Question: error when using seeFastqPlot
0
gravatar for setarosd
3.0 years ago by
setarosd0
setarosd0 wrote:

I get the following error message when trying to plot my statslist obtained by seeFastq:

Error: Unknown parameters: binwidth, bins, origin, right

I followed the manual pages for seeFastq() and seeFastqPlot() and this is the code I used to get the stats plot:

> fqlist <- seeFastq(fastq=infile1(args), batchsize=10000, klength=8)
> pdf("results/fastqReport.pdf", height=18, width=4*length(fqlist))
> seeFastqPlot(fqlist)

The fqlist object seems to be fine (see output of str(fqlist) at end of post).

I guess this is a problem that has to do with the geom_histogram function in ggplot2, as googling revealed the same error for another package that uses this function (see https://github.com/hadley/ggplot2/issues/1465). I am not sure, though. Hope you can help.

Thank you,

Sabrina


Below is some more info on the versions I am using (including output of systemInfo() and traceback()).

I am using ggplot2 version 2.0.0, R version 3.2.3


Output of systemInfo()

R version 3.2.3 (2015-12-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

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] systemPipeR_1.4.7          RSQLite_1.0.0              DBI_0.3.1                  ShortRead_1.28.0           GenomicAlignments_1.6.3   
 [6] SummarizedExperiment_1.0.2 Biobase_2.30.0             BiocParallel_1.4.3         Rsamtools_1.22.0           Biostrings_2.38.3         
[11] XVector_0.10.0             GenomicRanges_1.22.3       GenomeInfoDb_1.6.1         IRanges_2.4.6              S4Vectors_0.8.7           
[16] BiocGenerics_0.16.1       

loaded via a namespace (and not attached):
 [1] genefilter_1.52.0      splines_3.2.3          lattice_0.20-33        colorspace_1.2-6       rtracklayer_1.30.1    
 [6] Category_2.36.0        GenomicFeatures_1.22.8 base64enc_0.1-3        XML_3.98-1.3           RBGL_1.46.0           
[11] survival_2.38-3        GOstats_2.36.0         RColorBrewer_1.1-2     lambda.r_1.1.7         plyr_1.8.3            
[16] stringr_1.0.0          zlibbioc_1.16.0        munsell_0.4.2          gtable_0.1.2           futile.logger_1.4.1   
[21] hwriter_1.3.2          latticeExtra_0.6-26    biomaRt_2.26.1         AnnotationDbi_1.32.3   GSEABase_1.32.0       
[26] Rcpp_0.12.3            xtable_1.8-0           edgeR_3.12.0           scales_0.3.0           checkmate_1.7.0       
[31] limma_3.26.5           graph_1.48.0           annotate_1.48.0        sendmailR_1.2-1        brew_1.0-6            
[36] BatchJobs_1.6          rjson_0.2.15           ggplot2_2.0.0          fail_1.3               digest_0.6.9          
[41] stringi_1.0-1          BBmisc_1.9             grid_3.2.3             tools_3.2.3            bitops_1.0-6          
[46] magrittr_1.5           RCurl_1.95-4.7         futile.options_1.0.0   GO.db_3.2.2            pheatmap_1.0.8        
[51] Matrix_1.2-3           AnnotationForge_1.12.2


Output from traceback()

8: stop("Unknown parameters: ", paste(extra, collapse = ", "), call. = FALSE)
7: layer(data = data, mapping = mapping, stat = stat, geom = GeomBar,
       position = position, show.legend = show.legend, inherit.aes = inherit.aes,
       params = list(binwidth = binwidth, bins = bins, origin = origin,
           right = right, na.rm = na.rm, ...))
6: geom_histogram(fill = "#0072B2", stat = "identity")
5: fastqPlot(x = fqlist[z])
4: FUN(X[[i]], ...)
3: lapply(names(fqlist), function(z) fastqPlot(x = fqlist[z]))
2: lapply(names(fqlist), function(z) fastqPlot(x = fqlist[z]))
1: seeFastqPlot(fqlist)


Output from str(fqlist):

