changed name of plotting functions to avoid conflicts with ggVennDiagram

NAMESPACE

@@ -3,10 +3,10 @@
 export("%>%")
 export(biblioverApp)
 export(biblioverlap)
+export(matching_summary_plot)
 export(merge_input_files)
 export(merge_results)
-export(plot_matching_summary)
-export(plot_upset)
-export(plot_venn)
+export(upset_plot)
+export(venn_plot)
 importFrom(magrittr,"%>%")
 importFrom(rlang,.data)

R/06-plots_and_app.R

@@ -71,7 +71,7 @@ add_logo_to_plot <- function(plot,
 #' Extracting list of uuid columns from biblioverlap results
 #'
 #' @description
-#' Helper function to [plot_venn()] and [plot_upset()] that extracts overlapping data stored in the UUID column.
+#' Helper function to [venn_plot()] and [upset_plot()] that extracts overlapping data stored in the UUID column.
 #'
 #' @param db_list - list of matched dataframes (with UUID column added by biblioverlap)
 #'
@@ -103,9 +103,9 @@ get_uuid_list <- function(db_list) {
 #' biblioverlap_results$summary
 #'
 #' #Plotting the matching summary
-#' plot_matching_summary(biblioverlap_results$summary)
+#' matching_summary_plot(biblioverlap_results$summary)
 #'
-plot_matching_summary <- function(matching_summary_df, add_logo = TRUE, text_size = 15, ...) {
+matching_summary_plot <- function(matching_summary_df, add_logo = TRUE, text_size = 15, ...) {
   summary_plot <- matching_summary_df %>%
     ggplot2::ggplot(ggplot2::aes(x = .data$category, y = .data$n_docs, fill = .data$doc_subset)) +
     ggplot2::geom_bar(stat = 'identity', position = 'stack') +
@@ -137,9 +137,9 @@ plot_matching_summary <- function(matching_summary_df, add_logo = TRUE, text_siz
 #' lapply(biblioverlap_results$db_list, head, n=1)
 #'
 #' #Plotting the Venn diagram
-#' plot_venn(biblioverlap_results$db_list)
+#' venn_plot(biblioverlap_results$db_list)
 #'
-plot_venn <- function(db_list, add_logo = TRUE, ...) {
+venn_plot <- function(db_list, add_logo = TRUE, ...) {
   uuid <- get_uuid_list(db_list)
   venn <- ggVennDiagram::ggVennDiagram(uuid, ...) +
     ggplot2::scale_fill_gradient(low = "#A7C7E7", high = "#08306B") +
@@ -169,9 +169,9 @@ plot_venn <- function(db_list, add_logo = TRUE, ...) {
 #' lapply(biblioverlap_results$db_list, head, n=1)
 #'
 #' #Plotting the UpSet plot
-#' plot_upset(biblioverlap_results$db_list)
+#' upset_plot(biblioverlap_results$db_list)
 #'
-plot_upset <- function(db_list, add_logo = TRUE, ...) {
+upset_plot <- function(db_list, add_logo = TRUE, ...) {
   uuid <- get_uuid_list(db_list)
   upset <- UpSetR::upset(UpSetR::fromList(uuid),
                          main.bar.color = "#08306B",

README.Rmd

@@ -72,25 +72,25 @@ biblioverlap_results <- biblioverlap(ufrj_bio_0122, matching_fields = matching_c
 sapply(biblioverlap_results, class)
 ```
 
-The package also features some functions for plotting the results of `biblioverlap()`. For instance, the `plot_matching_summary()` function can be used to convert the summary of the matching procedure into a bar plot.
+The package also features some functions for plotting the results of `biblioverlap()`. For instance, the `matching_summary_plot()` function can be used to convert the summary of the matching procedure into a bar plot.
 
 ```{r matching_summary}
 #Plotting the matching results summary
-plot_matching_summary(biblioverlap_results$summary)
+matching_summary_plot(biblioverlap_results$summary)
 ```
 
-The `plot_venn()` function uses the UUID column to plot the results of the matching procedure as a Venn diagram. 
+The `venn_plot()` function uses the UUID column to plot the results of the matching procedure as a Venn diagram. 
 
 ```{r venn}
 #Plotting the Venn diagram
-plot_venn(biblioverlap_results$db_list)
+venn_plot(biblioverlap_results$db_list)
 ```
 
-Similarly, the `plot_upset()` function uses the UUID column to generate a UpSet plot, which is generally better for visualizing intersections between 5 or more datasets.
+Similarly, the `upset_plot()` function uses the UUID column to generate a UpSet plot, which is generally better for visualizing intersections between 5 or more datasets.
 
 ```{r upset}
 #Plotting the UpSet plot
-plot_upset(biblioverlap_results$db_list)
+upset_plot(biblioverlap_results$db_list)
 
 ```