Add an annotation track for specific SNPs

[sarahbrotman]

I would like to add a SNP annotation track to my plotgardener plot. I am able to do so using annoHighlight(), however I want to add ~2,000 SNPs which is unrealistic to do one-by-one and takes a long time in a for loop. Is there a way to plot many SNPs at once? I have also tried using plotRanges(), however only a few lines show up and they are too thin to see on the rest of my plot which is about 700kb. Here is my code so far:

library(plotgardener)
library(AnnotationHub)
library(TxDb.Hsapiens.UCSC.hg38.knownGene)
library(org.Hs.eg.db)


tagSNPs <- read.delim("allTagSNPs_forPlot.txt", header = T, stringsAsFactors = F)

pageCreate(
  width = 6, height = 3, default.units = "inches",
  showGuides = FALSE, xgrid = 0, ygrid = 0
)

ideogramPlot <- plotIdeogram(
  chrom = "chr17", assembly = "hg38",
  orientation = "h",
  x = 0.25, y = 0.25, width = 5.75, height = 0.3, just = "left"
)

region <- pgParams(chrom = "chr17", chromstart = 45578810, chromend = 46277280)
H4 <- pgParams(chrom = "chr17", chromstart = 45637307, chromend = 45637307)
H5 <- pgParams(chrom = "chr17", chromstart = 46095849, chromend = 46095849)
H6 <- pgParams(chrom = "chr17", chromstart = 45593653, chromend = 45593653)
H8 <- pgParams(chrom = "chr17", chromstart = 45588844, chromend = 45588844)

annoHighlight(
  plot = ideogramPlot, params = region,
  fill = "red",
  y = 0.05, height = 0.4, just = c("left", "top"), default.units = "inches"
)

annoZoomLines(
  plot = ideogramPlot, params = region,
  y0 = 0.5, x1 = c(0.25, 6), y1 = 1.25, default.units = "inches"
)

genes <- plotGenes(
  assembly = "hg38",
  chrom = "chr17", chromstart = 45578810, chromend = 46277280,
  y = 1.5, x = 0.3, width = 5.5, just = c("left", "top")
)

plotGenomeLabel(
  chrom = "chr17",
  chromstart = 45578810, chromend = 46277280,
  assembly = "hg38",
  scale = "Mb",
  x = 0.3, y = 2.5, length = 5.5, default.units = "inches"
)

for (i in 1:nrow(tagSNPs)) {
  
  # Extract the chrom, chromstart, and chromend for the current SNP
  chrom <- tagSNPs$chrom[i]
  chromstart <- as.numeric(tagSNPs$start[i])
  chromend <- as.numeric(tagSNPs$end[i]-1)
  
  # Create the region using pgParams() for the current SNP
  SNP <- pgParams(chrom = chrom, chromstart = chromstart, chromend = chromend)
  
  # Create fill color
  fill_color <- ifelse(tagSNPs$haplotype[i] == "H4", "#40004B", 
                       ifelse(tagSNPs$haplotype[i] == "H5", "#A6DBA0", 
                              ifelse(tagSNPs$haplotype[i] == "H6", "#762A83", "#D9F0D3")))
  
  # Apply annoHighlight for this SNP region
  annoHighlight(
    plot = genes, params = SNP,
    fill = fill_color,
    y = 2.1, height = 0.1, just = c("left", "top"), default.units = "inches"
  )
  
  
}

# plotRanges(
#   data = tagSNPs, chrom = "chr17",
#   chromstart = 45578800, chromend = 46277280,
#   assembly = "hg38",
#   order = "random",
#   collapse = TRUE,
#   fill = colorby("haplotype", palette =
#                    colorRampPalette(c("#40004B", "#A6DBA0", "#762A83", "#D9F0D3"))),
#   x = 0.5, y = 0.25, width = 5.5, height = 0.1,
#   just = c("left", "top"), default.units = "inches"
# )

[allTagSNPs_forPlot.txt](https://github.com/user-attachments/files/18578918/allTagSNPs_forPlot.txt)