Update documentation (and indentation)

llrs · Sep 27, 2023 · 6c8c0c6 · 6c8c0c6
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -39,13 +39,14 @@ Suggests:
     rmarkdown,
     spelling,
     targetscan.Hs.eg.db,
-    testthat,
+    testthat (>= 3.0.0),
     WGCNA
 VignetteBuilder:
     knitr
 biocViews: StatisticalMethod, Clustering, GeneExpression, Network,
     Pathways, NetworkEnrichment, SystemsBiology
+Config/testthat/edition: 3
 Encoding: UTF-8
 Language: en-US
-RoxygenNote: 7.2.3
 Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.2.3
diff --git a/NEWS.md b/NEWS.md
@@ -1,6 +1,10 @@
 # BioCor 1.26
 
-* Added support for plots of similarities
+* Added support for plots of similarities with `plot_data()` and 
+  `plot_similarity()`.
+* Removed internal data accidentally exposed (It was only used for testing).
+* Fix problem with documenting the package via roxygen2.
+* Remove the `\describe{}` macro used in some pages.
 
 # Changes in version 1.19.1
 

diff --git a/R/AintoB.R b/R/AintoB.R
@@ -31,25 +31,25 @@
 #' AintoB(A, B)
 #' @export
 AintoB <- function(A, B) {
-    if (!is.matrix(A) || !is.matrix(B)) {
-        stop("Input should be matrices")
-    }
-    # Select the order for columns
-    if (ncol(A) <= ncol(B) && nrow(A) <= nrow(B)) {
-        mc <- match(colnames(A), colnames(B))
-        mr <- match(rownames(A), rownames(B))
-    } else {
-        stop(
-            "Impossible to insert matrix A into matrix B\n",
-            "Matrix A is bigger than matrix B."
-        )
-    }
-    # Omit those with NA
-    nar <- is.na(mr)
-    nac <- is.na(mc)
-    mr <- mr[!nar]
-    mc <- mc[!nac]
+  if (!is.matrix(A) || !is.matrix(B)) {
+    stop("Input should be matrices")
+  }
+  # Select the order for columns
+  if (ncol(A) <= ncol(B) && nrow(A) <= nrow(B)) {
+    mc <- match(colnames(A), colnames(B))
+    mr <- match(rownames(A), rownames(B))
+  } else {
+    stop(
+      "Impossible to insert matrix A into matrix B\n",
+      "Matrix A is bigger than matrix B."
+    )
+  }
+  # Omit those with NA
+  nar <- is.na(mr)
+  nac <- is.na(mc)
+  mr <- mr[!nar]
+  mc <- mc[!nac]
 
