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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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median option lost target when use plotmafSummary function #141

Closed ShixiangWang closed 6 years ago

ShixiangWang commented 6 years ago

Hello @PoisonAlien ,

When I learn the usage of this package, I find something very strange. The median option do not function in plotmafSummary and lost its target.

When use command

plotmafSummary(maf = laml, rmOutlier = TRUE, addStat = 'median', dashboard = TRUE, titvRaw = FALSE)

get

image

When use command 

plotmafSummary(maf = laml.plus.gistic, rmOutlier = TRUE, addStat = 'median', dashboard = TRUE, titvRaw = FALSE)

get

image

the laml and laml.plus.gistic are objects from your extend data, I think you know what they mean.

Do you have any idea to work around?

PoisonAlien commented 6 years ago

Hi, Could you post your sessionInfo ?

ShixiangWang commented 6 years ago 
> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 17.10

Matrix products: default
BLAS: /home/diviner-wsx/anaconda/lib/R/lib/libRblas.so
LAPACK: /home/diviner-wsx/anaconda/lib/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=zh_CN.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=zh_CN.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=zh_CN.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=zh_CN.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] survminer_0.4.1      ggpubr_0.1.6         magrittr_1.5         survival_2.41-3     
 [5] bindrcpp_0.2         forcats_0.2.0        stringr_1.2.0        dplyr_0.7.4         
 [9] purrr_0.2.4          readr_1.1.1          tidyr_0.7.2          tibble_1.4.1        
[13] ggplot2_2.2.1        tidyverse_1.2.1      maftools_1.4.27      Biobase_2.38.0      
[17] BiocGenerics_0.24.0  RevoUtils_10.0.8     RevoUtilsMath_10.0.1

loaded via a namespace (and not attached):
  [1] colorspace_1.3-2           rjson_0.2.15               mclust_5.4                
  [4] circlize_0.4.3             XVector_0.18.0             GenomicRanges_1.30.3      
  [7] GlobalOptions_0.0.13       rstudioapi_0.7             ggrepel_0.7.0             
 [10] bit64_0.9-7                AnnotationDbi_1.40.0       lubridate_1.7.1           
 [13] xml2_1.1.1                 codetools_0.2-15           splines_3.4.3             
 [16] mnormt_1.5-5               doParallel_1.0.12          knitr_1.18                
 [19] jsonlite_1.5               Rsamtools_1.30.0           km.ci_0.5-2               
 [22] broom_0.4.3                gridBase_0.4-7             cluster_2.0.6             
 [25] compiler_3.4.3             httr_1.3.1                 assertthat_0.2.0          
 [28] Matrix_1.2-12              lazyeval_0.2.1             cli_1.0.0                 
 [31] prettyunits_1.0.2          tools_3.4.3                gtable_0.2.0              
 [34] glue_1.2.0                 GenomeInfoDbData_1.0.0     reshape2_1.4.3            
 [37] Rcpp_0.12.14               slam_0.1-42                cellranger_1.1.0          
 [40] NMF_0.21.0                 Biostrings_2.46.0          nlme_3.1-131              
 [43] rtracklayer_1.38.3         iterators_1.0.9            changepoint_2.2.2         
 [46] psych_1.7.8                rvest_0.3.2                rngtools_1.2.4            
 [49] XML_3.98-1.10              zlibbioc_1.24.0            zoo_1.8-0                 
 [52] scales_0.5.0               BSgenome_1.46.0            VariantAnnotation_1.24.5  
 [55] hms_0.4.0                  SummarizedExperiment_1.8.1 RColorBrewer_1.1-2        
 [58] ComplexHeatmap_1.17.1      yaml_2.1.16                memoise_1.1.0             
 [61] gridExtra_2.3              KMsurv_0.1-5               pkgmaker_0.22             
 [64] biomaRt_2.34.2             stringi_1.1.6              RSQLite_2.0               
 [67] S4Vectors_0.16.0           foreach_1.4.5              RMySQL_0.10.14            
 [70] GenomicFeatures_1.30.3     BiocParallel_1.12.0        shape_1.4.4               
 [73] GenomeInfoDb_1.14.0        rlang_0.1.6                pkgconfig_2.0.1           
 [76] matrixStats_0.53.1         bitops_1.0-6               lattice_0.20-35           
 [79] bindr_0.1                  cmprsk_2.2-7               GenomicAlignments_1.14.2  
 [82] labeling_0.3               cowplot_0.9.2              bit_1.1-12                
 [85] plyr_1.8.4                 R6_2.2.2                   IRanges_2.12.0            
 [88] DelayedArray_0.4.1         DBI_0.7                    pillar_1.0.1              
 [91] haven_1.1.0                foreign_0.8-69             RCurl_1.95-4.10           
 [94] crayon_1.3.4               modelr_0.1.1               survMisc_0.5.4            
 [97] wordcloud_2.5              GetoptLong_0.1.6           progress_1.1.2            
[100] grid_3.4.3                 readxl_1.0.0               data.table_1.10.4-3       
[103] blob_1.1.1                 digest_0.6.13              xtable_1.8-2              
[106] stats4_3.4.3               munsell_0.4.3              registry_0.5
PoisonAlien commented 6 years ago

Hi, Thanks for the report, it was indeed a bug. I have fixed it. Can you install the package from GitHub and see if you have the same issue ? Note that on May 1st new bioconductor releases (3_7), and I have made few changes to the package including to the mafsummary plot. You won't be able to add the label, and plot might look bit different.

ShixiangWang commented 6 years ago

OK, I am looking forward to the latest version. Would you update the usage of these functions at https://bioconductor.org/packages/release/bioc/vignettes/maftools/inst/doc/maftools.html? I think I need more time to be familiar with this powerful package.