Question: Printing arrayQualityMetrics report
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7.0 years ago by
David Westergaard280 wrote:
Hello, I am trying to include an arrayQualityMetrics report in my appendix, but I am finding it very difficult to produce a pretty version as a pdf. I have tried simply to print to file in both Google Chrome and Iceweasel, and both of them are having trouble placing the figures correctly in the pdf. I have also tried to convert index.html to LaTeX using html2latex, which did not work either. Is it possible to produce a non-interactive pdf (Or something similar) which can be included in a thesis, written in LaTe, from arrayQualityMetrtics? I could not find any information about this in the documentation. Best, David
modified 7.0 years ago by Wolfgang Huber13k • written 7.0 years ago by David Westergaard280
Answer: Printing arrayQualityMetrics report
0
7.0 years ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:
Dear David I get a reasonable PDF with default settings on Firefox 13 on a Mac OS X 10.6.8. I will send you this off-list. However, it is not perfect and some twiddling with printer formating may improve things. I do not perceive the production of reports in (or fully automated conversion into) PDF as a high priority, and since your use case is a 'one-off', why don't you take the LaTeX that you get from html2latex and manually edit it to your needs? After all, the report is not exactly a very complex document, just a couple of text blocks with figures interspersed. Hope this helps Wolfgang Jun/21/12 5:01 PM, David Westergaard scripsit:: > Hello, > > I am trying to include an arrayQualityMetrics report in my appendix, > but I am finding it very difficult to produce a pretty version as a > pdf. I have tried simply to print to file in both Google Chrome and > Iceweasel, and both of them are having trouble placing the figures > correctly in the pdf. I have also tried to convert index.html to LaTeX > using html2latex, which did not work either. > > Is it possible to produce a non-interactive pdf (Or something similar) > which can be included in a thesis, written in LaTe, from > arrayQualityMetrtics? I could not find any information about this in > the documentation. > > Best, > David > -- Best wishes Wolfgang Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber
Dear James that is one way to go about it. A more direct way for getting at this table is to keep the return value of the call to the function arrayQualityMetrics: myReport = arrayQualityMetrics( eset, ...) and access the table via myReport$arrayTable Please use arrayQualityMetrics >= 3.13.5 for this (unfortunately in previous versions due to an oversight of mine this object was not propagated all the way to the return value of arrayQualityMetrics). Version 3.13.5 is in svn and should also soon be on the website / in the package repository. It also fixes the 'intgroup' issue reported by Sonal and Tim. Best wishes Wolfgang James F. Reid scripsit 06/22/2012 10:11 AM: ...[snip] > you could extract the table contents using the readHTMLTable function > from the 'XML' package and for the figures just include the pdfs as > figures and add a caption to them. > > HTH, > J. Best wishes Wolfgang Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber ADD REPLYlink written 7.0 years ago by Wolfgang Huber13k Hi, I actually managed to produce a sufficient pdf to include just by upgrading my browser and fixing minor issues in inkscape. Thanks for the help, David 2012/6/22 Wolfgang Huber <whuber at="" embl.de="">: > Dear James > > that is one way to go about it. A more direct way for getting at this table > is to keep the return value of the call to the function arrayQualityMetrics: > > ?myReport = arrayQualityMetrics( eset, ...) > > and access the table via > > ?myReport$arrayTable > > Please use arrayQualityMetrics >= 3.13.5 for this (unfortunately in previous > versions due to an oversight of mine this object was not propagated all the > way to the return value of arrayQualityMetrics). > > Version 3.13.5 is in svn and should also soon be on the website / in the > package repository. It also fixes the 'intgroup' issue reported by Sonal and > Tim. > > ? ? ? ?Best wishes > ? ? ? ?Wolfgang > > > > > > James F. Reid scripsit 06/22/2012 10:11 AM: > > ...[snip] > > >> you could extract the table contents using the readHTMLTable function >> from the 'XML' package and for the figures just include the pdfs as >> figures and add a caption to them. >> >> HTH, >> J. > > > Best wishes > ? ? ? ?Wolfgang > > Wolfgang Huber > EMBL > http://www.embl.de/research/units/genome_biology/huber > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor