Displaying 3 results from an estimated 3 matches for "basepair".
2012 Jul 13
2
alternate tick labels and tick marks with lattice xyplot
...k marks. I can do this with the regular R plot function as
follows.
#A small version of my data looks like this
data<-data.frame(matrix(ncol=3,nrow=12))
data[,1]<-rep(c(1,2,3),c(4,4,4))
data[,2]<-rep(c(1,2,3,4),3)
data[,3]<-runif(12,0,1)
names(data)<-c("Chromosome", "BasePair", "Pvalue")
#using R's plot function, I would place the the chromosome label between
the
#tick marks as follows:
v1<-c(4,8)
v2<-c(2,6,10)
data$indice<-seq(1:12)
plot(data$indice, -log10(data$Pvalue), type="l", xaxt="n", main="Result",
xlab=...
2018 Mar 15
3
stats 'dist' euclidean distance calculation
...fference between x_i and y_i would be the number of allelic differences at each base pair site between samples. For example, the euclidean distance between Samp1 and Samp2 would be:
euclidean distance = sqrt( S1_L1 - S2_L1)^2 + (S1_L2 - S2_L2)^2 + (S1_L3 - S2_L3)^2 )
at locus 1: GG - AG --> one basepair difference --> (1)^2 = 1
at locus 2: <NA> - CA --> two basepair differences --> (2)^2 = 4
at locus 3: GG - GA --> one basepair difference --> (1)^2 = 1
euclidean distance = sqrt( 1 + 4 + 1 ) = sqrt( 6 ) = 2.44940
Calculating euclidean distances this way, the distance matrix s...
2007 Dec 03
3
overlapping labels
...uld use another set of
graphical functions (grid or lattice packages).
Does anybody have suggestions?
Thank you,
Filippo Biscarini
PS: These are the lines of codes that I have been using to generate the
plot.
plot(
prova$x,
prova$y,
type="b",
mar=c(0.5,0.5,0.5,0.5),
xlab="basepairs",
ylab=""
);
text(
prova$x,
prova$y,
prova$lab,
pos=3,
offset=2,
cex=0.5
);
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