TODOs in approximate order of importance (higher is more important). ASK JS GUYS: grey after mouseout on ff? Talked to JS guys, maybe has something to do with mouseenter and mouseleave http://bl.ocks.org/mbostock/5247027 ------------------------------- maybe has something to do with setInterval which is not executed in chrome when the browser window is inactive http://stackoverflow.com/questions/5927284 When testing code on travis, record how much time, disk space, memory for compilation and rendering steps, and write those values to a CSV file. Then make a time series plot of these data to see if the code is getting more or less efficient. This could be useful in packages other than animint, so I proposed a GSOC2015 project https://github.com/rstats-gsoc/gsoc2015/wiki/Test-timings-on-Travis DSL: allow for example geom_tile(aes(clickSelects1=var1, clickSelects2=var2)) which means that clicking a tile changes the selected values of BOTH selectors. DSL: customizable alpha/color/size/fill/linetype for selected geoms, using selected.alpha, selected.color, etc aesthetics, see examples/Climate-selected.R. The first implementation should only allow this at the geom level, e.g. geom_point(aes(clickSelects=var),selected.color="red") means to plot a bunch of points which are black if not selected and red if selected. In ggplot2-0.9.3.1, selected.color thus defined can be accessed as layer$stat_params$selected.color. In the future we can try an implementation at the aes level, e.g. geom_point(aes(clickSelects=var1,selected.color=var2)) means black if not selected and scale[var2] if selected. NOTE: should maintain compatibility with existing code, which assumes selected.color="black" and color="transparent" for e.g. geom_rect(aes(fill=numeric, clickSelects=id)) and otherwise, selected.alpha=1 and alpha=1/2. RENDER: Have you thought adding the ability about saving the visualization state? I know we have ability to change the default selection, but it would also be nice to save the state as a url fragment -- http://en.wikipedia.org/wiki/Fragment_identifier OPTIMIZATION: Why does it take so much memory to compile large data? e.g. My computer has 12GB RAM but starts swapping when I try to compile examples/vervet.R. OPTIMIZATION: Profile animint2dir() to see what part is slow, and speed it up! e.g. the last viz in https://github.com/tdhock/animint-examples/blob/master/examples/scaffolds.R took 15 minutes to compile on my computer. OPTIMIZATION: to save disk space, we can compress the TSV file standard web servers? With servers like gist.github.com, all .json files are served with Content-Encoding: gzip, so they use http://en.wikipedia.org/wiki/HTTP_compression over the network. In firefox Inspect Element -> network it seems like they do not compress .tsv files. In curl it seems like it depends on the --compress flag thocking@silene:~/projects/chip-seq-paper(master*)$ curl --compress -# --head https://gist.githubusercontent.com/tdhock/914ab9c19038cae238a4/raw/geom10_rect_profiles_chunk9.tsv |grep Content-Encoding Content-Encoding: gzip thocking@silene:~/projects/chip-seq-paper(master*)$ curl -# --head https://gist.githubusercontent.com/tdhock/914ab9c19038cae238a4/raw/geom10_rect_profiles_chunk9.tsv |grep Content-Encoding thocking@silene:~/projects/chip-seq-paper(master*)$ curl --compress -# --head https://gist.githubusercontent.com/tdhock/914ab9c19038cae238a4/raw/plot.json |grep Content-Encoding Content-Encoding: gzip thocking@silene:~/projects/chip-seq-paper(master*)$ curl -# --head https://gist.githubusercontent.com/tdhock/914ab9c19038cae238a4/raw/plot.json |grep Content-Encoding thocking@silene:~/projects/chip-seq-paper(master*)$ DSL: Allow other variable names for the same selection variable, e.g. insert and insert.show are 2 different columns in data=other.inserts, but they should both use the "insert" selection variable, in geom_point(aes(clickSelects=insert, showSelected=insert.show, data=other.inserts). See the example in https://github.com/tdhock/animint-examples/blob/master/examples/scaffolds.R#L65 A better way to define this would be aes(clickSelects=insert, showSelected.variable="insert", showSelected.value=insert.show) Such