#Figure 2 All Sweepos
Fig2 <- as.matrix(read.table("n398_AllSweepos_NONAME.txt",sep=","))
hist(Fig2,
  main="",
  xlab="Pairwise Nucleotide Identity",
  ylab="Number of Pairwise Comparisons",
  cex.lab=1.5,
  cex.axis=1.5,
  xlim=c(65,100),
  ylim=c(0,5000),
  breaks=50,
  col="gray",
  freq=TRUE)
abline(v = 90.5, col='red', lwd = 3)
abline(v = 93.5, col='red', lwd = 3)


#Figure 4 SPLCV vs. SPLCV, Before and After
Fig4_before <- as.matrix(read.table("n398_SPLCVvsSPLCV_NONAME.txt",sep=","))
Fig4_after <- as.matrix(read.table("n398_noname_SPLCV only_revised.txt",sep=","))
hist(Fig4_before,
  main="",
  xlab="Pairwise Nucleotide Identity",
  ylab="Number of Pairwise Comparisons",
  cex.lab=1.5,
  cex.axis=1.5,
  xlim=c(65,100),
  ylim=c(0,5000),
  breaks=50,
  col=rgb(0,0,1,1/4),
  freq=TRUE,
  )
hist(Fig4_after,
  xlim=c(65,100),
  ylim=c(0,5000),
  cex.lab=1.5,
  cex.axis=1.5,
  breaks=40,
  col=rgb(1,0,0,1/4),
  freq=TRUE,
  add=T)
abline(v = 90.5, col='red', lwd = 3)
abline(v = 93.5, col='red', lwd = 3)




#Supplemental Figure 2 SPLCV vs. Non-SPLCV, Before and After
Suppl2_before <- as.matrix(read.table("BEFORE REVISIONS n398 matrix no ID 100 corrected names_SPLCV vs. non-SPLCV.txt",sep=","))
Suppl2_after <- as.matrix(read.table("AFTER REVISIONS n398 matrix no self ID 100 revised classifications_SPLCV vs. non-SPLCV.txt",sep=","))
hist(Suppl2_before,
xlab="Pairwise Nucleotide Identity",
ylab="Number of Pairwise Comparisons",
xlim=c(65,100),
ylim=c(0,5000),
cex.lab=1.5,
cex.axis=1.5,
breaks=50,
col=rgb(0,0,1,1/4),
freq=TRUE,
)
hist(Suppl2_after,
xlim=c(65,100),
ylim=c(0,5000),
cex.lab=1.5,
cex.axis=1.5,
breaks=40,
col=rgb(1,0,0,1/4),
freq=TRUE,
add=T)
abline(v = 90.5, col='red', lwd = 3)
abline(v = 93.5, col='red', lwd = 3)
