I have a protein sequence alignement and for each position of the
alignement, I want to plot two values (one per sequence). Alignements look
like this:
MVAFKGVWTQAFWKAVTAEFL
--------MCSISRKMAAEFI
So, data for the plot would be something like this
Prot 1 values: 1 5 2 7 4 3 5 6 8 2 2 7 6 4 2 8 5 8 2 3 7 3
Prot 2 values: 1 8 5 0 5 3 4 1 2 2 3 7 0
Aligned Prot 1 seq: M V A F K G V W T Q A F W K A T V T A E F L
Aligned Prot 2 seq: - - - - - - - - M C S I S R K - M A A E F I
Gabor Grothendieck gently helped me (thank you Gabor) so now I can plot the
two time series, handle gaps (the '-' in the second sequence aligned)
and
change the values in X axis for the values of the first sequence. This can
be achieved by running this code:
x<-data.frame
(a=c(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22),b=c(1,5,2,7,4,3,5,6,8,2,2,7,6,4,2,8,5,8,2,3,7,3))
y1<-data.frame(a=c(9,10,11,12,13,14,15),b=c(1,8,5,0,5,3,4))
y2<-data.frame(a=c(17,18,19,20,21,22),b=c(1,2,2,3,7,0))
xts <- ts(x$b,start=x$a[1])
y1ts <- ts(y1$b,start=y1$a[1])
y2ts <- ts(y2$b,start=y2$a[1])
xaxislabels_1 <-
c('M','V','A','F','K','G','V','W','T','Q','A','F','W','K','A','T','V','T','A','E','F','L')
xaxislabels_2 <-
c('-','-','-','-','-','-','-','-','M','C','S','I','S','R','K','-','M','A','A','E','F','I')
ts.plot(xts,y1ts,y2ts,col=c("red","blue","blue"),
gpars = list(axes FALSE))
axis(2)
axis(1, at=1:22, labels=xaxislabels_1)
Now, how can I add the second sequence values in X axis just below the
values given in axis(1, at=1:22, labels=xaxislabels_1)?
Thanks in advance.
--
Felipe
[[alternative HTML version deleted]]
Gabor Grothendieck
2007-Nov-10 23:41 UTC
[R] Add another set of labels in a plot for X axis
Try this: axis(1, 1:22, paste(xaxislabels_1, xaxislabels_2, sep = "\n"), tcl = .3) On Nov 10, 2007 6:27 PM, Felipe <felipenaranja at gmail.com> wrote:> I have a protein sequence alignement and for each position of the > alignement, I want to plot two values (one per sequence). Alignements look > like this: > > MVAFKGVWTQAFWKAVTAEFL > --------MCSISRKMAAEFI > > So, data for the plot would be something like this > > > Prot 1 values: 1 5 2 7 4 3 5 6 8 2 2 7 6 4 2 8 5 8 2 3 7 3 > Prot 2 values: 1 8 5 0 5 3 4 1 2 2 3 7 0 > > Aligned Prot 1 seq: M V A F K G V W T Q A F W K A T V T A E F L > Aligned Prot 2 seq: - - - - - - - - M C S I S R K - M A A E F I > > Gabor Grothendieck gently helped me (thank you Gabor) so now I can plot the > two time series, handle gaps (the '-' in the second sequence aligned) and > change the values in X axis for the values of the first sequence. This can > be achieved by running this code: > > x<-data.frame > (a=c(1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22),b=c(1,5,2,7,4,3,5,6,8,2,2,7,6,4,2,8,5,8,2,3,7,3)) > y1<-data.frame(a=c(9,10,11,12,13,14,15),b=c(1,8,5,0,5,3,4)) > y2<-data.frame(a=c(17,18,19,20,21,22),b=c(1,2,2,3,7,0)) > xts <- ts(x$b,start=x$a[1]) > y1ts <- ts(y1$b,start=y1$a[1]) > y2ts <- ts(y2$b,start=y2$a[1]) > xaxislabels_1 <- > c('M','V','A','F','K','G','V','W','T','Q','A','F','W','K','A','T','V','T','A','E','F','L') > xaxislabels_2 <- > c('-','-','-','-','-','-','-','-','M','C','S','I','S','R','K','-','M','A','A','E','F','I') > ts.plot(xts,y1ts,y2ts,col=c("red","blue","blue"), gpars = list(axes > FALSE)) > axis(2) > axis(1, at=1:22, labels=xaxislabels_1) > > Now, how can I add the second sequence values in X axis just below the > values given in axis(1, at=1:22, labels=xaxislabels_1)? > > Thanks in advance. > > -- > Felipe > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >