Merge pull request #23 from sterrettJD/bioconductor

Setup bioconductor compatibility

Author: sterrettJD

.Rbuildignore

@@ -1,2 +1,11 @@
-^.*\.Rproj$
+^benchmarking/
+^.*\.pdf$
+^.*\.tar\.gz$
+^\.DS_Store$
+^\.git$
+^\.github$
+^\.gitignore$
+^\.Rhistory$
 ^\.Rproj\.user$
+^HoMiStats\.Rproj$
+^notes/

DESCRIPTION

@@ -1,19 +1,28 @@
 Package: HoMiStats
 Type: Package
 Title: Stats for host-microbiome dual transcriptomics
-Version: 0.1.0
-Author: John Sterrett
-Maintainer: John Sterrett <john.sterrett@colorado.edu>
-Description: Stats for host-microbiome dual transcriptomics
-    Contains tools for metatranscriptome differential expression and
-    for creating co-occurrence networks between host and microbial transcripts
-Imports: gamlss, gamlss.dist, broom, broom.mixed, ggplot2, tidyverse, lme4, ZIBR, dplyr, lmerTest, Matrix, parallel, foreach, doParallel, doSNOW, plyr, Rfast, AnnotationDbi, org.Hs.eg.db, DESeq2
-License: MIT
+Version: 0.99.0
+Authors@R: person("John", "Sterrett", 
+                email = "sterrettjd@protonmail.com", 
+                role = c("aut", "cre"),
+                comment = c(ORCID = "0000-0002-0931-7181"))
+Description: Statistical tooling for host-microbiome dual transcriptomics.
+    HoMiStats contains tools for metatranscriptome differential expression and
+    for creating co-occurrence networks between host and microbial transcripts.
+    Additionally, there are tools for transforming data and 
+    performing targeted (knowledge-guided) analyses to look for 
+    biologically-plausible associations in gene expression between 
+    hosts and microbes.
+Imports: gamlss, gamlss.dist, broom, broom.mixed, ggplot2, tidyverse, lme4, ZIBR, dplyr, lmerTest, Matrix, parallel, foreach, doParallel, doSNOW, plyr, Rfast, AnnotationDbi, org.Hs.eg.db, DESeq2, stats, utils, stringr
+License: MIT + file LICENSE
 Encoding: UTF-8
-LazyData: true
 Suggests: 
     knitr,
     rmarkdown,
     testthat (>= 3.0.0)
 VignetteBuilder: knitr
 Config/testthat/edition: 3
+URL: https://github.com/sterrettJD/HoMiStats
+BugReports: https://github.com/sterrettJD/HoMiStats/issues
+biocViews: GeneExpression, Regression, DifferentialExpression, Transcriptomics, Metagenomics, Microbiome, KEGG
+RoxygenNote: 7.3.2

LICENSE

@@ -0,0 +1,7 @@
+Copyright <2025> <John Sterrett>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

NAMESPACE

@@ -1,21 +1,25 @@
 exportPattern("^[[:alpha:]]+")
-import(gamlss)
-import(gamlss.dist)
 import(ZIBR)
-import(lme4)
-import(lmerTest)
 import(foreach)
 import(DESeq2)
+import(ggplot2)
+import(tidyverse)
+import(Matrix)
+importFrom(gamlss, gamlss)
+importFrom(gamlss, gamlss.control)
+importFrom(gamlss.dist, BEZI)
+importFrom(lmerTest, lmer)
+importFrom(lme4, findbars)
 importFrom(parallel, makeCluster)
 importFrom(parallel, stopCluster)
 importFrom(doParallel, registerDoParallel)
 importFrom(doSNOW, registerDoSNOW)
 importFrom(broom.mixed, tidy)
 importFrom(broom, tidy)
-importFrom("stats", "as.formula", "p.adjust")
-importFrom("utils", "setTxtProgressBar", "txtProgressBar")
+importFrom("stats", "as.formula", "p.adjust","lm", "var")
+importFrom("utils", "setTxtProgressBar", "txtProgressBar", "download.file")
 importFrom(plyr, mapvalues)
 importFrom(Rfast, comb_n)
 importFrom(AnnotationDbi, select)
 importFrom(org.Hs.eg.db, org.Hs.eg.db)
-
+importFrom(stringr, str_split)

