Strehler-Mildvan, s288c + Exg06 data, p=0.007

S288C is added to the natural isolates from QinEXG06.

#2013 Sep 30, Oct 1, Oct 3, add 's288c' into exg06 data

setwd("~/projects/jtb13")

 rm( list = ls() );
 list.files(, pattern="csv|tab")
 s288c = read.csv("s288c.RG.csv")

# tb = read.table("summary.new.by.strain.csv", header=T, sep="\t"); #incomplete data
 tb = read.table("061405.rls.for.publication.tab", header=T)
 names(tb) = c("strain","sample_size","ARLS","RLS.sd","R0","R.sd", "G","G.sd")
 tb$strain = as.character(tb$strain)
 tb.original = tb;
 tb[19,] = NA
 tb$strain[19] = 'S288c'
 tb[19, c("R0","G")] = t(c(s288c$V1[1],s288c$V2[1]))
 tb$strain[grep('RM11', tb$strain)] = 'RM11'

plot( log10(tb$R0) ~ tb$G, pch=19 )
text( tb$G, log10(tb$R0), tb$strain)

 tb = tb[-grep("BY4743", tb$strain), ]
 tb = tb[-grep("PSY", tb$strain), ]
 tb = tb[-grep("W303", tb$strain), ]
 tb = tb[-grep("SK1", tb$strain), ]

model = lm(log10(tb$R0) ~ tb$G )
summary( model ) #p=0.007, strehler-mildvan correlation! 

plot( log10(tb$R0) ~ tb$G, pch=19, xlim=c(0.06, 0.19), ylim=c(-3.6, -2), xlab='G',ylab='lnR' )
title("p=0.007, Strehler-Mildvan, natural isolates")
text( tb$G + 0.01*nchar(tb$strain)/4, log10(tb$R0)-0.1*nchar(tb$strain)/4, tb$strain, pos=3)
abline(model, col='red')