a syntax would also be useful to avoid the use of for loops when defining a data viz with many selection variables, as in https://github.com/tdhock/animint-examples/blob/master/examples/PSJ.R For loops are bad for two reasons: - more code to type (144 lines versus 122 lines), - and slower construction of the data viz (30 seconds versus 1 second). DSL/RENDER: after clicking and changing the displayed data subset, zoom/update the axes of related plots. For animations we clearly want to keep the same axes across animation frames, but for some other kinds of plots it would be nice if the axes automatically zoomed. We currently have theme_animint(update_axes=c("x", "y")) option for single selection variables for most supported geoms. There should also be a button next to each axis that you can click to toggle zooming on and off. The implementation for multiple selection vars may require some computation in the renderer. See this: https://github.com/tdhock/animint/pull/158 RENDER: move stats computation to the renderer, to support e.g. examples/stats.R RENDER: it would be nice to zoom by dragging a rectangle on the plot background, as in plotly. Then double-click to zoom back out. This lib might help do the heavy lifting -- https://github.com/romsson/dragit RENDER: It would be nice to be able to resize plots interactively, like we can do in shiny+ggvis. RENDER/DSL: Multiple selection via rectangular brush and/or lasso https://github.com/skokenes/D3-Lasso-Plugin RENDER: Easy legend decoding: draw an arrow next to the legend entry for the value of the element that the mouse is hovering over, e.g. http://www.highcharts.com/maps/demo/map-drilldown/dark-unica DSL: To accomplish interactivity like in this plot http://timelyportfolio.blogspot.ca/2014/05/pdf-chart-inkscape-svg-d3-interactive.html http://kbroman.github.io/qtlcharts/assets/chartexamples/iplotMScanone_example.html https://www.biostat.wisc.edu/~kbroman/D3/car_crashes/ we could write geom_tile(aes(hoverSelects=var)) which means that the selected value of var should be changed when the user hovers the mouse over any tile. Raise an error if hoverSelects is used with multiple selection. For the viz below http://cpsievert.github.io/LDAvis/newsgroup/newsgroup.html we could write geom_point(aes(hoverSelects=var, clickSelects=var)) There are thus two kinds of hoverSelects: when you hover away from a geom, (1) select the previous value or (2) keep the same value. We could use two different aesthetics: aes(hoverSelectsSticky) and aes(hoverSelectsLast). Or we could use a geom-level option geom_point(aes(hoverSelects=var), onMouseOut="selectLast") or geom_point(aes(hoverSelects=var), onMouseOut="keepSelection"). Or we could infer a default: aes(hoverSelects=var) implies (2) and aes(hoverSelects=var, clickSelects=var) implies (1). Which of these 3 methods should we use to define hoverSelects interactivity? GGPLOT: theme(legend.position) DSL: how to specify the layout of SVG elements on the page? - option list(layout=matrix of plot names) means render plots in an html table instead of in a line? - specifying newlines in the option list? list(timeSeries=ggplot(), newline=list(), scatter=ggplot()) means that we should layout the plots in a with 2 rows and 1 column. EXAMPLE: US state population since 1790, compare w/ other countries? http://en.wikipedia.org/wiki/List_of_U.S._states_by_historical_population http://fr.wikipedia.org/wiki/Histoire_démographique_de_la_France http://www.populstat.info/Asia/japanc.htm http://www.populstat.info/Americas/canadac.htm RENDER: Is it possible to fix geom_rect and geom_text vertical alignment? There is no equivalent of R's vjust in SVG. See examples/align_rect_text.R. DSL: if there was no duration specified, should time=list(variable=2000) imply duration=list(variable=1000)? DSL: geom_tallrect(aes(xmin=chromStart, xmax=chromEnd, fill=annotation), edit=TRUE) means that we would like to interactively edit the data in this geom. In particular it means that the specified aesthetics may be edited by the user (xmin, xmax, fill) but the non-specified aesthetics may not (e.g. color in the example above). Save