changing axis labels

[melodysyue]

For the dotplot function, how should I change the x/y axis labels. It seems like the regular ggplot functions (xlab, labs) don't work, the axis labels are still "query" and "target". I would like to label them with specific chromosome names. Thanks!

Here is my R code.
dotplot(ali1.pm, label_seqs=TRUE, order_by="provided", ordering=chr3)+
theme_bw(base_size=25)+
coord_cartesian(xlim=c(32e6, 34e6), ylim=c(45e6, 48e6))+
annotate("rect",xmin=chr3_start, xmax=chr3_end, ymin=-Inf, ymax=Inf, fill="purple", alpha=0.2)+
labs(x="NC_042537.1", y="NC_048567.1", title="Chromosome 3")

Here is the generated plot.

[edexter]

I'd like to bump this up as well. I'm running into the same problem.

[jayoung]

dotplot() has xlab/ylab arguments - it seems to work for me.

In your example I think it would be :

dotplot(ali1.pm, label_seqs=TRUE, 
    order_by="provided", ordering=chr3, 
    xlab="NC_042537.1", ylab="NC_048567.1") +
 (code for other layers)

does it work for you?