Hi Guys Now that I am able to create basic reports which already are a great time saver. I am wondering do I have some flexibility to decide where to render images and some page formatting options. For example I have three specific requirements at this point. 1. Left align the whole page. Currently a rendered table is centered cutting the displayed text as it is horizontally broad 2. put multiple images in a single row; in other words put 2-3 images side by side in a row. Thanks! -Abhi

Hi Abhi, I'm glad that you've gotten RpeortingTools working. Perhaps Josh can discuss a bit how to customize the alignment and spacing of the tables that are produced. I'm much less familiar with the CSS options that exist. For your second question, we can look to the examples in the microarray analysis vignette for some hints about how to do this. In the "Differential expression analysis using limma" section, there's a function for producing one plot per row in the table. We can extend this example like this: > library(hwriter) > makeNewImages <- function(df,...){ + imagenames1 <- paste0(df$ProbeId, "_1") + imagenames2 <- paste0(df$ProbeId, "_2") + imagenames3 <- paste0(df$ProbeId, "_3") + for (i in 1:nrow(df)){ + probeId <- df$ProbeId[i] + pl1 <- xyplot(...) + pl2 <- xyplot(...) + pl3 <- xyplot(...) + png(filename = paste0("./reports/figuresde_analysis/", + imagenames1[i])) + print(pl1) + dev.off() + png(filename = paste0("./reports/figuresde_analysis/", + imagenames2[i])) + print(pl2) + dev.off() + png(filename = paste0("./reports/figuresde_analysis/", + imagenames3[i])) + print(pl3) + dev.off() + + } + image.link1 <- hwriteImage(paste0("figuresde_analysis/", imagenames1), + table=FALSE, width=100) + image.link2 <- hwriteImage(paste0("figuresde_analysis/", imagenames1), + table=FALSE, width=100) + image.link3 <- hwriteImage(paste0("figuresde_analysis/", imagenames1), + table=FALSE, width=100) + df <- data.frame(df, Image1 = image.link1, Image2 = image.link2, Image3 = image.link3) + return(df) + } > publish(my.df, my.report, .modifyDF = makeNewImages) > finish(my.report) This will work easiest with lattice- or ggplot2-based graphics, because you can follow the pattern above. Otherwise, you can use recordPlot to capture the images as in the vignette. The above example also makes the three images in one function, but you could have three functions and pass a list of the three functions to .modifyDF, and achieve the same result. Let me know if you need any help with getting this to work. Cheers, Jason On Mon, Jun 17, 2013 at 3:45 PM, Abhishek Pratap <apratap@lbl.gov> wrote: > Hi Guys > > Now that I am able to create basic reports which already are a great > time saver. I am wondering do I have some flexibility to decide where > to render images and some page formatting options. > > For example I have three specific requirements at this point. > > 1. Left align the whole page. Currently a rendered table is centered > cutting the displayed text as it is horizontally broad > > 2. put multiple images in a single row; in other words put 2-3 images > side by side in a row. > > > Thanks! > -Abhi > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Jason A. Hackney, Ph.D. Bioinformatics and Computational Biology Genentech hackney.jason@gene.com 650-467-5084 [[alternative HTML version deleted]]