each TSV file with an _animint_id column which is unique for each drawn element. Start a web server that accepts POST requests and can edit the TSV files appropriately. This will probably take a lot of work, and a lot of geom-specific interactive editing code, so it is more of a research project than a feature request. RENDER: Should we download all data in the background, even for non-animated plots? I have started some work on the loadall branch, but the preliminary answer is NO -- the browser freezes and the plot does not respond to mouse clicks while the data is loading. DSL: Implement shape aesthetic with d3.svg.symbol() https://github.com/mbostock/d3/wiki/SVG-Shapes#symbol_type RENDER: Determine why border of tiles in pirates example does not seem to be rendering. RENDER: multiple animints inside of a single shiny app? This is probably just a theoretical issue. (why not just make a single animint?) 2016.11.02 PR#169 OPTIMIZATION: some un-necessary code was deleted in a cleanup effort by @faizan-khan-iit, thanks! 2016.08.21 PR#158 DSL/RENDER: Added theme_animint(update_axes=c("x", "y")) option for single selection showSelected variables. 2016.08.15 PR#166 BUGFIX: no more NA saved to tsv files (even when there is no common data tsv file). OPTIMIZATION: getCommonChunk is faster, now we only split by group (and vectorize over chunks rather than splitting on chunks and doing a for loop). Also checkCommon returns that a variable is NOT common as soon as we have at least two chunks for which that variable is different, for a given group (before, we were checking all chunks). TEST: getStyleValue now works even if there are some nodes which are missing the style attribute. COMPILER: when aes(group) is specified and we have NA values with a group, we add a new subgroup ID for each run of non-NA values. Normally in ggplot2 this is important since for example a line group with two runs of NA values will be rendered as three lines. This fixes the bug that was combining lines, see test-renderer4-NA-separate-lines.R 2016.08.14 PR#165 DATA: prostateLasso. BUGFIX: tooltips display correctly even after they have been updated via a selector change. BUGFIX: it is now OK to use .variable .value aes with the time selector. DSL: make_tallrect and new make_widerect use .variable and .value aes and key so that they now support smooth transitions. 2016.07.12 PR#157 GGPLOT: added support for stroke aesthetic in geom_point Covers #127 (test-renderer4-geom-point-stroke.R) 2016.07.06 PR#156 BUGFIX: tooltip and href now work properly when used together fixes #100 and #155 (test-renderer5-tooltip-interactivity.R) 2016.06.26 PR#135 GGPLOT: compiler works with ggplot2 >= 2.0 thanks to Kevin and (especially) Faizan! 2016.05.11 PR#152 GGPLOT: no warning when showSelected is used with stats which are known to work (hline, vline, abline). 2016.05.08 PR#146 GGPLOT: the compiler now stops with an informative error when stats are used with showSelected. New warning when position is used with showSelected. RENDER: aes(href) works when data_is_object (e.g. geom_polygon) 2016.05.07 PR#151 BUGFIX: common chunk data were not computed correctly when some chunks did not have all groups. 2016.03.23 PR#143 DSL: informative error when time option but no interactive aes specified. RENDER: "Show selection menus" instead of "Toggle selected variables" to be more consistent with the other buttons. 2016.03.22 PR#138 structure(viz, class="animint") works on the R command line (before, it only worked in Rmd files). BUGFIX: now we can render legends called "label" in Rmd (before, there was a conflict with bootstrap.js which is used to render Rmd, and defines a css style for a class called "label") BUGFIX: plots, legends, and legend entries in the same Rmd are now guaranteed to have different id. BUGFIX: animints with common chunk tsv files now work in Rmd. RENDER: selector.types defaults to multiple selection for variables which have legends somewhere in the data viz. 2016.03.15 PR#141 TEST: Added the test for Lilac Chaser Visual Illusion. test-renderer3-lilac_chaser.R 2016.03.14 PR#140 BUGFIX for geom_point(aes(color), fill=NA), new ensure_rgba for test infrastructure that can convert arbitrary colors to rgba format (respecting alpha opacity). 