v7.5.0 release: Ok up to the plot_insertion process, tested using the test file

README.md

@@ -198,6 +198,11 @@ Gitlab developers
 
 ## WHAT'S NEW IN
 
+### v7.5.0
+
+1) Ok up to the plot_insertion process, tested using the test file
+
+
 ### v7.4.0
 
 1) Ok up to global logo, tested using the test file

bin/plot_insertion.R

@@ -113,7 +113,7 @@ rm(tempo.cat)
 # window_size <- "50000 200000"
 # step <- "100"
 # file_name <- "test.fastq2"
-# cute <- "https://gitlab.pasteur.fr/gmillot/cute_little_R_functions/-/raw/v10.9.0/cute_little_R_functions.R"
+# cute <- "https://gitlab.pasteur.fr/gmillot/cute_little_R_functions/-/raw/v11.0.0/cute_little_R_functions.R"
 # log <-  "plot_insertion_report.txt"
 
 
@@ -423,7 +423,7 @@ if(ncol(obs.freq) > 0){
         line.size = 3, 
         color = fun_gg_palette(n = 7, kind = "dark")[6], # fun_gg_palette(n = 2) # fun_gg_palette(n = 2)[1]
         legend.width = 0, 
-        title = "TOTAL ZOOMED", 
+        title = "TOTAL", 
         x.lab = "Insertion number", 
         x.left.extra.margin = 0.05, 
         y.top.extra.margin = 0.05, 
@@ -452,7 +452,7 @@ if(ncol(obs.freq) > 0){
         line.size = 3, 
         color = fun_gg_palette(n = 7, kind = "dark")[6], # fun_gg_palette(n = 2) # fun_gg_palette(n = 2)[1]
         legend.width = 0, 
-        title = "TOTAL", 
+        title = "TOTAL ZOOMED", 
         x.lab = "Insertion number", 
         x.left.extra.margin = 0.05, 
         x.right.extra.margin = 0.05, 
@@ -603,6 +603,7 @@ for(i0 in window_size){
 
     if(ncol(total) > 0){
         # graph of total frequency
+        pdf(file = NULL) # send plots into a NULL file, no pdf file created. It is to draw the plot but then to save it using ggsave()
         res <- fun_gg_scatter(data1 = list(structure, total), 
         x = list("x", "center"), 
         y = list("y", "value"), 
@@ -613,13 +614,13 @@ for(i0 in window_size){
         dot.size = 0.7, 
         line.size = 1, 
         x.lab = xlab, 
-        x.lim = xlim, 
+        x.lim = c(0, genome_size), 
         x.tick.nb = 6, 
         x.second.tick.nb = 3, 
         x.left.extra.margin = 0, 
         x.right.extra.margin = 0, 
         y.lab = "Number of insertion sites", 
-        y.lim = ylim, 
+        y.lim = NULL, 
         y.tick.nb = 6, 
         y.second.tick.nb = 3, 
         y.top.extra.margin = 0, 
@@ -632,9 +633,9 @@ for(i0 in window_size){
         title.text.size = 7, 
         return = TRUE
         )
-        ggplot2::ggsave(paste0("total_insertion_site_freq_", i0, ".png"), plot = res$gtable, device = "png", width = 5000, height = 1800, units = "px", res = 300)
+        ggplot2::ggsave(paste0("plot_", file_name, "_insertion_bin_", i0, ".png"), plot = res$gtable, device = "png", width = 16.6, height = 6, units = "in", dpi = 300) # width = 5000, height = 1800, units = "px" normally but "px" not accepted in the r_ext container
     }else{
-        png(filename = paste0("total_insertion_site_freq_", i0, ".png"), width = 5000, height = 1800, units = "px", res = 300)
+        png(filename = paste0("plot_", file_name, "_insertion_bin_", i0, ".png"), width = 5000, height = 1800, units = "px", res = 300)
         fun_gg_empty_graph(text = "EMPTY pos FILE: NO PLOT DRAWN")
     }
 }

main.nf

@@ -1006,11 +1006,12 @@ process plot_insertion { // sections 24.7.2 and 45 of the labbook 20200520
 ![Figure 23: Raw insertion frequencies.](./figures/plot_${file_name}_insertion_raw.png){width=600}
 \\n\\n</center>\\n\\n<br /><br />\\n\\n
     ' >> report.rmd
-    count=0
+    echo -e "\\n\\n<br /><br />\\n\\n####  Binned frequencies\\n\\n" >> report.rmd
+    count=1
     for i in $window_size ; do
         echo -e '
 \\n\\n<br /><br />\\n\\n</center>\\n\\n
-![Figure \'\$((23 + \$count))\': \'\${i}\'](./figures/plot_${file_name}_insertion_bin_\'\${i}\'png){width=600}
+![Figure \'\$((23 + \$count))\': \'\${i}\'](./figures/plot_${file_name}_insertion_bin_\'\${i}\'.png){width=600}
 \\n\\n</center>\\n\\n
         ' >> report.rmd
         count=\$((count + 1))

nextflow.config

@@ -60,7 +60,7 @@ env {
     motif_rev='A[AT]C' // the antiparallel of motif_fw
     window_size = "50000" // written as R vector, width of the sliding window on the reference genome in bp
     step=100 // steps of the sliding window on the reference genome in bp
-    cute_path="https://gitlab.pasteur.fr/gmillot/cute_little_R_functions/-/raw/v10.9.0/cute_little_R_functions.R" // single character string indicating the file (and absolute pathway) of the required cute_little_R_functions toolbox. With ethernet connection available, this can also be used: "https://gitlab.pasteur.fr/gmillot/cute_little_R_functions/raw/v5.1.0/cute_little_R_functions.R" or local "C:\\Users\\Gael\\Documents\\Git_projects\\cute_little_R_functions\\cute_little_R_functions.R"
+    cute_path="https://gitlab.pasteur.fr/gmillot/cute_little_R_functions/-/raw/v11.0.0/cute_little_R_functions.R" // single character string indicating the file (and absolute pathway) of the required cute_little_R_functions toolbox. With ethernet connection available, this can also be used: "https://gitlab.pasteur.fr/gmillot/cute_little_R_functions/raw/v5.1.0/cute_little_R_functions.R" or local "C:\\Users\\Gael\\Documents\\Git_projects\\cute_little_R_functions\\cute_little_R_functions.R"
 }
 
 //////// end variables that will be used only in the main.nf