Try removing the line
x <- x[order(x[,1], decreasing=TRUE),]
Peter
On Tue, Aug 4, 2015 at 10:58 AM, April Smith <aprilgracesm...@gmail.com> wrote:
> Let me just preface that everything I know about writing code for R is self
> taught so this may be really basic but I can't figure it out!
>
> I am using someone else code to create plots. I would like to change the
> automatically generated colors to the same colors for every plot. The
> current code makes the highest line in the graph black, the second highest
> line red, 3rd blue, etc, regardless of what the line represents. I need to
> create 10 of these plots and it gets confusing when the black line means a
> different thing in each plot! Here is the line I need to adjust, I just
> don't know how.
>
> lines(1:orders, x[i,], col=i)
>
> Here is the code in entirety:
> plot.hill <- function(x, scales = c(0, 0.25, 0.5, 1, 2, 4, 8, 16, 32, 64,
> Inf), ...) {
> require(vegan)
> nsites <- if(is.null(ncol(x))) 1 else ncol(x)
> x <- renyi(t(x), scales=scales, hill=TRUE)
> orders <- length(scales)
> if(nsites > 1) {
> x <- x[order(x[,1], decreasing=TRUE),]
> OP <- matrix(". ", nsites,nsites)
> colnames(OP) <- rownames(OP) <- rownames(x)
> for(i in 1:(nsites-1))
> for(j in (i+1):nsites)
> if(all(x[i,] > x[j,])) {
> OP[i,j] <- "< "
> OP[j,i] <- "^ "
> }
> diag(OP) <- " "
> OP <- as.data.frame(OP)
> cat("The arrow < or ^ points to the more diverse site:\n")
> print(OP, na.print=" ")
> } else
> OP <- NULL
> plot(1:4,1:4,type="n",xlim=c(0.9,orders+0.1),ylim=range(0,x),axes=FALSE,
> ylab="Hill Diversity Numbers",xlab="Order", ...)
> axis(2)
> axis(1, at=1:orders, labels=scales)
> if(nsites > 1) {
> for(i in 1:nsites)
> lines(1:orders, x[i,], col=i)
> legend("topright", legend=row.names(x), col=1:nsites, lty=1, cex=0.7)
> } else
> lines(1:orders, x)
> invisible(OP)
> }
>
> [[alternative HTML version deleted]]
>
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and provide commented, minimal, self-contained, reproducible code.
