rcmdcheck

DESCRIPTION

@@ -1,12 +1,13 @@
 Package: stana
 Type: Package
-Title: Strain-level metagenomic analysis in R
+Title: Metagenotyping analysis in R
 Version: 0.99.0
 License: GPL-3
-Description: Analysis toolkit for intra-species diversity from metagenomics.
+Description: The package aims to analyze intra-species diversity from metagenomics. The package supports the loading functions for single nucleotide variants and copy number variant profiles, filtering, and statistical analysis.
 Authors@R: person("Noriaki", "Sato", email = "nori@hgc.jp", role = c("cre", "aut"))
 Depends: ggplot2, ggstar, ggraph, igraph
-Imports: GetoptLong, BiocFileCache, RCurl, vegan, methods, data.table, phangorn, RColorBrewer, ggtree, circlize, ComplexHeatmap, ggkegg, ape, dplyr, exactRankTests, ggblend, ggh4x, scales, tidygraph, ggplotify, ggtreeExtra, ggnewscale, scico, MKmisc, NMF, pillar, BiocStyle, cowplot, patchwork, reshape2, ggrepel, Boruta, tidyr, stringr
+Imports: GetoptLong, BiocFileCache, RCurl, vegan, methods, data.table, phangorn, RColorBrewer, ggtree, circlize, ComplexHeatmap, ggkegg, ape, dplyr, exactRankTests, ggblend, ggh4x, scales, tidygraph, ggplotify, ggtreeExtra, ggnewscale, scico, MKmisc, NMF, pillar, cowplot, patchwork, reshape2, Boruta, tidyr, stringr, clusterProfiler, grDevices, stats, utils
 Suggests: simplifyEnrichment, knitr, rmarkdown, NNLM, shiny, BiocStyle, matrixStats
 RoxygenNote: 7.3.2
+biocViews: Microbiome
 VignetteBuilder: knitr

NAMESPACE

@@ -139,6 +139,8 @@ importFrom(scico,scale_fill_scico_d)
 importFrom(stats,as.formula)
 importFrom(stats,dist)
 importFrom(stats,prcomp)
+importFrom(tidygraph,"%E>%")
+importFrom(tidygraph,"%N>%")
 importFrom(utils,object.size)
 importFrom(utils,read.table)
 importFrom(vegan,adonis2)

R/NMF.R

@@ -230,6 +230,7 @@ plotStackedBarPlot <- function(stana, sp, by="NMF") {
 #' @param rank if NMF is not performed, this performs the NMF beforehand.
 #' rank can be specified here.
 #' @export
+#' @return vegan::diversity results
 alphaDiversityWithinSpecies <- function(stana, species, method="shannon", rank=5) {
     if (is.null(stana@NMF[[species]])) {
         stana <- NMF(stana, species, rank=rank)
@@ -261,6 +262,7 @@ alphaDiversityWithinSpecies <- function(stana, species, method="shannon", rank=5
 #' @param return_data return only the data, not plot
 #' @param by NMF or coef matrix set to `coefMat` slot
 #' @export
+#' @return ggplot object
 plotAbundanceWithinSpecies <- function(stana, species, tss=TRUE, return_data=FALSE, by="NMF") {
 	if (by=="NMF") {
 	    if (is.null(stana@NMF[[species]])) {

R/alleleStat.R

@@ -42,8 +42,8 @@ alleleStat_metaSNV <- function(stana, sp, cl, deleteZeroDepth) {
 #' @param base "maj","ref", or "majref"
 #' @param deleteZeroDepth delete snvs with zero depth
 #' @export
+#' @return list of statistical values
 #' 
-
 alleleStat <- function(stana, sp=NULL, cl=NULL, base="maj",
 	deleteZeroDepth=FALSE) {
 	if (is.null(sp)) {sp <- stana@ids[1]}

R/annot.R

@@ -15,6 +15,7 @@
 #'        passed to anno_word_cloud
 #' @param argList will be passed to anno_word_cloud
 #' @export
+#' @return the results of anno_word_cloud
 anno_PATRIC_keywords <- function(split, genes, fnc="pathway_name",
   removeHigh=TRUE, removeAdditional=NULL, argList=list()) {
 

R/doBoruta.R

@@ -42,7 +42,7 @@ doBoruta <- function(stana, sp, cl=NULL, doFix=TRUE,
   }
   cat_subtle("# Feature number: ", dim(filtDf)[1], "\n", sep="")
   transDf <- data.frame(t(filtDf),
-                        check.names=F)
+                        check.names=FALSE)
   transDf <- transDf[intersect(row.names(transDf), cl |> unlist() |> unique()),]
   gr <- NULL
   for (cn in rownames(transDf)){

R/doGSEA.R

@@ -107,6 +107,7 @@ doGSEA <- function(stana, candSp=NULL, cl=NULL, eps=1e-2, how=sum,
 #' @param return_graph return only the tbl_graph
 #' @param layout graph layout in ggraph
 #' @export
+#' @importFrom tidygraph %N>% %E>%
 #' @return ggplot object
 plotGSEA <- function(stana, dataset_names=NULL, padjThreshold=0.05,
     return_graph=FALSE, layout="kk") {

R/plotHeatmap.R

@@ -16,7 +16,6 @@
 #' @param removeHigh remove high frequent words (preset)
 #' @param removeAdditional remove additional words specified
 #' @param max_words max words to plot
-#' @param seed random seed
 #' @param filter_zero_frac genes with zero abundance over fraction of samples as this value
 #' are removed before sample filtering. As typically gene matrix is large, for further filtering, please use `mat` option
 #' @param filter_max_frac remove genes with values below `filter_max_value` in this fraction of sample
@@ -25,11 +24,10 @@
 #' @importFrom ComplexHeatmap Heatmap
 #' @export
 #' 
-plotHeatmap <- function(stana, sp, cl=NULL, k=10, mat=NULL, seed=1,
+plotHeatmap <- function(stana, sp, cl=NULL, k=10, mat=NULL,
 	geneID=NULL, variable=0,
 	fnc="KEGG_Pathway", removeHigh=TRUE, removeAdditional=NULL, max_words=10,
     filter_zero_frac=0.8, filter_max_frac=0, filter_max_value=50) {
-	set.seed(seed)
 
 	if (!is.null(mat)) {
 		df <- mat

R/utils.R

@@ -15,7 +15,7 @@ cnDiscretize <- function(stana, species, cutoff=0.35) {
 #' @export
 #' @return stana
 setTree <- function(stana, species, tre) {
-	if (class(tre)!="phylo") {stop("Please provide phylo object")}
+	if (!is(tre, "phylo")) {stop("Please provide phylo object")}
 	stana@treeList[[species]] <- tre
 	return(stana)
 }

vignettes/usage_of_stana.Rmd

@@ -17,6 +17,7 @@ knitr::opts_chunk$set(echo = TRUE,
                       fig.height=5,
                       warning=FALSE,
                       message=FALSE)
+library(BiocStyle)
 ```
 
 # stana