diff --git a/R_scripts/eAED_files/eAED_statistics_Non-Annotated.txt b/R_scripts/eAED_files/eAED_statistics_Non-Annotated.txt
new file mode 100644
index 0000000..61f6a22
--- /dev/null
+++ b/R_scripts/eAED_files/eAED_statistics_Non-Annotated.txt
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diff --git a/R_scripts/eAED_statistics.R b/R_scripts/eAED_statistics.R
index 66fea36..2641470 100644
--- a/R_scripts/eAED_statistics.R
+++ b/R_scripts/eAED_statistics.R
@@ -1,24 +1,24 @@
 ## plot eAED
 ## grep '>' *maker.proteins.fasta | awk '{print $1":"$4}' | perl -ne '@array=split(":", $_); @name=split("-",$array[0]);print $name[1]."\t".$array[2];' > eAED_statistics*
-setwd("/Users/jfsh/DATA/spiders/DSil_genome/annotation/")
+setwd("/Users/jfsh/GIT_REPOS/Dysdera_silvatica_genome/")
 
 ## training Rounds
 breaks = seq(0, 1, by=0.02) 
-eAED_R1 <- read.table("eAED_files/eAED_statistics_contigs_R1_values.txt")
+eAED_R1 <- read.table("R_scripts/eAED_files/eAED_statistics_contigs_R1_values.txt")
 eAED_R1_table <- table(eAED_R1)
 eAED_R1_frame <- as.data.frame(eAED_R1_table)
 eAED_R1.cut = cut(eAED_R1$V1, breaks, right=FALSE) 
 eAED_R1.freq = table(eAED_R1.cut)
 cumfreq0_R1 = c(0, cumsum(eAED_R1.freq)/sum(eAED_R1.freq)) 
 
-eAED_R2 <- read.table("eAED_files/eAED_statistics_contigs_R2_values.txt")
+eAED_R2 <- read.table("R_scripts/eAED_files/eAED_statistics_contigs_R2_values.txt")
 eAED_R2_table <- table(eAED_R2)
 eAED_R2_frame <- as.data.frame(eAED_R2_table)
 eAED_R2.cut = cut(eAED_R2$V1, breaks, right=FALSE) 
 eAED_R2.freq = table(eAED_R2.cut)
 cumfreq0_R2 = c(0, cumsum(eAED_R2.freq)/sum(eAED_R2.freq)) 
 
-eAED_R3 <- read.table("eAED_files/eAED_statistics_contigs_R3_values.txt")
+eAED_R3 <- read.table("R_scripts/eAED_files/eAED_statistics_contigs_R3_values.txt")
 eAED_R3_table <- table(eAED_R3)
 eAED_R3_frame <- as.data.frame(eAED_R3_table)
 eAED_R3.cut = cut(eAED_R3$V1, breaks, right=FALSE) 
@@ -27,42 +27,55 @@ cumfreq0_R3 = c(0, cumsum(eAED_R3.freq)/sum(eAED_R3.freq))
 
 
 ## Final annotation
-eAED_first <- read.table("eAED_files/first_eAED_value.txt")
+eAED_first <- read.table("R_scripts/eAED_files/first_eAED_value.txt")
 eAED_first_table <- table(eAED_first)
 eAED_final_frame <- as.data.frame(eAED_first_table)
 eAED_first.cut = cut(eAED_first$V1, breaks, right=FALSE) 
 eAED_first.freq = table(eAED_first.cut)
 cumfreq0_first = c(0, cumsum(eAED_first.freq)/sum(eAED_first.freq)) 
-median_eAED_first = median(eAED_first$V1)
 
-eAED_second <- read.table("eAED_files/second_eAED_value.txt")
+eAED_second <- read.table("R_scripts/eAED_files/second_eAED_value.txt")
 eAED_second_table <- table(eAED_second)
 eAED_second_frame <- as.data.frame(eAED_second_table)
 eAED_second.cut = cut(eAED_second$V1, breaks, right=FALSE) 
 eAED_second.freq = table(eAED_second.cut)
 cumfreq0_second = c(0, cumsum(eAED_second.freq)/sum(eAED_second.freq)) 
-median_eAED_second = median(eAED_second$V1)
 
