Add R CMD fixes

DESCRIPTION

@@ -51,20 +51,15 @@ URL: https://github.com/maize-genetics/rPHG,
     https://rphg.maizegenetics.net/
 Imports:
     cli,
-    corrplot,
     curl,
-    GenomeInfoDb,
     GenomicRanges,
     ggplot2,
     httr,
     IRanges,
     jsonlite,
-    magrittr,
     methods,
-    parallel,
     rJava,
     rlang,
-    S4Vectors,
     tibble,
     visNetwork
 Depends:

R/class_haplotype_graph.R

@@ -6,6 +6,7 @@
 #' a \code{HaplotypeGraph} object defined in the PHG API
 #'
 #' @slot methodID A \code{\linkS4class{PHGMethod}} object
+#' @slot methodType The method type (e.g. PATHS, CONSENSUS, etc.)
 #' @slot nChrom Number of chromosomes
 #' @slot nNodes Number of nodes
 #' @slot nRefRanges Number of reference ranges

R/class_phg_con_server.R

@@ -77,6 +77,7 @@ setValidity("PHGServerCon", function(object) {
 #' @description \code{PHGServerCon} is the primary container for housing BrAPI
 #'    connection information.
 #'
+#' @param host A user defined URL
 #' @param port The host port. If \code{NULL}, a default port (e.g. \code{80} or
 #'    \code{443}) will be used depending on protocol.
 #' @param protocol Which protocol must be used to fetch the desired data? Must
@@ -126,7 +127,7 @@ PHGServerCon <- function(
         stop("Cannot resolve mandatory endpoint: {serverinfo}", call. = FALSE)
     }
 
-    new(
+    methods::new(
         Class    = "PHGServerCon",
         phgType  = "server",
         host     = host,

R/class_phg_method.R

@@ -7,6 +7,7 @@
 #'
 #' @slot methodID A PHG method identifier.
 #' @slot phgConObj A \code{\linkS4class{PHGCon}} object
+#' @slot isDemo A logical indicating if this method is for demoing
 #'
 #' @name PHGMethod-class
 #' @rdname PHGMethod-class
@@ -20,7 +21,7 @@ setClass(
     ),
     prototype = list(
         methodID  = "test",
-        phgConObj = new("PHGCon", phgType = "local", host = "localHost"),
+        phgConObj = methods::new("PHGCon", phgType = "local", host = "localHost"),
         isDemo    = FALSE
     )
 )
@@ -70,22 +71,22 @@ setValidity("PHGMethod", function(object) {
 #' @param methodID A PHG method identifier.
 #'
 #' @export
-PHGMethod <- function(phgConObj, methodId) {
+PHGMethod <- function(phgConObj, methodID) {
 
     demoMethodId <- "DEMO"
 
     # For demo purposes only! (useful for workshops)
     trueMethodId <- ifelse(
-        test = methodId == demoMethodId,
+        test = methodID == demoMethodId,
         yes  = "NAM_GBS_Alignments_PATHS",
-        no   = methodId
+        no   = methodID
     )
 
     methods::new(
         Class     = "PHGMethod",
         methodID  = trueMethodId,
         phgConObj = phgConObj,
-        isDemo    = methodId == demoMethodId
+        isDemo    = methodID == demoMethodId
     )
 }
 

R/read_hap_ids.R

@@ -50,7 +50,7 @@ hapIdsFromSever <- function(conObj, conMethod, conDemo) {
     )
 
     message(verbInfo[1])
-    initResp <- rPHG:::parseJSON(initRespUrl)
+    initResp <- parseJSON(initRespUrl)
     pageSizeDf <- initResp$result$pagination
 
     totalPages <- ifelse(
@@ -74,7 +74,7 @@ hapIdsFromSever <- function(conObj, conMethod, conDemo) {
     )
 
     message(verbInfo[2])
-    pb <- txtProgressBar(
+    pb <- utils::txtProgressBar(
         min     = 0,
         max     = totalPages,
         initial = 1,
@@ -84,8 +84,8 @@ hapIdsFromSever <- function(conObj, conMethod, conDemo) {
     )
     i <- 2
     for (url in respUrls) {
-        respVector[[i]] <- rPHG:::parseJSON(url)
-        setTxtProgressBar(pb, i)
+        respVector[[i]] <- parseJSON(url)
+        utils::setTxtProgressBar(pb, i)
         i <- i + 1
     }
     close(pb)
@@ -102,7 +102,7 @@ hapIdsFromSever <- function(conObj, conMethod, conDemo) {
     )
 
     colnames(fullResp) <- paste0("R", seq_len(ncol(fullResp)))
-    rownames(fullResp) <- rPHG:::samplesFromServer(conObj, conMethod, conDemo)
+    rownames(fullResp) <- samplesFromServer(conObj, conMethod, conDemo)
 
     return(fullResp)
 }

R/stats_mutual_info.R

@@ -3,7 +3,7 @@
 #
 # @param phgObj A `PHGDataSet` object
 calcMutualInfoFromPHGDataSet <- function(phgObj) {
-    phgHapIDMat     <- t(assay(phgObj))
+    phgHapIDMat     <- t(SummarizedExperiment::assay(phgObj))
     refRanges       <- colnames(phgHapIDMat)
     nRanges         <- length(refRanges)
     miMat           <- matrix(NA, nrow = nRanges, ncol = nRanges)

