Run circlize errors

Question

[Alex]

Hello,while I use my data run the circlize to plot the genomic Points track,It appear some Unexpected errors.all the points are gathered into several scaffold and some points out of track Note:6822 points are out of plotting region in sector 'scaffold_1', track '3'.

Note:7642 points are out of plotting region in sector 'scaffold_2', track '3'.

Note:7608 points are out of plotting region in sector 'scaffold_3', track '3'.

my bed1 files only have three column which only include chromosome and position and code is that： circos.genomicInitialize(bed1)

circos.genomicTrackPlotRegion(ylim=c(0,1),bg.col=rainbow(nrow(bed1)),track.height=0.1)

circos.genomicTrackPlotRegion(bed2,track.height=0.1,ylim = c(-1,1),panel.fun = function(region, value, ...) {circos.genomicPoints( region, value, pch = 16, cex = 0.1,...)})

Can anyone could how to explain it ?I am a new to plot the circos picture,Any help will be appreciated

Thanks

Answer 1

[theobroma22]

Take a second look at how your panel.fun is written and if you have three columns in your bed file I didn't see you set the numeric column argument.

[Alex]

yeah，I have solved it ,Thanks ,theobroma22

Alex