loss synteny blocks

[PengfeiInTuebingen]

Hi,

Thank you for developing such a useful tool. Recently, I encountered an issue while generating a riparian plot. When using the whole genome, I lose most of the synteny blocks (see image below).

Interestingly, I do get the synteny blocks when I highlight a specific chromosome (see image below).
,

Do you have any suggestions on how to resolve this issue?

The code for plot i used

ripDat <- plot_riparian(
  gsParam = gsParam, 
  #palette = customPal,
  braidAlpha = .75,
  invertTheseChrs = invchr,
  refGenome = "561",
  genomeIDs = c("P7","P6","P5","P4","P3","P2","P1"),
  syntenyWeight = 1,
  addThemes = ggthemes,
  chrFill = "lightgrey",
  useOrder = FALSE, 
  forceRecalcBlocks = FALSE)



roi <- data.frame(
  genome = c("P2"),
  chr = c("chr_25"), 
  color = c("#97d1d9"))

ripDat <- plot_riparian(
  gsParam = gsParam, 
  highlightBed = roi, 
  #backgroundColor = NULL, 
  invertTheseChrs = invchr,
  palette = customPal,
  refGenome = "561",
  genomeIDs = c("P7","P6","P5","P4","P3","P2","P1"),
  syntenyWeight = 1,
  addThemes = ggthemes,
  chrFill = "lightgrey",
  useOrder = FALSE)

Best,

PF