2016.03.08 PR#137 BUGFIX for geom_path(aes(group, key)) with animated transitions, see test-renderer3-path-key.R. 2016.03.01 PR#133 BUGFIX for an animint inside of shiny. Thanks to @lrmelt who brought up the issue #132. Now we have a test for animating, changing shiny widgets, and re-rendering an animint inside of a shiny app. 2016.02.29 PR#134 BUGFIX in merge_recurse when there are several geoms with different aes values that could be used to render legend entries, just take the last one (test-renderer3-roc.R). 2016.01.28 Depend ggplot2 < 2.0. BUGFIX: knit_print.animint seems to be working again with the most recent version of knitr/rmarkdown. Use rmarkdown::render("doc.Rmd") without the output_dir argument! https://github.com/rstudio/rmarkdown/issues/587#issuecomment-168437646 2015.12.09 PR#125 BUGFIX: geom_widerect should now render properly in all contexts. There was some problem when plot width << height which is now fixed. 2015.12.03 PR#124 animint2gist stops with the new max of 300 files per gist. 2015.12.01 PR#119 animint2gist now stops with an error when there are over 40 files (fixes #122) and when there is at least one file that is over 1MB, which would be truncated (fixes #121). Animations with geoms that have more than one chunk var start playing immediately. Compiler stops with an informative error "aes names must be unique" when the same interactive aes appears multiple times, e.g. aes(showSelected=var1, showSelected=var2) 2015.11.30 BUGFIX: axis hiding on maps works again, via 6 element_blank()s: theme(axis.line=element_blank(), axis.text=element_blank(), axis.ticks=element_blank(), axis.title=element_blank(), panel.background = element_blank(), panel.border = element_blank()) 2015.11.01 BUGFIX: facet_grid(var ~ ., space="free") now uses the correct amount of space between vertical panels, and we test for it in test-renderer2-ChromHMMiterations.R. BUGFIX: axis names are now correctly spaced in the middle between the extreme panel edges. 2015.10.26 DSL: geom_1(aes(color=something))+geom_2(aes(color=something.else)) is now an error. aes(color="constant") and aes(color=factor(x)) are also errors. The idea is to force the designer to use informative and consistent selector variable names for interactive legends. DATA: PredictedPeaks and test-renderer2-PredictedPeaks.R BUGFIX: do not call update_selector twice from selectize widgets, since we are now using setValue(values, true). DSL: selectize option list for determining which selector widgets to render. By default do not render a widget if there are more than 1000 values. 2015.10.18 GGPLOT: aes(hjust) support for values 0, 0.5, 1 (error for other values). geom_text(vjust) or aes(vjust) raises warning if values other than 0.5 are specified. RENDERER: do not show selector widgets for selectors that were created with .variable .value aesthetics. RENDERER: play() only after loading all animation chunks. BUGFIX: common/varied chunk code properly handles the example in test-renderer2-VariantModels.R. 2015.09.28 BUGFIX: common/varied chunk code properly handles the example in test-PeakConsistency.R -- no nest columns in common data, and each group of common data must have either 1 or N data, where N is the number of rows in each varied chunk. 2015.09.25 BUGFIX: multiple animints can be rendered in the same Rmd, and each animint does not affect any of the others. 2015.09.23 BUGFIX: tooltips render for geoms with clickSelects.variable/value. 2015.09.22 BUGFIX: geom_hline is now rendered properly. Test includes with and without the data= argument. 2015.09.18 BUGFIX: geom_line was not rendering properly when the x values were not saved in increasing order in the tsv files. Fixed by sorting before saving. 2015.09.17 OPTIMIZATION: the compiler will not save any geom1_chunk123.tsv files less than 4KB, unless specifically asked to do so using chunk_vars. OPTIMIZATION: @caijun's GSOC2015 project allows even more disk space savings, by saving data which is the same in every tsv file in geom1_common.tsv. http://kferris10.github.io/AnimintBlog/Optimization-of-Disk-Usage-for-animint/ 2015.09.16 BUGFIX: data renders properly when there are many facet rows or columns (before, there was some problem with scales that was causing negative data values). RENDER: theme(panel.margin=grid::unit(0, "lines")) is interpreted to mean no space between facets. Useful to save space with theme_bw(). 