-    B[mr, mc] <- A[!nar, !nac]
-    B
+  B[mr, mc] <- A[!nar, !nac]
+  B
 }
diff --git a/R/AllGenerics.R b/R/AllGenerics.R
@@ -1,39 +1,39 @@
-#' @export pathSim
-setGeneric("pathSim", function(pathway1, pathway2, info, ...)
-      standardGeneric("pathSim")
-  )
-
-#' @export mpathSim
-setGeneric("mpathSim", function(pathways, info, method, ...)
-      standardGeneric("mpathSim")
-  )
-
-#' @export geneSim
-setGeneric("geneSim", function(gene1, gene2, info, method, ...)
-      standardGeneric("geneSim")
-  )
-
-#' @export mgeneSim
-setGeneric("mgeneSim", function(genes, info, method, ....)
-      standardGeneric("mgeneSim")
-  )
-
-#' @export clusterSim
-setGeneric("clusterSim", function(cluster1, cluster2, info, method, ...)
-      standardGeneric("clusterSim")
-  )
-
-#' @export mclusterSim
-setGeneric("mclusterSim", function(clusters, info, method, ....)
-      standardGeneric("mclusterSim")
-  )
-
-#' @export clusterGeneSim
-setGeneric("clusterGeneSim", function(cluster1, cluster2, info, method, ...)
-      standardGeneric("clusterGeneSim")
-  )
-
-#' @export mclusterGeneSim
-setGeneric("mclusterGeneSim", function(clusters, info, method, ....)
-      standardGeneric("mclusterGeneSim")
-  )
+#' @export pathSim
+setGeneric("pathSim", function(pathway1, pathway2, info, ...)
+  standardGeneric("pathSim")
+)
+
+#' @export mpathSim
+setGeneric("mpathSim", function(pathways, info, method, ...)
+  standardGeneric("mpathSim")
+)
+
+#' @export geneSim
+setGeneric("geneSim", function(gene1, gene2, info, method, ...)
+  standardGeneric("geneSim")
+)
+
+#' @export mgeneSim
+setGeneric("mgeneSim", function(genes, info, method, ....)
+  standardGeneric("mgeneSim")
+)
+
+#' @export clusterSim
+setGeneric("clusterSim", function(cluster1, cluster2, info, method, ...)
+  standardGeneric("clusterSim")
+)
+
+#' @export mclusterSim
+setGeneric("mclusterSim", function(clusters, info, method, ....)
+  standardGeneric("mclusterSim")
+)
+
+#' @export clusterGeneSim
+setGeneric("clusterGeneSim", function(cluster1, cluster2, info, method, ...)
+  standardGeneric("clusterGeneSim")
+)
+
+#' @export mclusterGeneSim
+setGeneric("mclusterGeneSim", function(clusters, info, method, ....)
+  standardGeneric("mclusterGeneSim")
+)
diff --git a/R/BioCor-package.R b/R/BioCor-package.R
@@ -1,25 +1,19 @@
-#' BioCor: A package to calculate functional similarities
-#'
-#' Calculates a functional similarity measure between gene identifiers
-#' based on the pathways described on KEGG and REACTOME.
-#'
-#' @section Important functions:
-#' \describe{
-#' \item{[pathSim()]}{Calculates the similarity between two pathways}
-#' \item{[geneSim()]}{Calculates the similarity (based on pathSim)
-#' between two genes}
-#' \item{[clusterSim()]}{Calculates the similarity between two
-#' clusters of genes by joining pathways of each gene.}
-#' \item{[clusterGeneSim()]}{Calculates the similarity between two
-#' clusters of genes by comparing the similarity between the genes of a cluster
-#' }
-#' \item{[similarities()]}{Allows to combine the value of matrices of
-#' similarities}
-#' \item{[conversions()]}{Two functions to convert similarity
-#' measures}
-#' \item{[weighted()]}{Functions provided to combine similarities}
-#' }
-#' @name BioCor-package
-#' @aliases BioCor
-#' @docType package
-NULL
+#' BioCor: A package to calculate functional similarities
+#'
+#' Calculates a functional similarity measure between gene identifiers
+#' based on the pathways described on KEGG and REACTOME.
+#'
+#' @section Important functions:
+#'  - **[pathSim()]**: Calculates the similarity between two pathways.
+#'  - **[geneSim()]**: Calculates the similarity (based on pathSim)
+#'  between two genes.
+#'  - **[clusterSim()]**: Calculates the similarity between two
+#' clusters of genes by joining pathways of each gene.
+#'  - **[clusterGeneSim()]**: Calculates the similarity between two
+#' clusters of genes by comparing the similarity between the genes of a cluster.
+#'  - **[similarities()]**: Allows to combine the value of matrices of
+#' similarities.
+#'  - **[conversions()]**: Two functions to convert similarity
+#' measures.
+#'  - **[weighted()]**: Functions provided to combine similarities.
+'_PACKAGE'
diff --git a/R/auxiliar.R b/R/auxiliar.R
@@ -22,30 +22,30 @@
 #' 4494469/2886003](http://stackoverflow.com/a/4494469/2886003)
 combinadic <- function(n, r, i) {
 
-    # http://msdn.microsoft.com/en-us/library/aa289166(VS.71).aspx
-    # http://en.wikipedia.org/wiki/Combinadic
-    n0 <- length(n)
-    if (i < 1L || i > choose(n0, r)) {
-        stop("'i' must be 0 < i <= n0!/(n0-r)!")
-    }
-    largestV <- function(n, r, i) {
-        v <- n # Adjusted for one-based indexing
-        while (choose(v, r) >= i) { # Adjusted for one-based indexing
-            v <- v - 1L
-        }
-        return(v)
+  # http://msdn.microsoft.com/en-us/library/aa289166(VS.71).aspx
+  # http://en.wikipedia.org/wiki/Combinadic
+  n0 <- length(n)
+  if (i < 1L || i > choose(n0, r)) {
+    stop("'i' must be 0 < i <= n0!/(n0-r)!")
+  }
+  largestV <- function(n, r, i) {
+    v <- n # Adjusted for one-based indexing
+    while (choose(v, r) >= i) { # Adjusted for one-based indexing
+      v <- v - 1L
     }
+    return(v)
+  }
 
-    res <- rep(NA, r)
-    for (j in 1L:r) {
-        res[j] <- largestV(n0, r, i)
-        i <- i - choose(res[j], r)
-        n0 <- res[j]
-        r <- r - 1L
-    }
-    res <- res + 1L
-    res <- n[res]
-    return(res)
+  res <- rep(NA, r)
+  for (j in 1L:r) {
+    res[j] <- largestV(n0, r, i)
+    i <- i - choose(res[j], r)
+    n0 <- res[j]
+    r <- r - 1L
+  }
+  res <- res + 1L
+  res <- n[res]
+  return(res)
 }
 
