search

PoisonAlien / maftools

Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.
http://bioconductor.org/packages/release/bioc/html/maftools.html
MIT License
450 stars 222 forks source link

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

Open HummelFa opened 2 months ago

HummelFa commented 2 months ago

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

github-actions[bot] commented 3 weeks ago

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

github-actions[bot] commented 1 week ago

This issue was closed because it has been inactive for 14 days since being marked as stale.

HummelFa commented 1 week ago

Is there no one, who can give an answer, since I still have the problem?

PoisonAlien commented 1 week ago

Hi Fabian,

Sorry for the tardy response. I will look into it soon.