I have multiple plots made with ggplot2
that I arrange together using cowplot
. They all have the same length, and an x-axis with the same breaks at the same places, but with different labels.
This is a MWE:
mylist <- list()
mylist[["ID1"]][["sequence"]] <- "AGAATATTATACATTCATCT"
mylist[["ID2"]][["sequence"]] <- "GCTAGCGTTTAGTTTAGCTG"
mylist[["ID3"]][["sequence"]] <- "AACCCTTTAAACTCGAAGTA"
set.seed(123)
mylist[["ID1"]][["data"]] <- data.frame(time=1:100, value=rnorm(100, mean=10, sd=2))
mylist[["ID2"]][["data"]] <- data.frame(time=1:100, value=rnorm(100, mean=2, sd=1))
mylist[["ID3"]][["data"]] <- data.frame(time=1:100, value=rnorm(100, mean=5, sd=3))
indexes <- seq(5, 100, length.out=20)
all_df <- NULL
for (id in names(mylist)){
seqsplit <- unlist(strsplit(mylist[[id]][["sequence"]], ""))
ind_df <- data.frame(call=seqsplit, time=indexes)
final_df <- dplyr::left_join(mylist[[id]][["data"]], ind_df, by="time")
xcolors <- ifelse(seqsplit=="A", "green", ifelse(seqsplit=="C", "blue", ifelse(seqsplit=="G", "black", "red")))
P <- ggplot2::ggplot(final_df, ggplot2::aes(x=time, y=value)) +
ggplot2::geom_line(linewidth=0.5) +
ggplot2::scale_x_continuous(breaks=indexes, labels=seqsplit, expand=c(0,1)) +
ggplot2::scale_y_continuous(breaks=seq(-5, 15, 5), limits=c(-5,15)) +
ggplot2::theme_light() +
ggplot2::theme(axis.title=ggplot2::element_blank(),
axis.text.x=ggtext::element_markdown(face="bold", color=xcolors))
mylist[[id]][["plot"]] <- P
}
plot_list <- sapply(mylist, "[", "plot")
grDevices::pdf(file="test.pdf", height=4, width=10)
print(
cowplot::plot_grid(plotlist=plot_list, ncol=1)
)
grDevices::dev.off()
which produces:
What I want to accomplish now, is to make a common x-axis for all, with the common indexes
(or rather from 1 to the length of the sequences), that I would place on top of the cowplot
; something like this:
This would probably involve making the x-axis indexes ruler as a separate ggplot2
of the same width (accounting for the y-axis horizontal space and all), and then place it on the cowplot
with the appropriate relative height... any help is welcome!
One way is to add a secondary x-axis on the top of the first plot:
for (id in names(mylist)){
...
P <- ggplot(final_df, ggplot2::aes(x=time, y=value)) +
geom_line(linewidth=0.5) +
scale_y_continuous(breaks=seq(-5, 15, 5), limits=c(-5,15)) +
theme_light()
if(id=="ID1") {
P <- P + scale_x_continuous(breaks=indexes, labels=seqsplit, expand=c(0,1),
sec.axis = sec_axis(~.,
breaks=indexes, labels=seq_along(indexes))) +
theme(axis.title=element_blank(),
axis.text.x.top = ggtext::element_markdown(color='white', fill="steelblue",
padding=unit(c(1, 8, 1, 8), "pt")))
}
else {
P <- P + scale_x_continuous(breaks=indexes, labels=seqsplit, expand=c(0,1)) +
theme(axis.title=element_blank(),
axis.text.x=ggtext::element_markdown(face="bold", color=xcolors))
}
mylist[[id]][["plot"]] <- P
}