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bernatgel / karyoploteR

karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome
https://bernatgel.github.io/karyoploter_tutorial/
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kpPlotManhattan not plotting manhattan plot #127

Closed Maetchild closed 2 years ago

Maetchild commented 2 years ago

Hello,

I'm having troubles with kpPlotManhattan. It does plot the genomewideline and the suggestive one, but not the SNPs data.

My input GRobject is the following: Schermata 2022-07-07 alle 12 19 02

And I'm using this code: kp <- plotKaryotype(plot.type=2, genome=bos.genome, chromosomes = c("chr4", "chr16")) kpAxis(kp, ymax=20) kp <- kpPlotManhattan(kp, data=gr, pval=gr$p, ymax=20, points.col="2blues")

What I obtained is this, apparently it does not read my p-values: Schermata 2022-07-07 alle 12 17 01

I'm sure it's something stupid by my side, just I cannot understand what. Do you have any insight? (I'm using: _R version 4.2.1 (2022-06-23) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS High Sierra 10.13.4 other attached packages: BSgenome.Btaurus.UCSC.bosTau9_1.4.2 BSgenome_1.64.0
rtracklayer_1.56.1 Biostrings_2.64.0
XVector_0.36.0 dplyr_1.0.9
readxl_1.4.0 BiocManager_1.30.18
data.table_1.14.2 karyoploteR_1.22.0
regioneR_1.28.0 GenomicRanges_1.48.0
GenomeInfoDb_1.32.2 IRanges_2.30.0
S4Vectors_0.34.0 BiocGenerics0.42.0

Thank you so much!

Maetchild commented 2 years ago

Solved!! The chromosomes have to be expressed as "chr1", "chr2", ecc... and not as "1", "2",...

Great package by the way!!

bernatgel commented 2 years ago

Yes! This is a very common problem with karyoploteR! I'm debating between creating a page explaining the problem in the tutorial site, o trying to identify this problem on the fly and warn the user about it. But I'm sure it's been a problem difficult enough for many people to ditch it before using it. In any case, glad you found the problem!