annotate pubmed table

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,

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)

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)
+}
+

R/tables.R

@@ -108,19 +108,30 @@ 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,
                       dataset_name = "universal_pubmed",
                       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