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Question: Error with wavClusteR annotateClusters function
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gravatar for S.k
2.6 years ago by
S.k10
S.k10 wrote:

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

 

ADD COMMENTlink modified 2.6 years ago by federico.comoglio100 • written 2.6 years ago by S.k10
1
gravatar for federico.comoglio
2.6 years ago by
Switzerland
federico.comoglio100 wrote:

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

 

 

ADD COMMENTlink written 2.6 years ago by federico.comoglio100

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?

ADD REPLYlink written 2.6 years ago by S.k10

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

ADD REPLYlink written 2.6 years ago by federico.comoglio100
0
gravatar for federico.comoglio
2.6 years ago by
Switzerland
federico.comoglio100 wrote:

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 ) ) )

 

ADD COMMENTlink written 2.6 years ago by federico.comoglio100
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