Figure Updates

README.md

@@ -35,7 +35,15 @@ This repository includes all the scripts written to produce figures in the paper
     ```
     $ bash bin/get_data.sh
     ```
-
+## Rebuild Extened Figures
+
+```{r}
+Rscript -e "rmarkdown::render('bin/citations-graphs.Rmd', output_dir = 'bin')"      # Extended Figure 1
+Rscript -e "rmarkdown::render('bin/survey-figure.Rmd', output_dir = 'bin')"         # Extended Figure 2
+Rscript -e "rmarkdown::render('bin/tools-graphs.Rmd', output_dir = 'bin')"          # Extended Figure 3
+Rscript -e "rmarkdown::render('bin/workflows-graphs.Rmd', output_dir = 'bin')"      # Extended Figure 4
+Rscript -e "rmarkdown::render('bin/tutorials-graphs.Rmd', output_dir = 'bin')"      # Extended Figure 5
+```
 
 
 

bin/citations-graphs.Rmd

@@ -39,12 +39,12 @@ library(patchwork)
 ## Input data
 
 ```{r}
-years   <- fread("https://raw.githubusercontent.com/usegalaxy-eu/microgalaxy_technical_paper_2024/refs/heads/main/results/citations/years.csv")
-methods <- fread("https://raw.githubusercontent.com/usegalaxy-eu/microgalaxy_technical_paper_2024/refs/heads/main/results/citations/methods.csv")
-target_technical <- fread("https://raw.githubusercontent.com/usegalaxy-eu/microgalaxy_technical_paper_2024/refs/heads/main/results/citations/technical_target.csv")
-target_organisms <- fread("https://raw.githubusercontent.com/usegalaxy-eu/microgalaxy_technical_paper_2024/refs/heads/main/results/citations/targeted_organisms.csv")
+years            <- fread("https://raw.githubusercontent.com/usegalaxy-eu/microgalaxy_paper_2025/refs/heads/main/results/citations/years.csv")
+methods          <- fread("https://raw.githubusercontent.com/usegalaxy-eu/microgalaxy_paper_2025/refs/heads/main/results/citations/methods.csv")
+target_technical <- fread("https://raw.githubusercontent.com/usegalaxy-eu/microgalaxy_paper_2025/refs/heads/main/results/citations/technical_target.csv")
+target_organisms <- fread("https://raw.githubusercontent.com/usegalaxy-eu/microgalaxy_paper_2025/refs/heads/main/results/citations/targeted_organisms.csv")
 
-years$year <- seq(2005, 2025)
+years$year <- seq(2005, 2026)
 years <- years |> melt(id.vars = "year", value.factor = FALSE, variable.factor = FALSE)
 years$variable <- years$variable |> str_to_title()
 
@@ -70,15 +70,15 @@ gr1 <- years |>
     ggplot(aes(year, value)) +
 
     geom_point(aes(fill = variable), color = "grey25", 
-               shape = 21, size = 5.5, stroke = .25, 
+               shape = 21, size = 5.3, stroke = .25, 
                position = position_dodge(width = .9)) +
 
     geom_col(aes(fill = variable), color = "grey25", 
              linewidth = .15, 
              position = position_dodge(width = .9)) +
 
     geom_point(aes(color = variable),
-               size = 4.85,
+               size = 4.65,
                position = position_dodge(width = .9)) +
 
     scale_x_continuous(expand = c(0, 0)) +
@@ -138,7 +138,7 @@ gr2 <- p0 |>
 
         strip.text = element_text(face = "bold"),
 
-        axis.title.x = element_text(margin = margin(t = 10)),
+        axis.title.x = element_blank(), # element_text(margin = margin(t = 10)),
         axis.title.y = element_markdown(margin = margin(r = 10))
     ) +
 
@@ -157,22 +157,22 @@ multi <- (gr1 / gr2) +
 
 
 ```{r}
-outfolder <- "../results/citations/"
+outfolder <- "../docs/extended/"
 
 dir.create(outfolder, showWarnings = FALSE)
 
 ggsave(
-    plot = multi, filename = paste0(outfolder, "/citations.png"),
+    plot = multi, filename = paste0(outfolder, "/extended_figure_1.png"),
     width = 9, height = 10, units = "in", dpi = 600
 )
 
 ggsave(
-    plot = multi, filename = paste0(outfolder, "/citations.svg"),
+    plot = multi, filename = paste0(outfolder, "/extended_figure_1.svg"),
     width = 9, height = 10, units = "in", dpi = 600
 )
 
 ggsave(
-    plot = multi, filename = paste0(outfolder, "/citations.pdf"),
+    plot = multi, filename = paste0(outfolder, "/extended_figure_1.pdf"),
     width = 9, height = 10, units = "in", device = cairo_pdf
 )
 

bin/survey-figure.Rmd

@@ -19,7 +19,7 @@ library(stringr)
 ## Input data 
 
 ```{r}
-df <- "https://raw.githubusercontent.com/paulzierep/microgalaxy-survey/refs/heads/main/data/modified_answers.csv" |> fread()
+df <- "https://raw.githubusercontent.com/usegalaxy-eu/microgalaxy_technical_paper_2024/refs/heads/main/docs/supplementary/supplementary_table_2.tsv" |> fread()
 ```
 
 ### Correct column names 
@@ -221,6 +221,7 @@ library(ggh4x)
 
 library(shadowtext)
 
+library(paletteer)
 library(tidytext)
 ```
 
@@ -299,13 +300,13 @@ gr <- df_plot |>
 ```{r}
 # dir.create("survey-figure", showWarnings = FALSE)
 
-outfolder <- "../results/survey"
+outfolder <- "../docs/extended/"
 
 dir.create(outfolder, showWarnings = FALSE)
 
-ggsave(plot = gr, filename = paste0(outfolder, "/survey-results.png"), width = 9, height = 10, units = "in", dpi = 600)
-ggsave(plot = gr, filename = paste0(outfolder, "/survey-results.pdf"), width = 9, height = 10, units = "in", device = cairo_pdf)
-ggsave(plot = gr, filename = paste0(outfolder, "/survey-results.svg"), width = 9, height = 10, units = "in")
+ggsave(plot = gr, filename = paste0(outfolder, "/extended_figure_2.png"), width = 9, height = 10, units = "in", dpi = 600)
+ggsave(plot = gr, filename = paste0(outfolder, "/extended_figure_2.pdf"), width = 9, height = 10, units = "in", device = cairo_pdf)
+ggsave(plot = gr, filename = paste0(outfolder, "/extended_figure_2.svg"), width = 9, height = 10, units = "in")
 ```