From db120d5f489ae41702037b6224c7bdd800164d14 Mon Sep 17 00:00:00 2001
From: pcastellanoescuder <polcaes@gmail.com>
Date: Fri, 15 Dec 2023 14:42:05 -0500
Subject: [PATCH] annotate pubmed table

---
 DESCRIPTION              |  3 ++-
 NAMESPACE                |  1 +
 R/helper.R               | 18 ++++++++++++++++++
 R/tables.R               | 15 +++++++++++++--
 man/make_pubmed_table.Rd |  3 ++-
 man/pubmed_title.Rd      | 14 ++++++++++++++
 6 files changed, 50 insertions(+), 4 deletions(-)
 create mode 100644 man/pubmed_title.Rd

diff --git a/DESCRIPTION b/DESCRIPTION
index 665407c..89a7c74 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: ddh
 Type: Package
 Title: Utility Functions and Data Sets for Data-driven Hypothesis
-Version: 0.3.19
+Version: 0.3.20
 Authors@R: c(
     person(given = "Matthew",
            family = "Hirschey",
@@ -58,6 +58,7 @@ Imports:
     rayvertex,
     remotes,
     rlang,
+    rvest,
     scales,
     stringr,
     tibble,
diff --git a/NAMESPACE b/NAMESPACE
index 64e6b06..3aaa172 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -105,6 +105,7 @@ export(make_tissue)
 export(make_top_table)
 export(make_umap_plot)
 export(plot_size_finder)
+export(pubmed_title)
 export(scale_color_ddh_c)
 export(scale_color_ddh_d)
 export(scale_fill_ddh_c)
diff --git a/R/helper.R b/R/helper.R
index a4c0cde..97b7cf9 100644
--- a/R/helper.R
+++ b/R/helper.R
@@ -889,3 +889,21 @@ good_file_namer <- function(input = list){
   }
   return(good_file_name)
 }
+
+#' Extract PubMed Title from PubMed ID
+#'
+#' @param pmid PubMed ID
+#'
+#' @export
+pubmed_title <- function(pmid) {
+  paper_url <- glue::glue("https://pubmed.ncbi.nlm.nih.gov/{pmid}/")
+
+  paper_title <- rvest::read_html(paper_url) %>%
+    rvest::html_nodes("title") %>%
+    rvest::html_text()
+
+  paper_title <- gsub(" - PubMed", "", paper_title[1])
+
+  return(paper_title)
+}
+
diff --git a/R/tables.R b/R/tables.R
index bba3cb1..bcf3bea 100644
--- a/R/tables.R
+++ b/R/tables.R
@@ -108,10 +108,11 @@ make_compound_table <- function(input = list(),
 #' @export
 #' @examples
 #' make_pubmed_table(input = list(type = 'gene', content = 'ROCK1'))
+#' make_pubmed_table(input = list(type = 'gene', content = 'ROCK1'), title = TRUE)
 #' \dontrun{
 #' make_pubmed_table(input = list(type = 'gene', content = 'ROCK1'))
 #' }
-make_pubmed_table <- function(input = list()) {
+make_pubmed_table <- function(input = list(), n_papers = 10, title = FALSE) {
   make_pubmed_table_raw <- function() {
     pubmed_table <-
       get_data_object(object_name = input$content,
@@ -119,8 +120,18 @@ make_pubmed_table <- function(input = list()) {
                       pivotwider = TRUE) %>%
       dplyr::mutate(year = as.numeric(year),
                     pmid = as.numeric(pmid)) %>%
-      dplyr::arrange(as.numeric(pmid)) %>%
+      dplyr::arrange(dplyr::desc(year)) %>%
+      dplyr::slice(1:n_papers) %>%
       dplyr::select(id, pmid, year, pmcid)
+
+    if (title) {
+      pubmed_table <- pubmed_table %>%
+        dplyr::rowwise() %>%
+        dplyr::mutate(Title = pubmed_title(pmid)) %>%
+        dplyr::ungroup() %>%
+        dplyr::relocate(Title, .after = pmid)
+    }
+
     return(pubmed_table)
   }
   #error handling
diff --git a/man/make_pubmed_table.Rd b/man/make_pubmed_table.Rd
index ea65f7d..995f024 100644
--- a/man/make_pubmed_table.Rd
+++ b/man/make_pubmed_table.Rd
@@ -4,7 +4,7 @@
 \alias{make_pubmed_table}
 \title{Pubmed Table}
 \usage{
-make_pubmed_table(input = list())
+make_pubmed_table(input = list(), n_papers = 10, title = FALSE)
 }
 \arguments{
 \item{input}{Expecting a list containing type and content variable.}
@@ -20,6 +20,7 @@ This is a table function that takes a gene name and returns a pubmed Table
 }
 \examples{
 make_pubmed_table(input = list(type = 'gene', content = 'ROCK1'))
+make_pubmed_table(input = list(type = 'gene', content = 'ROCK1'), title = TRUE)
 \dontrun{
 make_pubmed_table(input = list(type = 'gene', content = 'ROCK1'))
 }
diff --git a/man/pubmed_title.Rd b/man/pubmed_title.Rd
new file mode 100644
index 0000000..248c5df
--- /dev/null
+++ b/man/pubmed_title.Rd
@@ -0,0 +1,14 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/helper.R
+\name{pubmed_title}
+\alias{pubmed_title}
+\title{Extract PubMed Title from PubMed ID}
+\usage{
+pubmed_title(pmid)
+}
+\arguments{
+\item{pmid}{PubMed ID}
+}
+\description{
+Extract PubMed Title from PubMed ID
+}