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sendplot

sendplot. Lori Shepherd April 06, 2009. sendplot. The Problem: The Approach:. How can we quickly generate useful data and get it back to scientists/collaborators with minimal requirements/effort on their end?.

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sendplot

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  1. sendplot Lori Shepherd April 06, 2009

  2. sendplot The Problem: The Approach: How can we quickly generate useful data and get it back to scientists/collaborators with minimal requirements/effort on their end? We have developed an R package called sendplot based on Dr. Sucheston’s visualization demo given on September 4, 2007

  3. What is sendplot? sendplot generates an interactive layout of plots. each plot may be interactive or static What is meant by interactivity is that information specific to a point or image region is displayed when the mouse scrolls over the area A png file and an html file are sent to end user; it can be sent to and run on any machine with a web browser that has javascript capabilities

  4. End Result Result is two files: 1. png file 2. html file The researcher/collaborator need only to open the html file in order to have an interactive graph to view data. It can be customized on the programmers end to show any data the researcher requests or would find useful

  5. System Requirementsfor Programmer • R www.r-project.org/ • libtiff www.libtiff.org/ All system requirements are free for download A version of this software that will no longer need system requirements, except R, is being created. Please check future releases. Previous versions of this software, available on CRAN, do not require system requirements except for R. The functionality is limited to only one plot in the layout being interactive, while the other plots of the layout are static. It also may require more steps for the user.

  6. Main sendplot functions • initSplot : this function creates an object of the type ’Splot’ which holds all information to generate a static layout of plots. • makeImap : this function adds image mapping information to the Splot object to allow for figure interactivity. • makeSplot : this function produces an interactive (or static) layout of plots.

  7. Wrappers Functions • xy.send : this function produces an interactive xy plot without any additional plots (i.e., just a single scatter-plot). • imagesend : this function produces an interactive image plot without any additional plots (i.e., just a single image plot). • heatmap.send : this function is a wrapper for the R stats package heatmap. This will create an interactive heatmap image. NOTE: The majority of the code for this function is verbatim from the R package stats heatmap function. This function was designed to work as a wrapper to utilize the same functionality and plotting as the heatmap function with sendplot’s interactive functionality.

  8. Object Oriented Approach • sendplot takes on an object oriented feel: • creating an object (initSplot) • manipulating the object (makeImap) • acting on the object to display contents (makeSplot) Let’s look at sendplot functions a little more closely...

  9. initSplot: initializing object initSplot( mat, plot.calls, Iflag=NA, figTypes=NA, mai.mat=NA, mai.prc=FALSE, plot.extras = NA, source.plot=NA, image.size="800x1100", pointsize=12, res=NA, ps.paper="letter",ps.width=8,ps.height=11, returnVl=T, saveFlag=F,saveName="Splot.RData")

  10. initSplot: initializing object initSplot( mat, plot.calls, Iflag=NA, figTypes=NA, mai.mat=NA, mai.prc=FALSE, plot.extras = NA, source.plot=NA, image.size="800x1100", pointsize=12, res=NA, ps.paper="letter",ps.width=8,ps.height=11, returnVl=T, saveFlag=F,saveName="Splot.RData")

  11. How it works: initSplot argument mat determines the layout of the plots using R’s layout function. mat is a numeric matrix with numbers 1:number of desired plots. 0 indicates area with no plot 4 4 4 4 4 4 4 4 0 0 0 0 0 4 4 4 4 4 4 4 4 0 0 0 0 0 1 1 1 1 1 1 1 1 3 3 3 3 3 1 1 1 1 1 1 1 1 3 3 3 3 3 1 1 1 1 1 1 1 1 3 3 3 3 3 1 1 1 1 1 1 1 1 3 3 3 3 3 1 1 1 1 1 1 1 1 3 3 3 3 3 1 1 1 1 1 1 1 1 3 3 3 3 3 2 2 2 2 2 2 2 2 3 3 3 3 3 2 2 2 2 2 2 2 2 3 3 3 3 3 2 2 2 2 2 2 2 2 3 3 3 3 3 2 2 2 2 2 2 2 2 3 3 3 3 3

  12. How it works: plot.calls is a character vector with the plot call that will be executed plot.calls = c( "boxplot(count ~ spray, data = InsectSprays, col = 'lightgray')", "plot(1:3,1:3, col='blue', xlab='', ylab=''); points(1:2, 2:3, col='red')", "image(1:2,1:3, z=matrix(myX,ncol=3,nrow=2), xlab='', ylab='')", "plot(cos, xlim = c(-pi,3*pi), n = 1001, col = 'blue', xlab='', ylab='')" you can combined calls with a semicolon “plot(1:3,1:3, col='blue', xlab='', ylab=''); points(1:2, 2:3, col='red')"

  13. initSplot: initializing object initSplot( mat, plot.calls, Iflag=NA, figTypes=NA, mai.mat=NA, mai.prc=FALSE, plot.extras = NA, source.plot=NA, image.size="800x1100", pointsize=12, res=NA, ps.paper="letter",ps.width=8,ps.height=11, returnVl=T, saveFlag=F,saveName="Splot.RData") Let’s look at an example...

