kpPlotGenes: Overlapping gene names margin increase

[Hanuphant]

Hi Bernat,

Thanks for this versatile tool. I had a query where we can adjust the gene margin a bit more to accommodate the gene names as well along with the names. I was hoping if someone could help me out in this regard.

The current plots that I have now look this.

I do understand the genes are too small to be plot and have labels, but I was hoping how I could increase the gap between overlapping gene names a bit more.

Attached is my code for plotting.

kp <- plotKaryotype(plot.type = 2, zoom = SNAPC3.region, cex = 1, plot.params = pp)
kpDataBackground(kp, data.panel = 1, col = "grey98")
kpPlotGenes(kp, gene.data, r0 = 0.2, r1 = 0.4, gene.name.cex = 0.8, data.panel = 2, gene.margin = 1, col = "darkmagenta", gene.name.col = "black", gene.name.position = "top")
kpDataBackground(kp, data.panel = 2, col = "grey98", r0 = 0.6, r1 = 0.7)

[Hanuphant]

Is there a way to subset gene.data based on the gene_ids so I can plot the gene ids I'd want. Something which works like this (obviously this doesn't work)?

gene.data <- gene.data$genes[gene.data$genes$gene_id %in% ranges.df[ranges.df$coverage == unique(ranges.df$coverage)[1],]$names]

[Hanuphant]

I do see we can use Txdb objects to customize the gene names and was wondering how can I filter Txdb object so that I can get what I want?

[h20gg702]

Hi, I faced the same problem and found the solution. I used the following script to filter the gene which I want to.

`kp <- plotKaryotype(zoom = grW, cex=1, plot.type=2,
main=position)
kpAddBaseNumbers(kp, tick.dist = 10000, minor.tick.dist = 2000,
add.units = TRUE, cex=1, digits = 6)

genes.data <- makeGenesDataFromTxDb(TxDb.Hsapiens.UCSC.hg38.knownGene,
karyoplot=kp,
plot.transcripts = TRUE,
plot.transcripts.structure = TRUE)
###--- merge all trascripts of each gene into one and addGeneNames ---###
genes.data <- addGeneNames(genes.data)
genes.data <- mergeTranscripts(genes.data)

Keep only the gene data for gene "54507"

genes.data$genes <- genes.data$genes[genes.data$genes$gene_id == "54507", ]

Keep only the transcripts data for gene "54507"

genes.data$transcripts <- genes.data$transcripts["54507"]

kpPlotGenes(kp, data=genes.data, r0=0, r1=0.35, gene.name.cex = 1, data.panel = 1)`

I do see we can use Txdb objects to customize the gene names and was wondering how can I filter Txdb object so that I can get what I want?