Error with wavClusteR annotateClusters function
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S.k ▴ 10
@sk-10106
Last seen 6.2 years ago

I am getting an error when trying to run the annotateClusters function from the wavClusteR pipeline. All the other steps in the pipeline work. It appears to be an issue with the plotting. Any ideas? This step is quite far down the analysis pipeline, so I am not sure what other items might be relevant for sharing in order to troubleshoot the issue. The source data is a sorted bam file produced by bowtie/samtools, using mm10 samples. So far I have encountered this error with all of the samples I have tried to process. 

 

> annotateClusters( clusters = wavclusters,
+                txDB = txDB,
+                plot = TRUE,
+                verbose = TRUE)
Extracting genomic features from TranscriptDb object...
Computing overlaps with genomic features on the sense strand...
Considering non-mapped clusters and computing overlaps with genomic features on the antisense strand...
Error in labeller(label_df) :
  argument "value" is missing, with no default

 

> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.3 (Final)

locale:
[1] C

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

other attached packages:
 [1] GenomicFeatures_1.22.13            AnnotationDbi_1.32.3
 [3] Biobase_2.30.0                     BSgenome.Mmusculus.UCSC.mm10_1.4.0
 [5] BSgenome_1.38.0                    rtracklayer_1.30.4
 [7] wavClusteR_2.4.1                   Rsamtools_1.22.0
 [9] Biostrings_2.38.4                  XVector_0.10.0
[11] GenomicRanges_1.22.4               GenomeInfoDb_1.6.3
[13] IRanges_2.4.8                      S4Vectors_0.8.11
[15] BiocGenerics_0.16.1

loaded via a namespace (and not attached):
 [1] SummarizedExperiment_1.0.2 reshape2_1.4.1
 [3] splines_3.2.3              lattice_0.20-33
 [5] colorspace_1.2-6           chron_2.3-47
 [7] XML_3.98-1.4               survival_2.39-2
 [9] foreign_0.8-66             DBI_0.4
[11] BiocParallel_1.4.3         RColorBrewer_1.1-2
[13] splus2R_1.2-0              lambda.r_1.1.7
[15] foreach_1.4.3              plyr_1.8.3
[17] stringr_1.0.0              zlibbioc_1.16.0
[19] munsell_0.4.3              gtable_0.2.0
[21] futile.logger_1.4.1        codetools_0.2-14
[23] labeling_0.3               latticeExtra_0.6-28
[25] biomaRt_2.26.1             wmtsa_2.0-0
[27] Rcpp_0.12.4                acepack_1.3-3.3
[29] scales_0.4.0               Hmisc_3.17-4
[31] gridExtra_2.2.1            ggplot2_2.1.0
[33] stringi_1.0-1              grid_3.2.3
[35] ade4_1.7-4                 tools_3.2.3
[37] bitops_1.0-6               magrittr_1.5
[39] ifultools_2.0-1            RCurl_1.95-4.8
[41] RSQLite_1.0.0              Formula_1.2-1
[43] cluster_2.0.4              futile.options_1.0.0
[45] seqinr_3.1-3               MASS_7.3-45
[47] Matrix_1.2-6               data.table_1.9.6
[49] iterators_1.0.8            mclust_5.2
[51] rpart_4.1-10               GenomicAlignments_1.6.3
[53] nnet_7.3-12                compiler_3.2.3

 

wavcluster • 897 views
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@federicocomoglio-4524
Last seen 5.0 years ago
Switzerland

The issue is independent of your data sets (in fact the example code from ?annotateClusters is sufficient to generate it), and is due to recent changes in ggplot2. I fixed the issue and pushed the code to BioC devel (https://github.com/Bioconductor-mirror/wavClusteR).

Hope this helps.

Let me know.

Federico

 

 

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Thank you for your help. I need to run the developer version of R/Bioconductor to get the changes? Any idea when this will be pushed out to official releases?

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You can also install the package from my GitHub repository with

library(devtools)
install_github(repo = "FedericoComoglio/wavClusteR", ref = "devel", build_vignettes = TRUE)

I would strongly advise to upgrade to R 3.3.0. Hope this helps, Federico

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@federicocomoglio-4524
Last seen 5.0 years ago
Switzerland

Hi,

 

 

 

thanks for your message. The error is generated by the call below. I will look into it asap and get back to you/push the relevant changes to the devel branch. Meanwhile, can you just provide the first - say 100 - entries of the wavclusters object?

 

p <- ggplot( data = summaryDf,
            aes( x = Percentage, y = Compartment ) ) + 
             geom_point( colour = 'royalblue', size = 2 ) + 
             facet_grid( group ~ ., scales = 'free', labeller = changeLab ) +
            theme_bw()
            labs( title = 'Cluster annotation' ) +
            theme( plot.title = element_text( size = rel( 1 ) ) )

 

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