R/stats_num_haplotypes.R

@@ -9,7 +9,7 @@ nHaploPerRefRangeFromPHGDataSet <- function(phgObj) {
         X      = SummarizedExperiment::assay(phgObj),
         MARGIN = 1,
         FUN    = function(x) {
-            length(unique(na.omit(x)))
+            length(unique(stats::na.omit(x)))
         }
     )
     nHapDf <- data.frame(

R/stats_taxa_by_node.R

@@ -33,7 +33,7 @@ taxaByNodeCore <- function(
         as.numeric()
 
     # Get ref range data frame
-    refRangeDataMini <- rowRanges(hapTableMini) |> as.data.frame()
+    refRangeDataMini <- SummarizedExperiment::rowRanges(hapTableMini) |> as.data.frame()
 
     # Group taxa by hap ID and ref range
     taxaGroups <- lapply(seq_len(ncol(currentMatrix)), function(i) {

R/utilities_general.R

@@ -111,7 +111,7 @@ parseConfigFile <- function(file) {
 
     properties <- vapply(FIELDS, \(x) getProperty(conLines, x), character(1))
 
-    return(setNames(as.list(properties), FIELDS))
+    return(stats::setNames(as.list(properties), FIELDS))
 }
 
 

R/utilities_stats.R

@@ -31,14 +31,14 @@ mutualInfoPair <- function(phgHapIDMat, twoRanges) {
 
     # Sum p(x, y)
     mmi <- matrix(
-        data = colMeans(model.matrix( ~ -1 + hapID[, 1]:hapID[, 2])),
+        data = colMeans(stats::model.matrix( ~ -1 + hapID[, 1]:hapID[, 2])),
         nrow = nHap1,
         ncol = nHap2
     )
 
     # p(x)p(y)
-    mm1 <- colMeans(model.matrix( ~ -1 + hapID[, 1]))
-    mm2 <- colMeans(model.matrix( ~ -1 + hapID[, 2]))
+    mm1 <- colMeans(stats::model.matrix( ~ -1 + hapID[, 1]))
+    mm2 <- colMeans(stats::model.matrix( ~ -1 + hapID[, 2]))
     mmm <- tcrossprod(mm1, mm2)
 
     # Sum p(x, y) log{p(x, y) / [p(x)p(y)]}

R/vis_plot_graph.R

@@ -46,7 +46,7 @@ plotGraphCore <- function(
     colnames(currentMatrix) <- as.numeric(gsub("R", "", colnames(currentMatrix)))
 
     # Get ref range data frame
-    refRangeDataMini <- as.data.frame(rowRanges(hapTableMini))
+    refRangeDataMini <- as.data.frame(SummarizedExperiment::rowRanges(hapTableMini))
 
     # Group taxa by hap ID and ref range
     taxaGroups <- lapply(seq_len(ncol(currentMatrix)), function(i) {

R/vis_plot_mutual_info.R

@@ -10,7 +10,7 @@ plotMutualInfoFromPHGDataSet <- function(phgObj) {
     mDf$X2 <- as.factor(as.numeric(gsub("R", "", mDf$X2)))
 
     p <- ggplot2::ggplot(mDf) +
-        ggplot2::aes(x = X1, y = X2, fill = mut) +
+        ggplot2::aes(x = rlang::.data$X1, y = rlang::.data$X2, fill = rlang::.data$mut) +
         ggplot2::geom_tile(
             color = "white",
             lwd = 0.5,

vignettes/rphg_installation.Rmd

@@ -7,7 +7,7 @@ output:
     toc_float: true
     number_sections: false
 vignette: >
-  %\VignetteIndexEntry{Getting Start with rPHG}
+  %\VignetteIndexEntry{Installing and setting up rPHG and rJava}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
   %\usepackage[utf8]{inputenc}

vignettes/rphg_walkthrough.Rmd

@@ -7,7 +7,7 @@ output:
     toc_float: true
     number_sections: false
 vignette: >
-  %\VignetteIndexEntry{Getting Start with rPHG}
+  %\VignetteIndexEntry{Introduction to rPHG}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
   %\usepackage[utf8]{inputenc}
@@ -144,20 +144,4 @@ configFile |>
     readPHGDataSet()
 ```
 
-## Analyzing and visualizing data
 
-# 
-
-# 
-
-# 
-
-# 
-
-# 
-
-# 
-
-# 
-
-#