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100 lines
2.9 KiB
100 lines
2.9 KiB
#!/usr/bin/env Rscript
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# Compare 2 versions of GCAT for a particular parameter
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# Karan Maini
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args <- commandArgs(TRUE)
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# Baaad....WORK.DIR = "/home/maini/Desktop/GCAT Test Script"
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# INPUT.1 = "GCAT2/output_gcat.fit_2013-11-18_12.23.34.txt"
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# INPUT.2 = "GCAT3/output_gcat.fit_2013-11-18_12.19.46.txt"
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# Read in the data
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in1 = read.table(args[1],header=T,sep="\t")
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in2 = read.table(args[2],header=T,sep="\t")
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parameter = args[3]
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# Compare values
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same = signif(in1$spec.growth,2) == signif(in2$spec.growth,2) & signif(in1$tot.growth,2) == signif(in2$tot.growth,2) & signif(in1$lag.time,2) == signif(in2$lag.time,2)
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same[is.na(in1$spec.growth) & is.na(in2$spec.growth)] = T
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# Write out the output
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#out = file(OUTPUT,open="w")
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#if (all(same)) { writeLines("No significant differences identified",con=out) }
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#close(out)
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# Manual exploration
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# Ascertain that results are quite different
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cat("Command:\nRscript compare_gcat_output.R",args[1],args[2],parameter)
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cat("\n\nSummary: \n\n")
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summary(same)
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head(same)
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cat("\n\nGCAT2: \n\n")
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head(in1)
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cat("\n\nGCAT3: \n\n")
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head(in2)
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cat("\n\nSpecific Growth Comparison Summary: \n\n")
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summary(in2$spec.growth/in1$spec.growth) # specific growth lower in GCAT 3
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cat("\n\nTotal Growth Comparison Summary: \n\n")
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summary(in2$tot.growth/in1$tot.growth)
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cat("\n\nLag Time Comparison Summary: \n\n")
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summary(in2$lag.time/in1$lag.time) # lag time also lower in GCAT 3
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# Baaad....WORK.DIR = "/home/maini/Desktop/GCAT Test Script/Comparison Plots"
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setwd("./Comparison Plots")
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pdf( paste( parameter,'Plot.pdf'),onefile=T)
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# ....plot code here....
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# Plot specific growth rate of GCAT 3 vs. GCAT 2
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x = in1$spec.growth
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y = in2$spec.growth
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plot(x,y,pch=16,main="Specific Growth", xlab="old GCAT", ylab="new GCAT")
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abline(0,1)
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abline(lm(y~x),lty=2)
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legend("bottomright",c("y=x line","regression line"),lty=c(1,2))
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# Plot total growth rate of GCAT 3 vs. GCAT 2
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x = in1$tot.growth
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y = in2$tot.growth
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plot(x,y,pch=16,main="Total Growth", xlab="old GCAT", ylab="new GCAT")
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abline(0,1)
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abline(lm(y~x),lty=2)
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legend("bottomright",c("y=x line","regression line"),lty=c(1,2))
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# Plot lag time of GCAT 3 vs. GCAT 2
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x = in1$lag.time
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y = in2$lag.time
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plot(x,y,pch=16,main="Lag Time", xlab="old GCAT", ylab="new GCAT")
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abline(0,1)
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abline(lm(y~x),lty=2)
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legend("bottomright",c("y=x line","regression line"),lty=c(1,2))
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# Plot Goodness of Fit of GCAT 3 vs. GCAT 2
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x = in1$good.fit
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y = in2$good.fit
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plot(x,y,pch=16,main="Goodness of Fit", xlab="old GCAT", ylab="new GCAT")
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abline(0,1)
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abline(lm(y~x),lty=2)
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legend("bottomright",c("y=x line","regression line"),lty=c(1,2))
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dev.off()
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# Investigate outliers
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subset(in1, is.finite(in1$spec.growth) & (in1$spec.growth < in2$spec.growth - 0.003))
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subset(in2, is.finite(in1$spec.growth) & (in1$spec.growth < in2$spec.growth - 0.003))
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# Clean up
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rm(list=ls())
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setwd("../") #move back to testing root directory |