieve calanguize_genomes script from the Github repository — retrieve_calanguize_genomes • CALANGO - +
    @@ -32,14 +32,14 @@
  • @@ -48,14 +48,14 @@
    • - +
    @@ -66,10 +66,10 @@

    Retrieve calanguize_genomes script from the Github repository

    -

    This script downloads the *calanguize_genomes.pl* Perl script from the -repository, together with associated README instructions for using the -script, managing dependencies, etc. It will extract the data into a folder -containing everything that is needed for preparing data for using +

    This script downloads the *calanguize_genomes.pl* Perl script from the +repository, together with associated README instructions for using the +script, managing dependencies, etc. It will extract the data into a folder +containing everything that is needed for preparing data for using CALANGO.

    @@ -83,28 +83,28 @@

    Retrieve calanguize_genomes script from the Github repository

    Arguments

    -
    target.dir
    + + +
    target.dir

    path to the folder where the files will be saved ( accepts relative and absolute paths)

    -
    method
    +
    method

    Method to be used for downloading files. Current download methods are "internal", "wininet" (Windows only) "libcurl", "wget" and "curl", and there is a value "auto": see _Details_ and _Note_ in the documentation of utils::download.file().

    -
    unzip
    +
    unzip

    The unzip method to be used. See the documentation of utils::unzip() for details.

    Value

    - - -

    No return value, called for side effects (see Description).

    +

    No return value, called for side effects (see Description).

    Details

    @@ -114,9 +114,9 @@

    Details

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
   CALANGO::retrieve_calanguize_genomes(target.dir = "./data")
-}
+} # }
    @@ -132,15 +132,15 @@

    Examples

    -

    Site built with pkgdown 2.0.6.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/retrieve_data_files.html b/docs/reference/retrieve_data_files.html index 1db314ec4..0038c64d8 100644 --- a/docs/reference/retrieve_data_files.html +++ b/docs/reference/retrieve_data_files.html @@ -1,14 +1,14 @@ -Retrieve data files from the Github repository — retrieve_data_files • CALANGORetrieve data files from the Github repository — retrieve_data_files • CALANGO - +
    @@ -33,14 +33,14 @@
  • @@ -49,14 +49,14 @@
    • - +
    @@ -70,8 +70,8 @@

    Retrieve data files from the Github repository

    This script downloads relevant data files from the CALANGO project repository. It will extract the data into a folder containing directories related to dictionary files, Gene Ontology annotation -files, tree files, etc. Note: you may need to edit the file paths in the -example scripts contained under the `parameters` subfolder of `target.dir`, +files, tree files, etc. Note: you may need to edit the file paths in the +example scripts contained under the `parameters` subfolder of `target.dir`, or pass an appropriate base path using parameter `basedir` in [run_CALANGO()].

    @@ -86,32 +86,32 @@

    Retrieve data files from the Github repository

    Arguments

    -
    target.dir
    + + +
    target.dir

    path to the folder where the files will be saved ( accepts relative and absolute paths)

    -
    method
    +
    method

    Method to be used for downloading files. Current download methods are "internal", "wininet" (Windows only) "libcurl", "wget" and "curl", and there is a value "auto": see _Details_ and _Note_ in the documentation of utils::download.file().

    -
    unzip
    +
    unzip

    The unzip method to be used. See the documentation of utils::unzip() for details.

    -
    ...
    +
    ...

    additional attributes (currently ignored)

    Value

    - - -

    No return value, called for side effects (see Description).

    +

    No return value, called for side effects (see Description).

    Details

    @@ -121,9 +121,9 @@

    Details

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
   CALANGO::retrieve_data_files(target.dir = "./data")
-}
+} # }
    @@ -139,15 +139,15 @@

    Examples

    -

    Site built with pkgdown 2.0.6.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/reference/run_CALANGO.html b/docs/reference/run_CALANGO.html index acfdd7f4a..04111f2de 100644 --- a/docs/reference/run_CALANGO.html +++ b/docs/reference/run_CALANGO.html @@ -1,10 +1,10 @@ -Run the CALANGO pipeline — run_CALANGO • CALANGORun the CALANGO pipeline — run_CALANGO • CALANGO - +
    @@ -29,14 +29,14 @@
  • @@ -45,14 +45,14 @@
    • - +
    @@ -79,43 +79,40 @@

    Run the CALANGO pipeline

    Arguments

    -
    defs
    + + +
    defs

    either a CALANGO-type list object or a path to a text file containing the required definitions (see Details).

