I tried to follow the instructions in section 3.5 from this link (https://bioconductor.org/packages/release/bioc/vignettes/motifStack/inst/doc/motifStack_HTML.html to plot logo stack with radial style. But I found the distance between the start of motif logos and the center are different, which makes the figure a little bit strange. Any suggestions or hints regarding this issue? Thanks in advance!

The code I used could be found as follows:

motifStack(motifs2, 

           layout="radialPhylog", 

           circle = 1.7,     

           cleaves = 0.2, 

           clabel.leaves = 1, 

           col.bg=rep(color, each=7), col.bg.alpha=0.3, 

           col.leaves=rep(color, each=7),

           col.inner.label.circle=rep(color, each=7), 

           inner.label.circle.width=0.05,

           col.outer.label.circle=rep(color, each=7), 

           outer.label.circle.width=0.02, 

           circle.motif= 1.5,    # The outer circle of motif

           angle=360)

Hi,

Thank you for trying motifStack.

Because the motifStack will automatically try to align the motifs, after alignment, the start position of the motifs will be different. If you do not want automatic alignment, please try to use  plotMotifStackWithRadialPhylog function.

Also, please try to set the circle.motif=NA.