Question

DEP package: error in plot_heatmap

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Rob • 0

@rob-21555

Last seen 3.0 years ago

Germany

I am using the DEP package from Bioconductor for some proteomics analysis. I found a bug in the plotheatmap function: it works well when the argument plot=TRUE (default), but it does return an error when plot= FALSE. I need this information to retrieve the coordinates to get the Genenames from my different clusters. Example from the default of DEP package:

library(DEP)
data <- UbiLength
data_unique <- make_unique(data, "Gene.names", "Protein.IDs", delim = ";")
columns <- grep("LFQ.", colnames(data_unique))
exp_design <- UbiLength_ExpDesign
se <- make_se(data_unique, columns, exp_design)
filt <- filter_missval(se, thr = 0)
imputed <- impute(filt, fun = "MinProb", q = 0.01)
diff <- test_diff(imputed, "control", "Ctrl")
dep <- add_rejections(diff, alpha = 0.05, lfc = 1)
plot_heatmap(dep, 'centered', kmeans = TRUE, k = 6, row_font_size = 3, plot=TRUE) #all good until here
plot_heatmap(dep, 'centered', kmeans = TRUE, k = 6, row_font_size = 3, plot=FALSE)

The last command will return the error:

  Error in rownames_to_column(., var = "protein") : 
  is.data.frame(df) is not TRUE

Can I do something to solve this issue?

DEP • 1.5k views

ADD COMMENT • link updated 5.3 years ago by arne.smits ▴ 70 • written 5.3 years ago by Rob • 0

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Dear robert.arsie,

Thank you for pointing out the bug. I am working on it and will let you know once a fix is available.

Best, Arne

ADD REPLY • link 5.3 years ago arne.smits ▴ 70

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> sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] imputeLCMD_2.0      impute_1.58.0       pcaMethods_1.76.0   Biobase_2.44.0      BiocGenerics_0.30.0 norm_1.0-9.5        tmvtnorm_1.4-10    
 [8] gmm_1.6-2           sandwich_2.5-1      Matrix_1.2-17       mvtnorm_1.0-10      DEP_1.6.0          

loaded via a namespace (and not attached):
 [1] ProtGenerics_1.16.0         bitops_1.0-6                matrixStats_0.54.0          doParallel_1.0.14           RColorBrewer_1.1-2         
 [6] GenomeInfoDb_1.20.0         MSnbase_2.10.0              tools_3.6.0                 R6_2.4.0                    DT_0.6                     
[11] affyio_1.54.0               lazyeval_0.2.2              colorspace_1.4-1            GetoptLong_0.1.7            tidyselect_0.2.5           
[16] compiler_3.6.0              preprocessCore_1.46.0       fdrtool_1.2.15              DelayedArray_0.10.0         scales_1.0.0               
[21] readr_1.3.1                 affy_1.62.0                 digest_0.6.19               XVector_0.24.0              pkgconfig_2.0.2            
[26] htmltools_0.3.6             limma_3.40.2                htmlwidgets_1.3             rlang_0.3.4                 GlobalOptions_0.1.0        
[31] rstudioapi_0.10             shiny_1.3.2                 shape_1.4.4                 zoo_1.8-5                   mzID_1.22.0                
[36] BiocParallel_1.17.18        dplyr_0.8.0.1               RCurl_1.95-4.12             magrittr_1.5                GenomeInfoDbData_1.2.1     
[41] MALDIquant_1.19.3           Rcpp_1.0.1                  munsell_0.5.0               S4Vectors_0.22.0            vsn_3.52.0                 
[46] MASS_7.3-51.4               SummarizedExperiment_1.14.0 zlibbioc_1.30.0             plyr_1.8.4                  grid_3.6.0                 
[51] promises_1.0.1              shinydashboard_0.7.1        crayon_1.3.4                lattice_0.20-38             circlize_0.4.6             
[56] hms_0.4.2                   mzR_2.18.0                  ComplexHeatmap_2.0.0        pillar_1.4.0                GenomicRanges_1.36.0       
[61] rjson_0.2.20                codetools_0.2-16            XML_3.98-1.19               glue_1.3.1                  BiocManager_1.30.4         
[66] png_0.1-7                   httpuv_1.5.1                foreach_1.4.4               tidyr_0.8.3                 gtable_0.3.0               
[71] purrr_0.3.2                 clue_0.3-57                 assertthat_0.2.1            ggplot2_3.1.1               mime_0.6                   
[76] xtable_1.8-4                later_0.8.0                 ncdf4_1.16.1                tibble_2.1.1                iterators_1.0.10           
[81] IRanges_2.18.0              cluster_2.0.9

ADD REPLY • link 5.3 years ago Rob • 0

score 1 · Accepted Answer · 2019-08-11

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arne.smits ▴ 70

@arnesmits-12878

Last seen 5.3 years ago

Dear robert.arsie,

A fix is available in the new version of DEP (version 1.6.1).

# Update Bioconductor packages:
BiocManager::install()

Best, Arne

ADD COMMENT • link 5.3 years ago arne.smits ▴ 70