From dcb118e3643086c48420709669094c0c383b3cfa Mon Sep 17 00:00:00 2001 From: "Jose F. Sanchez" Date: Fri, 7 Dec 2018 11:23:10 +0100 Subject: [PATCH] Version v1.1. draft genome --- .../eAED_statistics_Non-Annotated.txt | 2488 +++++++++++++++++ R_scripts/eAED_statistics.R | 77 +- 2 files changed, 2550 insertions(+), 15 deletions(-) create mode 100644 R_scripts/eAED_files/eAED_statistics_Non-Annotated.txt 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 @@ -0,0 +1,2488 @@ +0.00 +0.01 +0.25 +0.79 +0.76 +0.15 +0.00 +0.00 +0.54 +0.10 +0.09 +0.53 +0.13 +0.04 +0.00 +0.90 +0.00 +1.00 +0.00 +0.00 +0.00 +0.00 +0.02 +0.53 +0.13 +0.79 +0.05 +0.00 +0.64 +0.09 +0.46 +0.10 +0.49 +0.20 +0.67 +0.04 +0.69 +0.12 +0.23 +0.90 +0.61 +0.72 +0.33 +0.34 +0.00 +0.31 +0.00 +0.10 +0.67 +0.00 +0.57 +0.02 +0.12 +0.85 +0.04 +0.25 +0.58 +0.00 +0.23 +0.11 +0.00 +0.76 +0.23 +0.23 +0.00 +0.32 +0.11 +0.03 +1.00 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+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 +) +