Merge pull request #26 from waldronlab/16-update-student-vignettes-with-modern-analyses

16 update student vignettes with modern analyses

Author: cmirzayi

DESCRIPTION

@@ -1,12 +1,12 @@
 Package: bugSigSimple
-Version: 0.99.5
+Version: 0.99.6
 Date: 2022-03-07
 Title: Simple exploratory analysis of curated microbe signatures 
 Authors@R: c(person("Ludwig", "Geistlinger", email = "[email protected]", role = c("aut", "cre")),
     person("Chloe", "Mirzayi", email = "[email protected]", role = c("aut")),
     person("Fatima", "Zohra", email = "[email protected]", role = "aut"),
     person("Levi", "Waldron", email = "[email protected]", role = "aut"))
-Maintainer: Ludwig Geistlinger <ludwig.geistlinger@sph.cuny.edu>
+Maintainer: Chloe Mirzayi <chloe.mirzayi@sph.cuny.edu>
 Depends: R(>= 4.1.0)
 Imports: 
     curatedMetagenomicData,
@@ -31,12 +31,15 @@ Imports:
 Suggests: 
     BiocStyle, 
     knitr,
-    rmarkdown
+    rmarkdown,
+    broom,
+    jtools
 Remotes:
     waldronlab/BugSigDBStats,
     waldronlab/bugsigdbr
 Description: bugSigSimple provides simple exploratory analysis of curated microbe signatures from bugsigdb.org.
 License: Artistic-2.0
 VignetteBuilder: knitr
-RoxygenNote: 7.1.2
+RoxygenNote: 7.3.2
+Encoding: UTF-8
 URL: https://waldronlab.io/bugSigSimple

NAMESPACE

@@ -14,18 +14,21 @@ importFrom(dplyr,filter)
 importFrom(dplyr,first)
 importFrom(dplyr,group_by)
 importFrom(dplyr,mutate)
+importFrom(dplyr,n)
 importFrom(dplyr,n_distinct)
+importFrom(dplyr,reframe)
 importFrom(dplyr,relocate)
 importFrom(dplyr,rename)
 importFrom(dplyr,rowwise)
-importFrom(dplyr,summarize)
+importFrom(dplyr,select)
 importFrom(dplyr,ungroup)
 importFrom(kableExtra,kable_styling)
 importFrom(kableExtra,kbl)
 importFrom(stats,binom.test)
 importFrom(stats,quantile)
 importFrom(stringr,str_extract)
 importFrom(stringr,str_replace)
+importFrom(tidyr,all_of)
 importFrom(tidyr,separate)
 importFrom(utils,head)
 importFrom(utils,relist)

R/describe_curation.R

@@ -3,12 +3,14 @@
 #' @param dat data.frame produced by \link[bugsigdbr]{importBugSigDB}, subsetted as desired
 #' @param n number of taxa to return (if sig.type=="both", this is the number of taxa to return for each direction)
 #'
-#' @importFrom dplyr filter %>% mutate rowwise n_distinct group_by relocate rename first ungroup across
+#' @importFrom dplyr filter %>% mutate rowwise n_distinct group_by relocate rename first ungroup across n
 #' @importFrom utils relist head
 #' @importFrom stats quantile binom.test
 #' @importFrom kableExtra kbl kable_styling
 #' @importFrom tidyr separate
 #' @importFrom stringr str_replace str_extract
+#' @importFrom bugsigdbr getSignatures
+#' 
 #' @return kable table with increased and decreased taxa and a binomial test based on total number of studies in the data.frame
 #' @export
 #'
@@ -23,7 +25,7 @@ createTaxonTable <- function(dat, n=10){
     data.frame(getMostFrequentTaxa(dat, sig.type = "both", n = n),
                stringsAsFactors = FALSE) %>%
     mutate(metaphlan_name = Var1) %>%
-    tidyr::separate(
+    separate(
       col = Var1,
       sep = "\\|",
       into = dmap,
@@ -48,7 +50,7 @@ createTaxonTable <- function(dat, n=10){
       .countTaxon(dat = dat, x = x, direction = "decreased"))) %>%
     mutate(Taxon = gsub(".+\\|", "", output$metaphlan_name))
 