  14. plot.extras argument plot.extras=list( figure1= "rect(xleft=c(3,1), ytop=c(25,5),xright=c(4,2), ybottom=c(20,0)); title(main='A', cex=3)", figure2=list(c("polygon(x=c(2,2.5,3,2.5), y=c(1,2.5,1,1.5))"), c("title(main='B', cex=3)")), figure3 ="title(main='C', cex=3)", figure4="title(main='D', cex=3)“) Based on previous plot.calls, the rectangles in the box plot, the polygon in the scatterplot, and all plot titles (A,B,C,D) have not been drawn. How are these added?

  15. initSplot: initializing object initSplot( mat, plot.calls, Iflag=NA, figTypes=NA, mai.mat=NA, mai.prc=FALSE, plot.extras = NA, source.plot=NA, image.size="800x1100", pointsize=12, res=NA, ps.paper="letter",ps.width=8,ps.height=11, returnVl=T, saveFlag=F,saveName="Splot.RData")

  16. Now what... Now we have initialized an object, ‘Splot’. The object, at this point, contains information to make a static layout of plots. If the user wishes to add interactive capabilities, data needs to be added to the Splot object through makeImap If the user just wants a static layout of plots, the user may use the makeSplot function on the Splot object.

  17. makeImap: adding interactivity makeImap( Splot, x.pos, y.pos, figure=1, xy.type=NA, x.right.pos=NA, y.bottom.pos=NA, spot.radius = 5, x.labels=NA,y.labels=NA,xy.labels=NA, x.links=NA, y.links=NA,xy.links=NA, asLinks=NA, x.images=NA, y.images=NA, xy.images=NA, font.type="Helvetica",font.color="black", font.size="12",bg.color='#D6E3F6', fname.root="Splot",dir="./", automap=TRUE,automap.method="mode", bb.clr=NA,bb.cex=2, returnVl=T,saveFlag=F,saveName="Splot.RData“, cleanDir=T)

  18. makeImap: adding interactivity makeImap( Splot, x.pos, y.pos, figure=1, xy.type=NA, x.right.pos=NA, y.bottom.pos=NA, spot.radius = 5, x.labels=NA,y.labels=NA,xy.labels=NA, x.links=NA, y.links=NA,xy.links=NA, asLinks=NA x.images=NA, y.images=NA, xy.images=NA, font.type="Helvetica",font.color="black", font.size="12",bg.color='#D6E3F6', fname.root="Splot",dir="./", automap=TRUE,automap.method="mode", bb.clr=NA,bb.cex=2, returnVl=T,saveFlag=F,saveName="Splot.RData“, cleanDir=T)

  19. How it works: x.labels, ylabels, xy.labels stores information that will be displayed interactively x.labels/y.lables – data.frames xy.labels – list of matricies specific data x values x values y values This data will be mapped based on x and y values, and some internal calculations of the up left and lower right boundary points of the figure.

  20. How it works: x.links, y.links, xy.links work the same as x.lables, ylables, xy.labels storeing information that will be displayed interactively x.links/y.links – data.frames xy.lbls – list of matricies specific data x values x values y values The difference between the labels and the links sets are the links contain complete web links/hyperlinks to include in the tool tip; Similarly x.images, y.images, and xy.images behave the same but add images to the tool-tip

  21. How it works: It is also possible for the interactive points to be links themselves. This is controlled with the asLinks argument.

  22. makeImap: adding interactivity makeImap( Splot, x.pos, y.pos, figure=1, xy.type=NA, x.right.pos=NA, y.bottom.pos=NA, spot.radius = 5, x.labels=NA,y.labels=NA,xy.labels=NA, x.links=NA, y.links=NA,xy.links=NA, asLinks=NA, x.images=NA, y.images=NA, xy.images=NA, font.type="Helvetica",font.color="black", font.size="12",bg.color='#D6E3F6', fname.root="Splot",dir="./", automap=TRUE,automap.method="mode", bb.clr=NA,bb.cex=2, returnVl=T,saveFlag=F,saveName="Splot.RData“, cleanDir=T)

  23. Inner workings: The following need to be taken into account when determining the upper left and low right boundary coordinates • Operating System (windows, linux) • Graph type (scatter, image) • File type (ps, png) ps width and height resize All calculations are made within the function. Programmer does not have to be concerned

