Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Why are my lines in the GISTICChromPlot not straight? #1045

Open
HummelFa opened this issue Aug 25, 2024 · 1 comment
Open

Why are my lines in the GISTICChromPlot not straight? #1045

HummelFa opened this issue Aug 25, 2024 · 1 comment
Labels

Comments

@HummelFa
Copy link

So I loaded my GISTIC2.0 results via the following command:
laml_gistic = readGistic(gisticAllLesionsFile = "C:/Users/.../all_lesions.conf_90.txt", gisticAmpGenesFile = "C:/Users/.../amp_genes.conf_90.txt", gisticDelGenesFile = "C:/Users/.../del_genes.conf_90.txt", gisticScoresFile = "C:/Users/.../scores.gistic")

and created my ChromPlot using:
gisticChromPlot(laml_gistic, fdrCutOff = 0.25, markBands = "all", color = NULL, ref.build = "hg19", cytobandOffset = 0.015, txtSize = .8, cytobandTxtSize = 0.6, maf = NULL, mutGenes = NULL, y_lims = NULL, mutGenesTxtSize = 0.6)

But then, my output looks weird with obliquely lines like this:

image

What is the problem and why is it behaving like that? - How can I have just the usual straight lines?

ty!

Session info
R version 4.3.0 (2023-04-21 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22631)
Matrix products: default
locale:
[1] LC_COLLATE=German_Germany.utf8 LC_CTYPE=German_Germany.utf8 LC_MONETARY=German_Germany.utf8 LC_NUMERIC=C LC_TIME=German_Germany.utf8
time zone: Europe/Berlin
tzcode source: internal
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] openxlsx_4.2.6.1 dplyr_1.1.4 ggplot2_3.5.1 data.table_1.15.4 RaggedExperiment_1.24.2 GenomicRanges_1.52.1 GenomeInfoDb_1.36.4
[8] IRanges_2.34.1 S4Vectors_0.38.2 BiocGenerics_0.46.0 BiocManager_1.30.23 maftools_2.16.0
loaded via a namespace (and not attached):
[1] generics_0.1.3 utf8_1.2.4 bitops_1.0-7 stringi_1.8.4 lattice_0.21-8 digest_0.6.33
[7] magrittr_2.0.3 evaluate_0.24.0 grid_4.3.0 RColorBrewer_1.1-3 fastmap_1.1.1 Matrix_1.5-4
[13] zip_2.3.1 survival_3.5-5 fansi_1.0.6 scales_1.3.0 abind_1.4-5 cli_3.6.1
[19] rlang_1.1.1 crayon_1.5.3 XVector_0.40.0 Biobase_2.60.0 munsell_0.5.1 splines_4.3.0
[25] withr_3.0.1 DelayedArray_0.26.7 yaml_2.3.9 DNAcopy_1.74.1 S4Arrays_1.0.6 tools_4.3.0
[31] colorspace_2.1-1 GenomeInfoDbData_1.2.10 SummarizedExperiment_1.30.2 vctrs_0.6.5 R6_2.5.1 matrixStats_1.3.0
[37] lifecycle_1.0.4 zlibbioc_1.46.0 pkgconfig_2.0.3 pillar_1.9.0 gtable_0.3.5 Rcpp_1.0.13
[43] glue_1.7.0 tidyselect_1.2.1 xfun_0.45 tibble_3.2.1 rstudioapi_0.16.0 MatrixGenerics_1.12.3
[49] knitr_1.48 htmltools_0.5.6.1 rmarkdown_2.28 compiler_4.3.0 RCurl_1.98-1.14

Copy link

This issue is stale because it has been open for 60 days with no activity.

@github-actions github-actions bot added the stale label Oct 25, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
Projects
None yet
Development

No branches or pull requests

1 participant