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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
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gisticChromPlot Error #392

Closed Tinalxt closed 4 years ago

Tinalxt commented 5 years ago

Hi,

I used the gisticChromPlot function but got an error. I think that is because my data had not significant amp cnvs.

The code is as follow:

>laml.gistic = readGistic(gisticAllLesionsFile = all.lesions, gisticAmpGenesFile = amp.genes, 
                         gisticDelGenesFile = del.genes, gisticScoresFile = scores.gis, isTCGA = FALSE)
>gisticChromPlot(gistic = laml.gistic, markBands = "all")
Error in if (nrow(gis.scores[["Amp"]]) > 0) { : 
  argument is of length zero

I used the same files in R 3.5 and it was worked but not in R 3.6. Is this a problem caused by the version of R?

PoisonAlien commented 5 years ago

Hi, Its hard to guess the issue. Could you please post your sessionInfo? Also is there any chance to get a reproducible example data?

Tinalxt commented 5 years ago

Hi, Its hard to guess the issue. Could you please post your sessionInfo? Also is there any chance to get a reproducible example data? all_lesions.conf_99.txt del_genes.conf_99.txt amp_genes.conf_99.txt scores.gistic.txt

Hi, these are my files and sessioninfo. ─ Session info ───────────────────────────────────────────── setting value
version R version 3.6.1 (2019-07-05) os macOS Sierra 10.12.6
system x86_64, darwin15.6.0
ui RStudio
language (EN)
collate zh_CN.UTF-8
ctype zh_CN.UTF-8
tz Asia/Shanghai
date 2019-09-22

