Question: How to change the size of yaxis in motifstack
0
gravatar for saadmurtazakhan
3 months ago by
United States
saadmurtazakhan10 wrote:

Hi,

I am trying to use motifstack in bioconductor. I was wondering if there is any way to reduce the size of yaxis or limit the yaxis to a maximum value. I tried to use plotYaxis but I am unable to reduce the size of the yaxis. I was wondering how to do it.

thanks Saad

ADD COMMENTlink written 3 months ago by saadmurtazakhan10

Currently the yaxis is fixed by the max entropy of information. May I know why you want to change default yaxis?

ADD REPLYlink written 3 months ago by Ou, Jianhong1.2k

I have a motif and I am trying to look at the surrounding nucleotides distribution. So in the matrix I make all the motif positions to be zero and then look at the surrounding nucleotides but since they are too small I need to change the yaxis size. Please let me know how I go about in doing that.

ADD REPLYlink modified 3 months ago • written 3 months ago by saadmurtazakhan10

If that is the case, I would suggest you to set ic.scale into FALSE. Please have a try and let me know if that meet your requirement.

ADD REPLYlink written 3 months ago by Ou, Jianhong1.2k

That's probably not what I want.

With ic.scale=TRUE With ic.scale=TRUE

With ic.scale=FALSE With ic.scale=FALSE

ADD REPLYlink modified 3 months ago • written 3 months ago by saadmurtazakhan10

something like this (see vignette and help files for more details): plot(motif, ic.scale=FALSE, ylab="probability")

ADD REPLYlink written 3 months ago by Ou, Jianhong1.2k

@OU_jianhong is there a better work around than above. How Can I use ylim with plotmotifstack?

ADD REPLYlink written 3 months ago by saadmurtazakhan10

In current version, motifStack can not handle ylim. I want to fix the ylim when ic.scale is used. In your specific usage, you can have a try with plotMotifLogoA to plot the logos one by one like this (but I don't suggest you to do that): grid.newpage() vp <- viewport(x = .5, y=1.8, width = .9, height = 3.4) # adjust y and height to trim the plot. pushViewport(vp) plotMotifLogoA(motif) grid.xaxis(at=seq.int(ncol(motif@mat))-.5)/ncol(motif@mat), label = seq.int(ncol(motif@mat))) grid.yaxis(at=seq(0, .25, length=6), label=(0:5)/10) popViewport()

ADD REPLYlink written 3 months ago by Ou, Jianhong1.2k
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