2015.09.08 RENDER: For each selector variable, render a widget for selecting values using selectize.js 2015.08.31 BUGFIX: For geom_point(aes(fill=annotation, color=highly.divergent.regions)) the color legend now correctly shows a different stroke but the same fill for each . BUGFIX: interactive legends now work properly when selection/legend variable names contain dots (see test-malaria.R). BUGFIX: test-shiny.R works again thanks to remDr$switchToFrame. 2015.07.17 RENDER: Legends are now interactive and can be used to clickSelect. This means that aes(colour = variable) implies aes(showSelectedcolour = variable) for discrete variables. 2015.07.16 BUGFIX: geom_abline() stays on panel and theme(panel.grid = element_blank()) works. 2015.07.13 Fix bug where plots without minor y grid lines were not rendering. Update grid lines so that they inherit characteristics from default lines. 2015.07.03 Fix bug with geom_abline(). Automatically rebuild gh-pages tutorial when pushing to master. 2015.06.25 BUGFIX: Plots with only one grid line now render. 2015.06.23 BUGFIX: Panel backgrounds and borders can now handle rectangles of element_blank(). 2015.06.22 EXAMPLE: Incorporate example with pirates data. 2015.06.16 RENDER: Implement panel backgrounds, panel borders, and grid lines in plots. 2015.05.29 BUGFIX: warnings for opening pid.txt, closing unused connection and generating make_text.Rd. 2015.05.28 BUGFIX: ordering of legend entries now correctly reverses the order of numeric legend entries, so that smaller numbers appear lower in the legend. 2015.05.21 BUGFIX: linetypes, legend ordering, color=NA means "transparent" etc https://github.com/tdhock/animint/pull/72 BUGFIX: Testing should now work on Windows with Firefox. For complete details, see https://github.com/tdhock/animint/pull/70 2015.05.20 https://github.com/tdhock/animint/pull/48 RENDER: if the animation is paused when the user hides the animint window, then do not automatically start playing when the user shows the window. BUGFIX: aes(linetype) support for tall/wide rects. BUGFIX: facet_grid bugfix for when there is only 1 row or column. BUGFIX: R colors defined in parameters such as geom_line(colour="grey50") are now corrected translated to rgb(127, 127, 127) in JSON. 2015.05.11 For complete details, see https://github.com/tdhock/animint/pull/62 DSL: The url_prefix argument in animint2dir() was removed. Now the result will always be viewed at http://bl.ocks.org/:owner/raw/:id for better viewing. BUGFIX: The animint.js file introduces only 1 thing (animint) into the global JavaScript environment. Added continuous integration with wercker and made several improvements to testing infrastructure. 2015.03.31 BUGFIX: Various improvements including namespace handling. Fixes https://github.com/tdhock/animint/issues/49 https://github.com/tdhock/animint/issues/46 2015.03.30 Better testing "framework". See the testing page of the wiki for details https://github.com/tdhock/animint/wiki/Testing 2015.03.23 BUGFIX: hjust aesthetic for geom_text. R's valid hjust=0.5|1|0 is equivalent to CSS text-anchor: middle|end|start. 2015.01.27 Translate R/ggplot theme(axis.text.x=element_text(angle=70, hjust=1)) to HTML/SVG Thanks for the bug report @mswastik 2015.01.19 BUGFIX: no longer need to load knitr in a knitr document to print an animint plot. 2014.12.4 BUGFIX: do not stop when viz$timeSeries is a ggplot and viz$time is undefined. More informative error when viz$time does not contain the required elements named ms and variable. 2014.11.24 Added css.file argument to animint2dir 2014.11.13 knit_print.animint will now overwrite existing directories. This more closely mimics the default behavoir of knitr (everytime you re-knit, new figures/output files replace old ones). 2014.11.11 BUGFIX: Account for facet strip labels when placing multiple rows of panels. 