─ Packages ───────────────────────────────────────────── package version date lib source
assertthat 0.2.1 2019-03-21 [1] CRAN (R 3.6.0) bibtex 0.4.2 2017-06-30 [1] CRAN (R 3.6.0) Biobase 2.44.0 2019-05-02 [1] Bioconductor
BiocGenerics 0.30.0 2019-05-02 [1] Bioconductor
BiocManager 1.30.4 2018-11-13 [1] CRAN (R 3.6.0) BiocParallel 1.18.1 2019-08-06 [1] Bioconductor
Biostrings 2.52.0 2019-05-02 [1] Bioconductor
bitops 1.0-6 2013-08-17 [1] CRAN (R 3.6.0) BSgenome 1.52.0 2019-05-02 [1] Bioconductor
BSgenome.Hsapiens.UCSC.hg19 1.4.0 2019-08-26 [1] Bioconductor
circlize 0.4.7 2019-08-21 [1] CRAN (R 3.6.0) cli 1.1.0 2019-03-19 [1] CRAN (R 3.6.0) clue 0.3-57 2019-02-25 [1] CRAN (R 3.6.0) cluster 2.1.0 2019-06-19 [1] CRAN (R 3.6.1) codetools 0.2-16 2018-12-24 [1] CRAN (R 3.6.1) colorspace 1.4-1 2019-03-18 [1] CRAN (R 3.6.0) ComplexHeatmap 2.0.0 2019-05-02 [1] Bioconductor
crayon 1.3.4 2017-09-16 [1] CRAN (R 3.6.0) curl 4.0 2019-07-22 [1] CRAN (R 3.6.0) data.table 1.12.2 2019-04-07 [1] CRAN (R 3.6.0) DelayedArray 0.10.0 2019-05-02 [1] Bioconductor
digest 0.6.20 2019-07-04 [1] CRAN (R 3.6.0) doParallel 1.0.15 2019-08-02 [1] CRAN (R 3.6.0) dplyr 0.8.3 2019-07-04 [1] CRAN (R 3.6.0) foreach 1.4.7 2019-07-27 [1] CRAN (R 3.6.0) GenomeInfoDb 1.20.0 2019-05-02 [1] Bioconductor
GenomeInfoDbData 1.2.1 2019-08-25 [1] Bioconductor
GenomicAlignments 1.20.1 2019-06-18 [1] Bioconductor
GenomicRanges 1.36.0 2019-05-02 [1] Bioconductor
GetoptLong 0.1.7 2018-06-10 [1] CRAN (R 3.6.0) ggplot2 3.2.1 2019-08-10 [1] CRAN (R 3.6.0) GlobalOptions 0.1.0 2018-06-09 [1] CRAN (R 3.6.0) glue 1.3.1 2019-03-12 [1] CRAN (R 3.6.0) gridBase 0.4-7 2014-02-24 [1] CRAN (R 3.6.0) gtable 0.3.0 2019-03-25 [1] CRAN (R 3.6.0) IRanges * 2.18.2 2019-08-24 [1] Bioconductor
iterators 1.0.12 2019-07-26 [1] CRAN (R 3.6.0) jsonlite 1.6 2018-12-07 [1] CRAN (R 3.6.0) lattice 0.20-38 2018-11-04 [1] CRAN (R 3.6.1) lazyeval 0.2.2 2019-03-15 [1] CRAN (R 3.6.0) *maftools 2.0.16 2019-08-14 [1] Bioconductor*
magrittr 1.5 2014-11-22 [1] CRAN (R 3.6.0) Matrix 1.2-17 2019-03-22 [1] CRAN (R 3.6.1) matrixStats 0.54.0 2018-07-23 [1] CRAN (R 3.6.0) munsell 0.5.0 2018-06-12 [1] CRAN (R 3.6.0) NMF 0.21.0 2018-03-06 [1] CRAN (R 3.6.0) pheatmap 1.0.12 2019-01-04 [1] CRAN (R 3.6.0) pillar 1.4.2 2019-06-29 [1] CRAN (R 3.6.0) pixmap 0.4-11 2011-07-19 [1] CRAN (R 3.6.0) pkgconfig 2.0.2 2018-08-16 [1] CRAN (R 3.6.0) pkgmaker 0.27 2018-05-25 [1] CRAN (R 3.6.0) plyr 1.8.4 2016-06-08 [1] CRAN (R 3.6.0) png 0.1-7 2013-12-03 [1] CRAN (R 3.6.0) purrr 0.3.2 2019-03-15 [1] CRAN (R 3.6.0) R6 2.4.0 2019-02-14 [1] CRAN (R 3.6.0) randomcoloR 1.1.0 2017-12-08 [1] CRAN (R 3.6.0) RColorBrewer 1.1-2 2014-12-07 [1] CRAN (R 3.6.0) Rcpp 1.0.2 2019-07-25 [1] CRAN (R 3.6.0) RCurl 1.95-4.12 2019-03-04 [1] CRAN (R 3.6.0) registry 0.5-1 2019-03-05 [1] CRAN (R 3.6.0) reshape2 1.4.3 2017-12-11 [1] CRAN (R 3.6.0) rjson 0.2.20 2018-06-08 [1] CRAN (R 3.6.0) rlang 0.4.0 2019-06-25 [1] CRAN (R 3.6.0) rngtools 1.4 2019-07-01 [1] CRAN (R 3.6.0) Rsamtools 2.0.0 2019-05-02 [1] Bioconductor
rtiff 1.4.6 2019-03-21 [1] CRAN (R 3.6.0) rtracklayer 1.44.3 2019-08-24 [1] Bioconductor
Rtsne 0.15 2018-11-10 [1] CRAN (R 3.6.0) S4Vectors 0.22.0 2019-05-02 [1] Bioconductor
scales 1.0.0 2018-08-09 [1] CRAN (R 3.6.0) sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.6.0) shape 1.4.4 2018-02-07 [1] CRAN (R 3.6.0) stringi 1.4.3 2019-03-12 [1] CRAN (R 3.6.0) stringr 1.4.0 2019-02-10 [1] CRAN (R 3.6.0) SummarizedExperiment 1.14.1 2019-07-31 [1] Bioconductor
survival 2.44-1.1 2019-04-01 [1] CRAN (R 3.6.1) tibble 2.1.3 2019-06-06 [1] CRAN (R 3.6.0) tidyselect 0.2.5 2018-10-11 [1] CRAN (R 3.6.0) V8 2.3 2019-07-02 [1] CRAN (R 3.6.0) withr 2.1.2 2018-03-15 [1] CRAN (R 3.6.0) wordcloud 2.6 2018-08-24 [1] CRAN (R 3.6.0) XML 3.98-1.20 2019-06-06 [1] CRAN (R 3.6.0) xtable 1.8-4 2019-04-21 [1] CRAN (R 3.6.0) XVector 0.24.0 2019-05-02 [1] Bioconductor
zlibbioc 1.30.0 2019-05-02 [1] Bioconductor

PoisonAlien commented 5 years ago

Hello, Sorry for late reply, and Thank for the example files. Indeed there were no significant peaks in your dataset to highlight. However if you increase your fdrcutOff = 0.3 you will see some peaks getting highlighted. In any case, I have made tiny changes to the function to handle such situations. You can install it form GitHub if you would like. Please let me know if it helps.