Use as.table=TRUEto change the order of panels and groups(together with extended colvec) to change colo (u) rs.
edit : adjusted order of factor levels
mydf <-
data.frame (var, pos, yvar,
## fvar = factor(var,levels=unique(var)),
fvar = factor(var, levels = c(outer(2:1, 1:10, paste, sep="chr"))))
xyplot(yvar ~ pos| fvar,
groups=fvar,
data = mydf, layout = c(1,10,2), type = c("g", "h"),
col = c("darkolivegreen","purple"), lwd = 4, as.table=TRUE)
layout .

, " " :
library(latticeExtra)
useOuterStrips(xyplot(yvar ~ pos|factor(grp)*factor(chr),
groups=grp,
col=c("darkolivegreen","purple"),
data = mydf, layout = c(2,10), type = c("g", "h"),
lwd = 4, as.table=TRUE))