List of 1
 $ A_bac:List of 9
  ..$ fqstats: Named num [1:3] 10000 1560521 8
  .. ..- attr(*, "names")= chr [1:3] "batchsize" "nReads" "klength"
  ..$ astats :'data.frame':    125 obs. of  6 variables:
  .. ..$ Cycle: Ord.factor w/ 125 levels "1"<"2"<"3"<"4"<..: 1 2 3 4 5 6 7 8 9 10 ...
  .. ..$ min  : num [1:125] 2 27 33 33 33 37 37 37 37 37 ...
  .. ..$ low  : num [1:125] 14 27 33 33 33 37 37 37 37 37 ...
  .. ..$ mid  : num [1:125] 33 33 33 33 33 37 37 37 37 37 ...
  .. ..$ top  : num [1:125] 33 33 33 33 33 37 37 37 37 37 ...
  .. ..$ max  : num [1:125] 33 33 33 33 33 37 37 37 37 37 ...
  ..$ bstats :'data.frame':    500 obs. of  3 variables:
  .. ..$ Base     : Factor w/ 4 levels "A","C","G","T": 1 2 3 4 1 2 3 4 1 2 ...
  .. ..$ Frequency: num [1:500] 0.346 0.287 0.167 0.2 0.297 ...
  .. ..$ Cycle    : Ord.factor w/ 125 levels "1"<"2"<"3"<"4"<..: 1 1 1 1 2 2 2 2 3 3 ...
  ..$ cstats :'data.frame':    500 obs. of  3 variables:
  .. ..$ Quality: num [1:500] 25.8 27.7 30.2 32.2 31.9 ...
  .. ..$ Base   : Factor w/ 4 levels "A","C","G","T": 1 1 1 1 1 1 1 1 1 1 ...
  .. ..$ Cycle  : Ord.factor w/ 125 levels "1"<"2"<"3"<"4"<..: 1 2 3 4 5 6 7 8 9 10 ...
  ..$ dstats :'data.frame':    125 obs. of  3 variables:
  .. ..$ RelDiv: num [1:125] NA NA NA NA NA ...
  .. ..$ Method: num [1:125] 1 1 1 1 1 1 1 1 1 1 ...
  .. ..$ Cycle : Ord.factor w/ 125 levels "1"<"2"<"3"<"4"<..: 1 2 3 4 5 6 7 8 9 10 ...
  ..$ estats :'data.frame':    25 obs. of  3 variables:
  .. ..$ minQuality: Ord.factor w/ 5 levels ">0"<">10"<">20"<..: 1 2 3 4 5 1 2 3 4 5 ...
  .. ..$ Percent   : num [1:25] 100 82.6 32.5 14.7 0 ...
  .. ..$ Outliers  : Ord.factor w/ 5 levels "0"<"1"<"2"<"3"<..: 1 1 1 1 1 2 2 2 2 2 ...
  ..$ fstats :'data.frame':    38 obs. of  2 variables:
  .. ..$ Quality: Ord.factor w/ 38 levels "0"<"1"<"2"<"3"<..: 1 2 3 4 5 6 7 8 9 10 ...
  .. ..$ Percent: num [1:38(1d)] 0 0 0.01 0 0 0.02 0.03 0.01 0.01 0.07 ...
  .. .. ..- attr(*, "dimnames")=List of 1
  .. .. .. ..$ : chr [1:38] "0" "1" "2" "3" ...
  ..$ gstats :'data.frame':    125 obs. of  2 variables:
  .. ..$ Cycle  : Ord.factor w/ 125 levels "1"<"2"<"3"<"4"<..: 1 2 3 4 5 6 7 8 9 10 ...
  .. ..$ Percent: num [1:125] 0 0 0 0 0 0 0 0 0 0 ...
  ..$ hstats :'data.frame':    2 obs. of  2 variables:
  .. ..$ nOccurrences: Ord.factor w/ 2 levels "1"<"2": 1 2
  .. ..$ Percent     : num [1:2] 1e+02 2e-02

 

ADD COMMENTlink modified 3.0 years ago by Thomas Girke1.7k • written 3.0 years ago by setarosd0
Answer: error when using seeFastqPlot
0
gravatar for Thomas Girke
3.0 years ago by
Thomas Girke1.7k
United States
Thomas Girke1.7k wrote:

Thanks for pointing this out. You are correct this error is caused by a recent change in the behavior of geom_histogram from ggplot2. I will commit the fix today. It should appear in systemPipeR release >=1.4.8 and devel >=1.5.8 tomorrow or the day after, or today via svn/github.

Thomas

ADD COMMENTlink written 3.0 years ago by Thomas Girke1.7k
Thank you, Thomas. On 26.01.2016 11:33 AM, Thomas Girke [bioc] wrote: > Activity on a post you are following on support.bioconductor.org > <https: support.bioconductor.org=""> > > User Thomas Girke <https: support.bioconductor.org="" u="" 993=""/> wrote > Answer: error when using seeFastqPlot > <https: support.bioconductor.org="" p="" 77462="" #77470="">: > > Thanks for pointing this out. You are correct this error is caused by > a recent change in the behavior of |geom_histogram| from |ggplot2|. I > will commit the fix today. It should appear in systemPipeR release > >=1.4.8 and devel >=1.5.8 tomorrow or the day after, or today via > svn/github. > > Thomas > > ------------------------------------------------------------------------ > > Post tags: systempiper, seeFastqPlot, software error, ggplot2, > geom_histogram > > You may reply via email or visit > A: error when using seeFastqPlot >
ADD REPLYlink written 3.0 years ago by setarosd0
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