R/GMMs.R

@@ -1,16 +1,31 @@
 #' Download GMMs file
-#' @description Pulls the Raes lab gut metabolic modules file (v1.0.7). Will not overwrite an existing file.
+#' @description Pulls the Raes lab gut metabolic modules file (v1.0.7).
+#' This will not overwrite an existing file.
 #' @param filepath The filepath where the GMMs file should be downloaded
+#' @param version The version of GMMs to be used.
+#' As of April '24, the newest version is v1.07.
+#' This is used in pulling the data from the Raes lab GMMs github,
+#' so old versions that are not on the master branch
+#' may cause the filepath to not work.
+#' @param quietly A boolean denoting if the GMMs file
+#' should be downloaded quietly
 #' @return Nothing
+#'
+#' @examples
+#' pull_GMMs_file("loc_to_download.txt")
+#'
+#' # cleanup
+#' file.remove("loc_to_download.txt")
 #' @export
 #'
 pull_GMMs_file <- function(filepath, version="v1.07", quietly=TRUE){
     if(!file.exists(filepath)){
-        gmm.url <- paste0("https://raw.githubusercontent.com/raeslab/GMMs/master/GMMs.",
-                          version, ".txt")
+        gmm.url <- paste0("https://raw.githubusercontent.com/",
+                            "raeslab/GMMs/master/GMMs.",
+                            version, ".txt")
         download.file(gmm.url,
-                      filepath,
-                      quiet=quietly)
+                        filepath,
+                        quiet=quietly)
     } else {
         warning("File already exists.")
     }
@@ -20,12 +35,19 @@ pull_GMMs_file <- function(filepath, version="v1.07", quietly=TRUE){
 #' Adds KEGG line to the GMM matrix
 #' @description Parser for each line of the GMM file
 #' @param GMM.matrix The matrix with GMM data
-#' @param line A string containing the line to be parsed and added to the GMM matrix
-#' @param mod.name A string containing the name of the module for which current line is being parsed
-#' @param mod.number A string containing the ID of the module for which current line is being parsed
+#' @param line A string containing the line
+#' to be parsed and added to the GMM matrix
+#' @param mod.name A string containing the name of the module
+#' for which current line is being parsed
+#' @param mod.number A string containing the ID of the module
+#' for which current line is being parsed
 #' @return The updated matrix of GMMs, with the new line parsed and added
 #'
-add_K_line_to_matrix <- function(GMM.matrix, line, mod.name, mod.number){
+#' @importFrom stringr str_split
+#'
+#' @keywords internal
+#'
+.add_K_line_to_matrix <- function(GMM.matrix, line, mod.name, mod.number){
     # Splits line on either a comma or tab
     split.line <- stringr::str_split(line, "[,\t]")[[1]]
     new.GMM.matrix <- GMM.matrix
@@ -38,24 +60,37 @@ add_K_line_to_matrix <- function(GMM.matrix, line, mod.name, mod.number){
 }
 
 #' Gets the GMM matrix in a tabular format
-#' @description Download the GMM data (if needed) and parses this file to return a table with the GMMs and corresponding KOs
-#' @param filepath The filepath at which the GMMs file should be downloaded or found.
-#' @param version The version of GMMs to be used. As of April '24, the newest version is v1.07. This is used in pulling the data from the Raes lab GMMs github, so old versions that are not on the master branch may cause the filepath to not work.
-#' @param quietly A boolean denoting if the GMMs file should be downloaded quietly
-#' @param cleanup A boolean denoting if the filepath should be removed at the end of this function.
+#' @description Download the GMM data (if needed) and
+#' parses this file to return a table with the GMMs and corresponding KOs
+#' @param filepath The filepath at which
+#' the GMMs file should be downloaded or found.
+#' @param version The version of GMMs to be used.
+#' As of April '24, the newest version is v1.07.
+#' This is used in pulling the data from the Raes lab GMMs github,
+#' so old versions that are not on the master branch
+#' may cause the filepath to not work.
+#' @param quietly_download A boolean denoting if the GMMs file
+#' should be downloaded quietly
+#' @param cleanup A boolean denoting if the filepath
+#' should be removed at the end of this function.
 #' @return A tabular version of the GMMs as a dataframe
+#'
+#' @examples
+#' GMM.df <- get_GMM_matrix()
+#'
 #' @export
 #'
 get_GMM_matrix <- function(filepath="GMMs.txt", version="v1.07",
-                           quietly_download=TRUE, cleanup=TRUE){
+                            quietly_download=TRUE, cleanup=TRUE){
     if(!file.exists(filepath)){
-        pull_GMMs_file(filepath=filepath, version=version, quietly=quietly_download)
+        pull_GMMs_file(filepath=filepath, version=version,
+                        quietly=quietly_download)
     }
 
     GMM.fileconts <- readLines(filepath)
 
-    GMM.matrix <- matrix(data=c("KEGG","Module","Module ID"), nrow=1, ncol=3)
-    for(i in 1:length(GMM.fileconts)){
+    GMM.matrix <- matrix(data=c("KEGG", "Module", "Module ID"), nrow=1, ncol=3)
+    for(i in seq_len(length(GMM.fileconts))){
         line <- GMM.fileconts[i]
         # if new module, get its name and number
         if(grepl("^MF\\d{4}", line)){
@@ -65,7 +100,8 @@ get_GMM_matrix <- function(filepath="GMMs.txt", version="v1.07",
         }
         # If KO line, add that info to the matrix
         else if(grepl("^K\\d{5}", line)){
-            GMM.matrix <- add_K_line_to_matrix(GMM.matrix, line, mod.name, mod.number)
+            GMM.matrix <- .add_K_line_to_matrix(GMM.matrix, line, 
+                                                mod.name, mod.number)
         }
     }
 
@@ -78,7 +114,7 @@ get_GMM_matrix <- function(filepath="GMMs.txt", version="v1.07",
     GMM.matrix <- GMM.matrix[GMM.matrix$KEGG!="",]
 
     if(cleanup){
-        message(paste("Deleting", filepath))
+        message("Deleting ", filepath)
         file.remove(filepath)
     }
     return(GMM.matrix)