    -
    type
    +
    type

    type of analysis to perform. Currently only "correlation" is supported.

    -
    cores
    -

    positive integer, how many CPU cores to use (multicore -acceleration does not work in Windows systems). Setting -this parameter overrides any `cores` field from `defs`. Multicore support is -currently implemented using the `parallel` package, which uses forking -(which means that multicore support is not available under Windows)

    +
    cores
    +

    positive integer, how many CPU cores to use. Setting +this parameter overrides any `cores` field from `defs`.

    -
    render.report
    +
    render.report

    logical: should a HTML5 report be generated?

    -
    basedir
    -

    path to base folder to which all relative paths in `defs` +

    basedir
    +

    path to base folder to which all relative paths in `defs` refer to.

    Value

    - - -

    Updated `defs` list, containing:

    • All input parameters originally passed or read from a `defs` file +

      Updated `defs` list, containing:

      • All input parameters originally passed or read from a `defs` file (see **Details**).

        • -

      • Derived fields loaded and preprocessed from the files indicated in +

      • Derived fields loaded and preprocessed from the files indicated in `defs`.

        • -

      • Several statistical summaries of the data (used to render the - report), including correlations, contrasts, covariances, p-values and +

      • Several statistical summaries of the data (used to render the + report), including correlations, contrasts, covariances, p-values and other summary statistics.

      Results are also saved to files under `defs$output.dir`.

    @@ -170,7 +167,7 @@

    Details

    Examples

    - 
    if (FALSE) {
+    
    if (FALSE) { # \dontrun{
 
 ## Install any missing BioConductor packages for report generation 
 ## (only needs to be done once)
@@ -183,7 +180,7 @@ 
    Examples
    
 
 # Run CALANGO
 res <- run_CALANGO(defs, cores = 2)
-}
+} # }
    @@ -199,15 +196,15 @@

    Examples

    -

    Site built with pkgdown 2.0.6.

    +

    Site built with pkgdown 2.1.0.

    - - + + diff --git a/docs/sitemap.xml b/docs/sitemap.xml index 914e995e5..750123e09 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -1,8547 +1,2851 @@ - - - - /404.html - - - /LICENSE-text.html - - - /articles/CALANGO_Parameters.html - - - /articles/CALANGO_examples.html - - - /articles/examples-page.html - - - /articles/index.html - - - /articles/results/Example1_domain2GO_count/about.html - - - /articles/results/Example1_domain2GO_count/correlation_Plots/GO_0000270.html - - - /articles/results/Example1_domain2GO_count/correlation_Plots/GO_0000270_boxplot.html - - - /articles/results/Example1_domain2GO_count/correlation_Plots/GO_0000271.html - - - /articles/results/Example1_domain2GO_count/correlation_Plots/GO_0000271_boxplot.html - - - /articles/results/Example1_domain2GO_count/correlation_Plots/GO_0000287.html - - - /articles/results/Example1_domain2GO_count/correlation_Plots/GO_0000287_boxplot.html - - - 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+/reference/index.html +/reference/install_and_update_packages.html +/reference/install_bioc_dependencies.html +/reference/make_report.html +/reference/retrieve_calanguize_genomes.html +/reference/retrieve_data_files.html +/reference/run_CALANGO.html + diff --git a/man/retrieve_calanguize_genomes.Rd b/man/retrieve_calanguize_genomes.Rd index 259ad5d5d..852f3e015 100644 --- a/man/retrieve_calanguize_genomes.Rd +++ b/man/retrieve_calanguize_genomes.Rd @@ -7,7 +7,8 @@ retrieve_calanguize_genomes( target.dir, method = "auto", - unzip = getOption("unzip") + unzip = getOption("unzip"), + overwrite = TRUE ) } \arguments{ @@ -21,6 +22,10 @@ documentation of \code{utils::download.file()}.} \item{unzip}{The unzip method to be used. See the documentation of \code{utils::unzip()} for details.} + +\item{overwrite}{If TRUE, overwrite existing files in target the folder +(the equivalent of unzip -o), otherwise ignore such files (the equivalent of +unzip -n).} } \value{ No return value, called for side effects (see Description).