  24. makeImap: adding interactivity makeImap( Splot, x.pos, y.pos, figure=1, xy.type=NA, x.right.pos=NA, y.bottom.pos=NA, spot.radius = 5, x.labels=NA,y.labels=NA,xy.labels=NA, x.links=NA, y.links=NA,xy.links=NA, asLinks=NA, x.images=NA, y.images=NA, xy.images=NA font.type="Helvetica",font.color="black", font.size="12",bg.color='#D6E3F6', fname.root="Splot",dir="./", automap=TRUE,automap.method="mode", bb.clr=NA,bb.cex=2, returnVl=T,saveFlag=F,saveName="Splot.RData“, cleanDir=T)

  25. Some example tool-tips... This is default setting. font.type="Helvetica“ font.color="black“ font.size="12“ bg.color='#D6E3F6' font.type=“arial“ font.color=“hotpink“ font.size=“20“ bg.color=“blue” font.type="Helvetica“ font.color=“cyan“ font.size="15“ bg.color=‘black' these are the same tool-tips that are generated in the vignette example and utilized in the example that can be downloaded from the sendplot home page off the University at Buffalo Biostatistics research software page

  26. Some example tool-tips... Notice the transparency by using empty string font.type=“arial“ font.color=“green“ font.size=“14“ bg.color=“” font.type=“sans-serif“ font.color=“purple“ font.size=“30“ bg.color='#D6E3F6' these are the same tool-tips that are generated in the vignette example and utilized in the example that can be downloaded from the sendplot home page off the University at Buffalo Biostatistics research software page

  27. makeImap: adding interactivity makeImap( Splot, x.pos, y.pos, figure=1, xy.type=NA, x.right.pos=NA, y.bottom.pos=NA, spot.radius = 5, x.labels=NA,y.labels=NA,xy.labels=NA, x.links=NA, y.links=NA,xy.links=NA, asLinks=NA, x.images=NA, y.images=NA, xy.images=NA, font.type="Helvetica",font.color="black", font.size="12",bg.color='#D6E3F6', fname.root="Splot", dir="./", automap=TRUE,automap.method="mode", bb.clr=NA,bb.cex=2, returnVl=T, saveFlag=F, saveName="Splot.RData“, cleanDir=T)

  28. Now what... Now we have initialized an object, ‘Splot’. Added data to the Splot object for interactivity through makeImap Now it time to make the files that will be send to end user

  29. makeSplot makeSplot( Splot, fname.root="Splot", dir="./", overwriteSourcePlot = NA, makeInteractive=TRUE, overrideInteractive=NA, Default=TRUE, header="v3", window.size = "800x1100", returnObj = FALSE, getLims=FALSE)

  30. makeSplot makeSplot( Splot, fname.root="Splot", dir="./", overwriteSourcePlot = NA, makeInteractive=TRUE, overrideInteractive=NA, Default=TRUE, header="v3", window.size = "800x1100", returnObj = FALSE, getLims=FALSE)

  31. makeSplot makeSplot( Splot, fname.root="Splot", dir="./", overwriteSourcePlot = NA, makeInteractive=TRUE, overrideInteractive=NA, Default=TRUE, header="v3", window.size = "800x1100", returnObj = FALSE, getLims=FALSE)

  32. Screenshot of HTML

  33. Wrappers Functions • xy.send : this function produces an interactive xy plot without any additional plots (i.e., just a single scatter-plot). • imagesend : this function produces an interactive image plot without any additional plots (i.e., just a single image plot). • heatmap.send : this function is a wrapper for the R stats package heatmap. This will create an interactive heatmap image. NOTE: The majority of the code for this function is verbatim from the R package stats heatmap function. This function was designed to work as a wrapper to utilize the same functionality and plotting as the heatmap function with sendplot’s interactive functionality.

  34. See vignette for some additional functions and other examples

  35. So... Result is two files: 1. png file 2. html file The researcher/collaborator need only to open the html file in order to have an interactive graph to view data. It can be customized on the programmers end to show any data the researcher requests or would find useful Additional files may have been created, however only the main html file and png file are needed

  36. Download • UB Biostatistics website • CRAN: http://sphhp.buffalo.edu/biostat/research/software/sendplot/index.php http://cran.r-project.org/

  37. Up and Coming • Improvements we are implementing in future version releases: • add option for multiple tool-tip display

  38. See Also A Bioinformatics wrapper has been created : iGenomicViewer available for download from the University at Buffalo Biostatistics research software page creates an interactive layout of plots for ANY genomic data

  39. Acknowledgments • Andrew Bruno • Lara Sucheston • Kenneth Manly • Dan Gaile

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