2014.10.29 DSL: aes(tooltip=text) for specifying the text to show when you hover the mouse over something, e.g. issue #1. 2014.10.26 BUGFIX: When using facet_grid() + coord_equal() with multiple rows, the rows after the first row were not placed properly. 2014.10.21 User can play/pause the animation, and adjust animation time and transition durations. 2014.10.15 "shiny bindings" are now possible using the renderAnimint() and animintOutput() convenience functions. See here for simple shiny app: https://github.com/tdhock/animint/tree/master/inst/examples/shiny You can also incorporate animint plots into interactive documents: https://github.com/tdhock/animint/tree/master/inst/examples/rmarkdown You can view a live version of these examples here: https://cpsievert.shinyapps.io/animintShiny https://cpsievert.shinyapps.io/animintRmarkdown 2014.10.13 BUGFIX: Main title will no longer overlap with facet titles -- see https://github.com/tdhock/animint/issues/26 Also, space management between panels was reduced/improved. 2014.10.10 GGPLOT: geom_widerect is now defined in geoms.R and it is rendered by animint.js. BUGFIX: when nest_order contains PANEL and group, group should come last. 2014.10.9 BUGFIX: use eActions(enter_elements) to prevent them from flying in from the upper left. 2014.9.26 DSL: multiple selection! Now you can declare each interaction variable as either single or multiple selection using an option list: selector.types=list(year="single", country="multiple"). If this option list is not specified, single selection is used by default for all selectors. The interface to multiple selection should be simple: click a country to toggle the selection state from off to on. 2014.8.25 GGPLOT: facet_* and coord_fixed are now fully functional. BUGFIX: ticks/labels for scale_x_time are rendered properly. 2014.6.10 Restore support for numeric legends. 2014.6.2 DSL: Custom title for the generated HTML page using option title="TITLE". This title is also used for the animint2gist description. DSL: aes(href=sprintf("http://genome.ucsc.edu/%s", id)) to have clicking open a new web browser tab at that URL. OUTPUT: gg2animint is now deprecated, use animint2dir instead. animint2gist now checks for and ignores directories and files of size 0, which were causing Error: client error: (422) Unprocessable Entity (WebDAV; RFC 4918) 2014.5.22 All tests are now working. The animist2gist function posts relevant files as a gist and allows one to automatically view/share plots via http://bl.ocks.org Moved a number of packages from DEPENDS to IMPORTS (except for ggplot2 and proto). Also added gistr to SUGGESTS as it is needed for animist2gist. 2014.5.17 Fixed the "too many legend entires" bug. For more info, see the commit that introduced the bug (and the note on why it doesn't work) https://github.com/tdhock/animint/commit/069c167117c169dea9277608e8a0cbed3c75fcff 2014.5.16 The new knit_print.animint function tells knitr how to print objects of class "animint". This allows one to embed multiple animint plots in a single HTML via R Markdown and knitr. This is currently only possible with the dev version of knitr, but this won't be a problem when v1.6 is released to CRAN 2014.5.15 Use a local file server if the servr package is installed. 2014.5.9 Download progress table at the bottom of the plot. - click a button to show or hide the entire table. BUGFIX: geom_rect(size=0) is now correctly translated to . 2014.5.5 duration=list(complexity.i=2000) means a smooth transition over 2 seconds ONLY when the complexity.i selector is updated. e.g. for geom_ribbon(aes(showSelected=sample1, showSelected2=sample2, showSelected3=complexity.i, showSelected4=set.name), this means that there should be no smooth transition when we click to update sample1, sample2, or set.name. See https://github.com/tdhock/animint-examples/blob/master/examples/chip.seq.R Specify aes(key=variable) for constancy in transitions: http://bost.ocks.org/mike/constancy/ I found a real data set where this is necessary: https://github.com/tdhock/animint-examples/blob/master/examples/chip.seq.R 2014.4.30 The designer can specify chunk variables via geom_line(aes(showSelected=var1, showSelected2=var2, showSelected3=var3), chunk_vars=c("var1", "var2")). 