inter.intra.plot: Histogram of the intra- and interspecific distances

In sidier: Substitution and Indel Distances to Infer Evolutionary Relationships

Description

Plot histogram for inter and intra-specific distances together

Usage

inter.intra.plot(dismat=NA, xlim=NULL,ylim=NULL,
intra.col="gray",intra.density=0,intra.n=30,plot="N",
inter.col="black",inter.density=0,inter.n=30,legend=TRUE,
main="",xlab="Genetic distances",ylab=NULL)

Arguments

dismat	a symmetric matrix containing the pairwise genetic distances between individual sequences.
xlim	a vector containing the minimum and maximum value in the x-axis
ylim	a vector containing the minimum and maximum value in the y-axis
intra.col	the colour for the intraspecific distance distribution
intra.density	a numeric, the density of shading lines for the intraspecific distance distribution
intra.n	a numeric, the number of categories to represent in the intraspecific distance distribution
plot	a string, "freq" to represent frequency values in the y-axis and "N" for number of occurrences
inter.col	the colour for the interspecific distance distribution
inter.density	a numeric, the density of shading lines for the interspecific distance distribution
inter.n	a numeric, the number of categories to represent in the interspecific distance distribution
legend	a logic, "TRUE" to show plot legend
main	a string containing the title of the plot
xlab	a string with the label of the x-axis
ylab	a string with the label of the x-axis

Value

A list with two elements:

Intraspecific	a vector containing all the intraspecific distances.
Interspecific	a vector containing all the interspecific distances.

Author(s)

A.J. Muñoz-Pajares

Examples

# # Generating a distance matrix:
# 
# my.mat<-matrix(nrow=100,ncol=100,
# dimnames=list(paste("sp",rep(1:2,50),
# sep=""),paste("sp",rep(1:2,50),sep="")))
# L<-my.mat[seq(1,nrow(my.mat),2),seq(1,ncol(my.mat),2)]
# my.mat[seq(1,nrow(my.mat),2),seq(1,ncol(my.mat),2)]<-rnorm(0.15,n=L,sd=0.01)
# my.mat[seq(2,nrow(my.mat),2),seq(2,ncol(my.mat),2)]<-rnorm(0.15,n=L,sd=0.01)
# my.mat[seq(1,nrow(my.mat),2),seq(2,ncol(my.mat),2)]<-rnorm(0.3,n=L,sd=0.04)
# my.mat[seq(2,nrow(my.mat),2),seq(1,ncol(my.mat),2)]<-rnorm(0.3,n=L,sd=0.04)
# #Converting to symmetric
# my.mat<-as.matrix(as.dist(my.mat))  
# inter.intra.plot(dismat=my.mat)
# inter.intra.plot(dismat=my.mat,intra.n=10)
# inter.intra.plot(dismat=my.mat,plot="Freq",intra.n=10)

sidier documentation built on June 25, 2021, 5:10 p.m.