 # seq2mat ####
@@ -68,15 +68,15 @@ combinadic <- function(n, r, i) {
 #' @seealso [upper.tri()] and [lower.tri()]
 #' @author Lluís Revilla
 seq2mat <- function(x, dat) {
-    if (length(dat) != choose(length(x), 2L)) {
-        stop("Data is not enough big to populate the matrix")
-    }
-    out <- matrix(ncol = length(x), nrow = length(x))
-    out[upper.tri(out)] <- unlist(dat, use.names = TRUE)
-    out[lower.tri(out)] <- t(out)[lower.tri(t(out))]
-    diag(out) <- 1L
-    rownames(out) <- colnames(out) <- x
-    return(out)
+  if (length(dat) != choose(length(x), 2L)) {
+    stop("Data is not enough big to populate the matrix")
+  }
+  out <- matrix(ncol = length(x), nrow = length(x))
+  out[upper.tri(out)] <- unlist(dat, use.names = TRUE)
+  out[lower.tri(out)] <- t(out)[lower.tri(t(out))]
+  diag(out) <- 1L
+  rownames(out) <- colnames(out) <- x
+  return(out)
 }
 
 # duplicateIndices ####
@@ -96,13 +96,13 @@ seq2mat <- function(x, dat) {
 #' duplicateIndices(c("52", "52", "53", "55", "55")) # Repeated elements
 #' duplicateIndices(c("52", "55", "53", "55", "52")) # Mixed repeated elements
 duplicateIndices <- function(vec) {
-    if (!is.character(vec)) {
-        stop("Expected a list of characters to find duplicates on it")
-    }
-    sapply(unique(vec[duplicated(vec)]), function(x) {
-        b <- seq_len(length(vec))
-        b[vec == x]
-    }, simplify = FALSE)
+  if (!is.character(vec)) {
+    stop("Expected a list of characters to find duplicates on it")
+  }
+  sapply(unique(vec[duplicated(vec)]), function(x) {
+    b <- seq_len(length(vec))
+    b[vec == x]
+  }, simplify = FALSE)
 }
 
 # removeDup ####
@@ -128,23 +128,23 @@ duplicateIndices <- function(vec) {
 #' remat <- removeDup(mat, dupli)
 #' remat
 removeDup <- function(cor_mat, dupli) {
-    if (!all(sapply(cor_mat, isSymmetric))) {
-        stop(
-            "All the matrices of mat should be symmetric and with the same ",
-            "column names and rownames"
-        )
-    }
-    cor_mat <- Map(function(mat, x = dupli) {
-        rem.colum <- sapply(x, function(y, m) {
-            mean.column <- apply(m[, y], 2L, mean, na.rm = TRUE)
-            i <- which.max(abs(mean.column))
-            # Select those who don't bring more information
-            setdiff(y, y[i])
-        }, m = mat)
+  if (!all(sapply(cor_mat, isSymmetric))) {
+    stop(
+      "All the matrices of mat should be symmetric and with the same ",
+      "column names and rownames"
+    )
+  }
+  cor_mat <- Map(function(mat, x = dupli) {
+    rem.colum <- sapply(x, function(y, m) {
+      mean.column <- apply(m[, y], 2L, mean, na.rm = TRUE)
+      i <- which.max(abs(mean.column))
+      # Select those who don't bring more information
+      setdiff(y, y[i])
+    }, m = mat)
 
-        mat[-rem.colum, -rem.colum]
-    }, cor_mat)
-    return(cor_mat)
+    mat[-rem.colum, -rem.colum]
+  }, cor_mat)
+  return(cor_mat)
 }
 
 #' Invert a list
@@ -157,11 +157,11 @@ removeDup <- function(cor_mat, dupli) {
 #' @author Lluís Revilla
 #' @export
 inverseList <- function(x) {
-    stopifnot(length(names(x)) == length(x))
-    stopifnot(all(sapply(x, function(x) {
-        is.character(x) || is.na(x)
-    })))
-    genes <- unlist(x, use.names = FALSE)
-    pathways <- rep(names(x), lengths(x))
-    split(pathways, genes)
+  stopifnot(length(names(x)) == length(x))
+  stopifnot(all(sapply(x, function(x) {
+    is.character(x) || is.na(x)
+  })))
+  genes <- unlist(x, use.names = FALSE)
+  pathways <- rep(names(x), lengths(x))
+  split(pathways, genes)
 }