figure scripts updates

scripts/plot_figure_1_questions.R

@@ -142,7 +142,7 @@ if ( both ){
 }
 
 if (refs && both && tricolor){
-    file_to_save <- "figures/SM_Figure_1_genomic_studies.pdf"
+    file_to_save <- "figures/SM_Figure_3_genomic_studies.pdf"
 }
 
 pdf(file_to_save, width = 8, height = height, pointsize = 8)

scripts/plot_figure_2_heterozygosity.R

@@ -128,7 +128,7 @@ plot_corpus <- function(presentation = F){
     axis(1, labels = hyb_origins, at = 1:3, tick = F, line = F, cex.axis = general_cex)
 
     # Apis elipse
-    filledellipse(rx1 = 0.15, ry1 = 1.5, col = ellipse_col, angle = 0, dr = 0.1, mid = c(1.24, 1.5))
+    filledellipse(rx1 = 0.13, ry1 = 1.4, col = ellipse_col, angle = 0, dr = 0.1, mid = c(1.28, 1.5))
     if ( presentation & !split_axis ) {
       filledellipse(rx1 = 3.5, ry1 = 0.21, col = ellipse_col, angle = 90.8, dr = 0.1, mid = c(1.97, 9.3))
       filledellipse(rx1 = 3.8, ry1 = 0.2, col = ellipse_col, angle = 87.5, dr = 0.1, mid = c(3.13, 6))
@@ -148,11 +148,11 @@ plot_corpus <- function(presentation = F){
     }
     if ( split_axis ){
         if ( homoeolog ){
-            filledellipse(rx1 = 3.6, ry1 = 0.28, col = ellipse_col, angle = 90, dr = 0.1, mid = c(2.05, 14.55))
+            filledellipse(rx1 = 3.6, ry1 = 0.28, col = ellipse_col, angle = 90, dr = 0.1, mid = c(2.15, 14.55))
             # Meloidogyne
-            filledellipse(rx1 = 3.8, ry1 = 0.24, col = ellipse_col, angle = 86.5, dr = 0.1, mid = c(3.17, 6))
+            filledellipse(rx1 = 3.9, ry1 = 0.22, col = ellipse_col, angle = 88, dr = 0.1, mid = c(3.12, 6))
             # diploscapter
-            filledellipse(rx1 = 0.16, ry1 = 1.3, col = ellipse_col, angle = 0, dr = 0.1, mid = c(2.67, 4.6))
+            filledellipse(rx1 = 0.098, ry1 = 1.8, col = ellipse_col, angle = 0, dr = 0.1, mid = c(2.77, 5.5))
         } else {
             filledellipse(rx1 = 6.5, ry1 = 0.25, col = ellipse_col, angle = 90, dr = 0.1, mid = c(2.06, 17.5))
         }
@@ -180,9 +180,9 @@ plot_corpus <- function(presentation = F){
            c("gamete duplication",
              "terminal fusion",
              "central fusion",
-             "unknown meiosis",
+             "unknown meiotic",
              "unknown",
-             "functional mitosis"),
+             "functional mitotic"),
            col = pal, pch = c(rep(20,6)), cex = ifelse(presentation, 1.5, 1.2))
     # legend('topleft', bty = 'n',
     #        c("gamete duplication", "terminal fusion", "central fusion", "unknown automixis", "unknown", "functional apomixis",
@@ -198,6 +198,10 @@ plot_ploits <- function(hyb_origin = "no", presentation = F){
     subset <- subset[order(subset$callular_mechanism),]
     subset <- subset[!is.na(subset$heterozygosity),]
 
+    if (hyb_origin == "yes"){
+        subset <- subset[c(2,1,5,3,6:9,4),]
+    }
+
     at <- which(hyb_origin == hyb_origins)
     misplacement <- seq(from = -0.45, to = 0.45, length = nrow(subset) + 2)[2:(nrow(subset)+1)]
     # symbols <- c(NA, 19, 17, 15)
@@ -259,7 +263,7 @@ if ( homoeolog ){
 
     misplacement <- seq(from = -0.45, to = 0.45, length = unknown_repr + 2)[2:(unknown_repr+1)]
     print(misplacement)
-    xpos <- 2 + misplacement[c(4,5,6,7)]
+    xpos <- 2 + misplacement[c(5:8)]
     # symbols <- c(NA, 19, 17, 15)
     # conture_symbols <- c(NA, 21, 24, 22)
     rotifers_to_plot <- rotifers_ohno - (g_to - g_from)

scripts/plot_figure_S4_expected_heterozygosity_structure.R → scripts/plot_figure_S6_expected_heterozygosity_structure.R