-    output %>% tidyr::separate(col="Taxon", into=c("Taxonomic Level", "Taxon Name"), sep="__") %>%
+    output %>% separate(col="Taxon", into=c("Taxonomic Level", "Taxon Name"), sep="__") %>%
     mutate(`Taxonomic Level` = unname(dmap[`Taxonomic Level`])) %>%
     rowwise() %>%    
     mutate( `Binomial Test pval` = .createBinomTestSummary(increased_signatures, total_signatures, wordy = FALSE)) %>%
@@ -60,7 +62,7 @@ createTaxonTable <- function(dat, n=10){
   if (direction[1] %in% c("increased", "decreased")){
     dat <- filter(dat, `Abundance in Group 1` == direction[1])
   }
-  allnames <- bugsigdbr::getSignatures(dat, tax.id.type = "metaphlan")
+  allnames <- getSignatures(dat, tax.id.type = "metaphlan")
   sum(vapply(allnames, function(onesignames) x %in% onesignames, FUN.VALUE = 1L))
 }
 
@@ -86,22 +88,23 @@ createTaxonTable <- function(dat, n=10){
 
 #' Create a table of all studies currently in data.frame
 #'
-#' @param dat data.frame produced by \link[bugsigdbr]{importBugSigDB}, subsetted as desired
+#' @param bsdb.df \code{data.frame} produced by \link[bugsigdbr]{importBugSigDB}, pre-filtered as desired
+#' @param includeAlso \code{character} with column names to additionally include in the output table (default = `NULL`)
 #'
-#' @importFrom dplyr group_by summarize  %>%
+#' @importFrom dplyr group_by %>% select relocate reframe across n
+#' @importFrom tidyr all_of
 #' @importFrom kableExtra kbl kable_styling
 #' @return a data.frame of basic study information. Can be wrapped in 
-#' kable_styling(kbl(.)) to format nicely.
+#' kable_styling(kbl(...)) to format nicely.
 #' @export
 #'
 #' @examples
 #' full.dat <- bugsigdbr::importBugSigDB()
 #' createStudyTable(full.dat)
-#' ## kable_styling(kbl(createStudyTable(full.dat))) #for html styling
 
 createStudyTable <- function(bsdb.df, includeAlso = NULL) {
   # input check
-  if (!is_null(includeAlso)) {
+  if (!is.null(includeAlso)) {
     if (!all(includeAlso %in% colnames(bsdb.df))) {
       stop(paste(
         "The following columns are not found in the input data frame:",
@@ -153,7 +156,18 @@ globalVariables(
     "Freq",
     "species",
     "kingdom",
-    "Var1"
+    "Var1",
+    # the following are necessary after the merged data
+    "Authors",
+    "Year",
+    "BasicID",
+    "PMID",
+    "URL",
+    "uniqueRank",
+    "Study code",
+    "Group 0 sample size",
+    "Group 1 sample size",
+    "N_signatures"
   )
 )
 

R/simple.R

@@ -87,6 +87,7 @@ getMostFrequentTaxa <- function(dat, n=10, sig.type=c("both", "increased", "decr
 #' more PMID codes associated with the same ID and adds a .1, .2, for each 
 #' duplication
 #' 
+#' @param bsdb.df \code{data.frame} produced by \link[bugsigdbr]{importBugSigDB}, pre-filtered as desired
 
 .make_unique_study_ID <- function(bsdb.df){
   bsdb_with_StudyCode <- bsdb.df %>% 

man/createStudyTable.Rd

@@ -42,7 +42,7 @@ suppressPackageStartupMessages({
 
 ```{r}
 # use version="devel" and cache = FALSE to take the latest version from bugsigdb.org
-dat <- bugsigdbr::importBugSigDB(version = "devel", cache = FALSE) 
+dat <- bugsigdbr::importBugSigDB(cache = FALSE) 
 dim(dat)
 names(dat)
 ```
@@ -85,6 +85,7 @@ subset.final <-
   filter(`Body site` == "Meconium") %>%
   arrange(PMID)
 ```
+
 Show key characteristics of the included signatures:
 
 ```{r}
@@ -107,13 +108,17 @@ sort(setdiff(subset.dat$PMID, subset.final$PMID))
 # Table of studies
 
 These are the studies included in the review:
+
 ```{r}
-bugSigSimple::createStudyTable(subset.final)
+createStudyTable(subset.final) %>% 
+  kbl() %>% 
+  kable_styling()
 ```
 
 # Summary of taxa reported
 
 This table summarizes the results for the top `n` most frequently identified taxa.
+
 ```{r}
 kable_styling(kbl(bugSigSimple::createTaxonTable(subset.final, n = 20)))
 ```