Create a new .R file to plot figures for the paper

data-raw/data_prep.R

@@ -47,46 +47,3 @@ ufrj_bio_0122 <- lapply(df_list, function(df) {
 
 #Saving as package data
 usethis::use_data(ufrj_bio_0122, compress = 'xz')
-
-
-
-#Generating a venn diagram that show the intersects calculated in each round of pairwise comparisons (at first, this image will only be displayed in the paper)
-
-#Source: https://stackoverflow.com/questions/72651478/how-do-i-make-certain-regions-of-of-my-venn-diagram-colored-and-have-the-rest-bl
-
-library(ggVennDiagram)
-library(ggplot2)
-
-test_data = list(A = 1:1, B = 1:1, C = 1:1, D = 1:1)
-
-p <- ggVennDiagram(test_data, label_size = 15,
-                   set_size = 15, label_alpha = 0) +
-  scale_color_manual(values = rep("black", 4))
-
-#Names to be plotted instead of intersection counts
-new_names <-c('A', 'B', 'C', 'D',
-              'AB', 'AC', 'AD', 'BC', 'BD', 'CD',
-              'ABC', 'ABD', 'ACD', 'BCD',
-              'ABCD')
-
-p$layers[[1]]$mapping <- aes(fill = name) #Each name (intersection) can have an associated color now
-p$layers[[4]]$data$both <- new_names #Changing 'both' data column to have the intersect names, which will then be plotted instead
-
-
-p + scale_fill_manual(values = c(A = 'red',
-                                 A..B = 'red',
-                                 A..C = 'red',
-                                 A..D = 'red',
-                                 A..B..C = 'red',
-                                 A..B..D = 'red',
-                                 A..C..D = 'red',
-                                 A..B..C..D = 'red',
-                                 B = 'blue',
-                                 B..C = 'blue',
-                                 B..D = 'blue',
-                                 B..C..D = 'blue',
-                                 C = 'darkgreen',
-                                 C..D = 'darkgreen',
-                                 D = 'darkgreen'
-) ) + #Specifying a color for each intersect
-  theme(legend.position = '') #removing legend

data-raw/paper_figs.R

@@ -0,0 +1,97 @@
+############## Figures for the biblioverlap paper ###################
+
+library(ggVennDiagram) #Need to load ggVennDiagram first because it masks `plot_venn` and `plot_upset` functions from biblioverlap
+library(biblioverlap)
+library(dplyr)
+library(ggplot2)
+library(patchwork)
+
+################ Running biblioverlap for example dataset ################
+results <- biblioverlap(ufrj_bio_0122)
+db_list <- results$db_list
+
+
+################ Getting biblioverlap's plots ###########################
+plot_matching_summary(results$summary, add_logo = FALSE)
+plot_venn(db_list, add_logo = FALSE) #gets masked when loading ggVennDiagram alongside biblioverlap
+plot_upset(db_list, add_logo = FALSE) #gets masked when loading ggVennDiagram alongside biblioverlap
+
+
+############### Generating a venn diagram that show the intersects calculated in each round of pairwise comparisons ###########################
+#Source: https://stackoverflow.com/questions/72651478/how-do-i-make-certain-regions-of-of-my-venn-diagram-colored-and-have-the-rest-bl
+
+test_data = list(A = 1:1, B = 1:1, C = 1:1, D = 1:1)
+
+p <- ggVennDiagram(test_data, label_size = 15,
+                   set_size = 15, label_alpha = 0) +
+  scale_color_manual(values = rep("black", 4))
+
+#Names to be plotted instead of intersection counts
+new_names <-c('A', 'B', 'C', 'D',
+              'AB', 'AC', 'AD', 'BC', 'BD', 'CD',
+              'ABC', 'ABD', 'ACD', 'BCD',
+              'ABCD')
+
+p$layers[[1]]$mapping <- aes(fill = name) #Each name (intersection) can have an associated color now
+p$layers[[4]]$data$both <- new_names #Changing 'both' data column to have the intersect names, which will then be plotted instead
+
+
+p + scale_fill_manual(values = c(A = 'red',
+                                 A..B = 'red',
+                                 A..C = 'red',
+                                 A..D = 'red',
+                                 A..B..C = 'red',
+                                 A..B..D = 'red',
+                                 A..C..D = 'red',
+                                 A..B..C..D = 'red',
+                                 B = 'blue',
+                                 B..C = 'blue',
+                                 B..D = 'blue',
+                                 B..C..D = 'blue',
+                                 C = 'darkgreen',
+                                 C..D = 'darkgreen',
+                                 D = 'darkgreen'
+) ) + #Specifying a color for each intersect
+  theme(legend.position = '') #removing legend
+
+
+########### Generating venn diagrams for subsets of the data ##################
+
+#Open access docs
+open_access_docs <- lapply(db_list, function(db) {
+  filter(db, !(`Open Access Colour` %in% c('', 'unknown')))
+})
+open_access <- plot_venn(open_access_docs, add_logo = FALSE, label = c("count")) +
+  labs(title = 'Open Access') +
+  theme(plot.title = element_text(size = 15, hjust = 0.5),
+        legend.position = 'none')
+
+#Closed access docs
+closed_access_docs <- lapply(db_list, function(db) {
+  filter(db, `Open Access Colour` == '')
+})
+closed_access <- plot_venn(closed_access_docs, add_logo = FALSE, label = c("count")) +
+  labs(title = 'Closed Access') +
+  theme(plot.title = element_text(size = 15, hjust = 0.5),
+        legend.position = 'none')
+
+#Docs 10 or more citações
+i10_docs <- lapply(db_list, function(db) {
+  filter(db, `Citing Works Count` >= 10)
+})
+i10 <- plot_venn(i10_docs, add_logo = FALSE, label = c("count")) +
+  labs(title = '10 or more citations') +
+  theme(plot.title = element_text(size = 15, hjust = 0.5),
+        legend.position = 'none')
+
+#Preprints
+preprint_docs <- lapply(db_list, function(db) {
+  filter(db, `Publication Type` == 'preprint')
+})
+preprints <- plot_venn(preprint_docs, add_logo = FALSE, label = c("count")) +
+  labs(title = 'Preprints') +
+  theme(plot.title = element_text(size = 15, hjust = 0.5),
+        legend.position = 'none')
+
+
+open_access + closed_access + i10 + preprints + plot_annotation(tag_levels = 'A')