@@ -24,7 +24,7 @@ total_heterozygosities <- seq(0, 8, len = 100)
 triallelic_exp <- sapply(total_heterozygosities, get_exp_triallelic)
 
 # tiff("figures/supp_fig4_expected_triallelic.tiff", width = 800, height = 600, 'px', res = 100, compression = 'rle')
-pdf("figures/SM_Figure_4_expected_triallelic.pdf", width = 8, height = 6)
+pdf("figures/SM_Figure_6_expected_triallelic.pdf", width = 8, height = 6)
 
 plot(triallelic_exp ~ total_heterozygosities,
      xlab = 'Heterozygosity [%]',

scripts/plot_figure_S7_TEs_vs_mode_and_origin.R → scripts/plot_figure_S8_TEs_vs_mode_and_origin.R

@@ -94,7 +94,7 @@ plot_ploits <- function(hyb_origin = "no", .var = "repeats"){
 ####
 plot_tab <- genome_tab[!is.na(genome_tab$TEs),]
 
-tiff("figures/SM_Figure_7_TEs.tiff",
+tiff("figures/SM_Figure_8_TEs.tiff",
      width = 8, height = 8, units = 'in', res = 90)
 # # png('figures/Supp_fig2b_TEs.png')
 

scripts/print_values_for_manu.R

@@ -8,15 +8,27 @@ tab_file <- 'tables/genome_table.tsv'
 genome_tab <- read.table(tab_file, header = T, stringsAsFactors = F, skip = 1, check.names = F)
 
 # get unique species
-genome_tab <- genome_tab[!genome_tab$code %in% c('Ps591', 'Ps791', 'Dpul1', 'Dpul2', 'Dpul3', 'Dpul4', 'Mjav1', 'Mare1', 'Mare3', 'Minc1'),]
+genome_tab <- genome_tab[!genome_tab$code %in% c('Ps591', 'Ps791', 'Dpul1', 'Dpul4', 'Mjav1', 'Mare1', 'Mare3', 'Minc1'),]
 
 diploids <- genome_tab$ploidy == 2 & !is.na(genome_tab$ploidy)
 otherploids <- genome_tab$ploidy != 2 & !is.na(genome_tab$ploidy)
 
 number_of_species <- length(unique(genome_tab$species))
 
+genome_tab$callular_mechanism[is.na(genome_tab$callular_mechanism)] <- "unknown"
+genome_tab$hybrid_origin[is.na(genome_tab$hybrid_origin)] <- "unknown"
+cellular_mechs <- aggregate(callular_mechanism ~ species, data=genome_tab, FUN=function(x){x[1]})
+
+mitotic_parth <- genome_tab[genome_tab$callular_mechanism == 'functional_apomixis',]
+table(aggregate(ploidy ~ species, data=mitotic_parth, FUN=function(x){x[1]})$ploidy)
+
+meiotic_parth <- genome_tab[!genome_tab$callular_mechanism %in% c('functional_apomixis', 'unknown'),]
+table(aggregate(ploidy ~ species, data=meiotic_parth, FUN=function(x){x[1]})$ploidy)
+
+hybrid_orig <- aggregate(hybrid_origin ~ species, data=genome_tab, FUN=function(x){x[1]})
+
 # # genomes
-cat("Number of reanalyzed genomes: ", number_of_species, "\n")
+cat("Number of reanalyzed species: ", number_of_species, "\n")
 
 # genome sizes
 cat("Range of haploid sizes [Mbp]:", paste(range(c(genome_tab[,'assembly_size[M]'], genome_tab[,'haploid_length[M]']), na.rm=T)), "\n")