-eAED_third <- read.table("eAED_files/third_eAED_value.txt")
+eAED_third <- read.table("R_scripts/eAED_files/third_eAED_value.txt")
 eAED_third_table <- table(eAED_third)
 eAED_third_frame <- as.data.frame(eAED_third_table)
 eAED_third.cut = cut(eAED_third$V1, breaks, right=FALSE) 
 eAED_third.freq = table(eAED_third.cut)
 cumfreq0_third = c(0, cumsum(eAED_third.freq)/sum(eAED_third.freq))
-median_eAED_third = median(eAED_third$V1)
+
+## TR1
+mean_eAED_TR1 = mean(eAED_R1$V1)
+median_eAED_TR1 = median(eAED_R1$V1)
+## TR2
+mean_eAED_TR2 = mean(eAED_R2$V1)
+median_eAED_TR2 = median(eAED_R2$V1)
+## TR3
+mean_eAED_TR3 = mean(eAED_R3$V1)
+median_eAED_TR3 = median(eAED_R3$V1)
+
+## FT1
+mean_eAED_FT1 = mean(eAED_first$V1)
+median_eAED_FT1 = median(eAED_first$V1)
+## FT2
+mean_eAED_FT2 = mean(eAED_second$V1)
+median_eAED_FT2 = median(eAED_second$V1)
+## FT3
+mean_eAED_FT3 = mean(eAED_third$V1)
+median_eAED_FT3 = median(eAED_third$V1)
 
 #################
 ## set plot
 breaks = seq(0, 1, by=0.02) 
-median_R1 = median(eAED_R1$V1)
-median_R2 = median(eAED_R1$V1)
-median_R3 = median(eAED_R3$V1)
-
 plot(breaks,cumfreq0_R1,ylab="Cummulative Fraction of Annotation", xlab="eAED value", lty=2, type="l",col="deepskyblue", cex.lab=1.5, cex.axis=1.5, cex.main=1.5)
 abline(h=0.5, lty=4, col="grey")
 legend(
   "bottomright", ## POSITION 
-  c("50%", "","R1", "R2", "R3","","test1","test2","test3"), # puts text in the legend 
+  c("50%", "","TR1", "TR2", "TR3","","FT1","FT2","FT3"), # puts text in the legend 
   lty=c(4,0,2,2,2,0,1,1,1),               # gives the legend appropriate symbols (lines)
   lwd=c(2), ## width
   cex = 1.3,
@@ -75,3 +88,37 @@ lines(breaks,cumfreq0_R3,type="l",lty=2,col="darkslateblue")
 lines(breaks,cumfreq0_first,type="l",lty=1,col="chartreuse")
 lines(breaks,cumfreq0_second,type="l",lty=1,col="chartreuse3")
 lines(breaks,cumfreq0_third,type="l",lty=1,col="darkolivegreen")
+
+
+## Non annotated proteins
+eAED_non_annotated <- read.table("R_scripts/eAED_files/eAED_statistics_Non-Annotated.txt")
+breaks = seq(0, 1, by=0.02) 
+eAED_non_annotated_table <- table(eAED_non_annotated)
+eAED_non_annotated_frame <- as.data.frame(eAED_non_annotated_table)
+eAED_non_annotated.cut = cut(eAED_non_annotated$V1, breaks, right=FALSE) 
+eAED_non_annotated.freq = table(eAED_non_annotated.cut)
+cumfreq0_non_annotated = c(0, cumsum(eAED_non_annotated.freq)/sum(eAED_non_annotated.freq)) 
+
+plot(breaks,cumfreq0_non_annotated,ylab="Cummulative Fraction of Annotation",xlab="eAED value")
+lines(breaks,cumfreq0_non_annotated)
+
+## fiable
+# median
+median_eAED_non_annotated = median(eAED_non_annotated$V1)
+#abline(v=median_eAED_non_annotated, lty=2,col="blue")
+median_eAED_non_annotated
+
+# mean
+mean_eAED_non_annotated = mean(eAED_non_annotated$V1)
+abline(v=mean_eAED_non_annotated,lty=2,col="orange")
+abline(h=0.5, lty=4, col="grey")
+mean_eAED_non_annotated
+
+legend(
+  "bottomright", ## POSITION 
+  c("eAED", "mean"), # puts text in the legend 
+  lty=c(1,2),               # gives the legend appropriate symbols (lines)
+  lwd=c(3,3), ## width
+  col=c("black","orange") # gives the legend lines the correct color
+)
+