GenomicLabels clumped together

[jinghuazhao]

I have data such as these,

chr start end log10p label category chr9 107543283 107543283 10.9065783148378 ABCA1 1 chr17 66863433 66863433 6.18708664335714 ABCA8 4 ...

but circos.genomicLabels put all labels, just in the first two quadrants,

The code seems fairly standard,

circos.clear() circos.par(start.degree = 90, track.margin = c(0.005, 0.005), cell.padding = c(0.001, 0.01, 0.01, 0.001)) circos.initializeWithIdeogram(chromosome.index=paste0("chr",1:22),plotType = NULL) circos.genomicLabels(QTL_labels, labels=QTL_labels[["label"]], side = "outside", cex = 0.3, line_lwd = 0.8, padding=0.8, connection_height = convert_height(8, "mm"), line_col = QTL_labels[["category"]], col = QTL_labels[["category"]])

Are there any suggestions? Thank you!

[jpmcelderry]

I'm having the same issue:

The code looks like this:

circos.par(start.degree=85,gap.degree=10,xaxis.clock.wise=FALSE)
circos.genomicInitialize(chrM,plotType = NULL)
circos.genomicTrack(chrM,ylim=c(-10,10),track.margin=c(.005,0.005), panel.fun = function(region, value, ...) {
  circos.rect(xleft=chrM$start,ybottom = 0,xright = chrM$stop,ytop = CELL_META$cell.ylim[2]*chrM$strand,col=1:nrow(chrM))
  circos.genomicAxis(h="bottom",direction="inside",labels.cex=0.8,major.by = 1000)
},
track.height = 0.1, bg.border = NA)
circos.genomicLabels(chrM,labels.column = 5,side="inside",
                     col=c(1:(nrow(chrM)-1),1),line_col = c(1:(nrow(chrM)-1),1))

where chrM is just a standard BED file formatted like so:

  chrom start stop strand   name complex 
1  chrM     0  576      0 D-Loop   other
2  chrM   577  647      1     TF mt tRNA
3  chrM   648 1601      1   RNR1 mt rRNA
4  chrM  1602 1670      1     TV mt tRNA
5  chrM  1671 3229      1   RNR2 mt rRNA
6  chrM  3230 3304      1    TL1 mt tRNA

I've tried downgrading to 0.4.10 as others suggested which fixed this problem but created others, and I'm currently using the latest version of circlize available on GitHub.

[jinghuazhao]

Thank you so much @jpmcelderry; I have used CRAN version (0.4.14) for other successful plots and for this data and version 0.4.15 at the GitHub the problem goes away.

[jokergoo]

I will update the new version to CRAN in the next few weeks.

[jpmcelderry]

I will update the new version to CRAN in the next few weeks.

@jokergoo I'm still having this issue even with version 0.4.15. I've tried updating everything except R itself currently (I'm on version 4.1.1). One thing that did help was commenting out "xaxis.clock.wise=FALSE", which for some reason restored proper behavior but to only part of the plot.

[jokergoo]

@jpmcelderry maybe I haven't completely fixed this bug. Can you also send me the data and code so that I can have a test on it?

[jpmcelderry]

@jokergoo

The code is part of a larger script, but here are the relevant portions:

library(tidyverse)
library(ComplexHeatmap)
library(broom)
library(ggpubr)
library(ggrepel)
library(ggsci)
library(gridExtra)
library(circlize)

chrM <- read_delim(file = "chrM_genes.txt",delim='\t',col_names = TRUE,col_types = "cnnn")%>%
  `colnames<-`(c('name','start','stop','strand'))%>%
  mutate(name=str_sub(name,4,nchar(name)),chrom="chrM")%>%
  select(chrom,start,stop,strand,name)

circos.clear()
circos.par(start.degree=85,gap.degree=10)#,xaxis.clock.wise=FALSE)
circos.genomicInitialize(chrM,plotType = NULL)
circos.genomicTrack(ylim=c(-10,10),track.margin=c(.005,0.005), panel.fun = function(region, value, ...) {
  circos.rect(xleft=chrM$start,ybottom = 0,xright = chrM$stop,ytop = CELL_META$cell.ylim[2]*chrM$strand,col=1:nrow(chrM))
  circos.genomicAxis(h="bottom",direction="inside",labels.cex=0.8,major.by = 1000)
},
track.height = 0.1, bg.border = NA)
circos.genomicLabels(chrM,labels.column = "name",side="inside",
                     col=c(1:(nrow(chrM)-1),1),line_col = c(1:(nrow(chrM)-1),1),connection_height = mm_h(8),padding=0.2)

The annotations file is attached. Appreciate your help!

chrM_genes.txt

[jinghuazhao]

I use R 4.2.0 and 0.4.15 works OK for my problem but not this one.

[jokergoo]

Hi @jinghuazhao , thanks for the data. Yes that was a bug. Now I have fixed it. Please update from GitHub.

[jinghuazhao]

Thank you @jpmcelderry and @jokergoo for the information and bug fix -- I will update these from GitHub. Best. Jing Hua

[jpmcelderry]

@jokergoo Update worked, thank you! It seems that setting the "xaxis.clock.wise" option to 'FALSE' still causes the labels to clump, but most importantly default facing is working again. Thank you!

[jokergoo]

Thanks for discovering it! Now it is fixed.

[jpmcelderry]

Amazing, thank you so much @jokergoo