2014.4.28 scale_x_continuous(LABEL) specifies the x axis label. Previously, we could only use xlab(LABEL). 2014.4.25 theme_animint(width=600, height=600) instead of option lists which make us repeat the plot names... I made tdhock/ggplot2@98cefe4d653ce8f214177b66dc030c2f3c725ffb which lets you say theme(validate=FALSE) to avoid calling validate_element. This works with tdhock/animint@c4ff92d8c4edf523d20c6022fb3b515b19974b8b and I submitted an issue https://github.com/hadley/ggplot2/issues/938 and pull request. 2014.4.22 BUGFIX: the geom drawing order is respected now, even if there are some geoms which are absent for the current selection. This is implemented by putting the geoms on each layer in a g element with class e.g. geom7_vline_scatter. The g element is initialized on plot startup, and never is deleted, even if there are 0 geoms in the current selection. BUGFIX: in the JavaScript, when there are zero groups of line/ribbon data to display for the current selection, just draw nothing (before there was an error since the code was written as though there was 1 instead of 0 groups). 2014.4.16 BUGFIX: toJSON gives an infinite recursion error for converting R functions to JSON, and R functions are sometimes used as ggplot params/stat_params. But we do not want to pass these to JSON anyway, so we just ignore them. 2014.4.7 BUGFIX: make_text now works even if it appears before/after certain other data. See examples/make_text_bug.R The default/first selection can be specified by an option first=list(year=1960, country=c("Japan", "United States"). Stop with an error if multiple values are specified for a single selection variable. BUGFIX: Animation now works even for non-numeric variables, e.g. examples/canada-cities.R. For animations, start downloading the next chunk for that geom, until all data is loaded, even if it is not needed on screen right now. For large data sets such as the scaffold data, breaking the CSV database from 21 to 94032 CSV files resulted in a 10x increase in disk space usage (but faster loading of the first data subset), for 653018 rows of data. Forcing max 1 chunk variable means only 18045 CSV files which is more space/time efficient. Also, plot.json only stores the chunk ids, not the full filenames (less repetition). thocking@silene:~/projects/scaffold-viz$ ls boxes-nochunks|grep csv|wc -l 21 thocking@silene:~/projects/scaffold-viz$ ls boxes-fewer-chunks|grep tsv|wc -l 18045 thocking@silene:~/projects/scaffold-viz$ ls boxes-chunks|grep tsv|wc -l 94032 thocking@silene:~/projects/scaffold-viz$ du -hs boxes-*chunks 45M boxes-nochunks 99M boxes-fewer-chunks 400M boxes-chunks I uploaded these visualizations and timed page loading in chromium: http://cbio.ensmp.fr/~thocking/scaffold-viz5/ 44.1MB transferred 27.95 s transfers ALL the data. slow part is 3 csv files, each around 13 MB. http://cbio.ensmp.fr/~thocking/boxes-fewer-chunks/ transfers only the first subset. 5.6MB transferred 7.73 s. plot.json is only 304KB, slow part is 1.6MB geom7_point_box_chunk1057.tsv. http://cbio.ensmp.fr/~thocking/boxes-chunks/ 12.1MB transferred 9.61 s transfers only the first subset. slow part is 8.7MB plot.json. 2014.4.4 Download progress table at the bottom of the plot. - row for every geom. - columns: geom, selected chunk, status, downloaded, total. BUGFIX: stop with an error if width or height list contains plot names that do not exist! BUGFIX: when there are commas in text labels, animint.js now parses the data correctly, since we use tsv instead of csv. See examples/align_rect_text.R. Speedy web page loading: on compile, divide data into chunks --- separate csv files. In general a chunk of data will be shown onscreen at the same time, but we should not make chunks with only 1 row e.g. for the WorldBank viz, geom_points should have 1 chunk per year, geom_text country labels should have 1 chunk per country, and geom_text year labels should have just 1 chunk which covers all years. On page load, start downloading the first chunk for each geom. 2014.3.19 For geoms with fill=a numeric variable, changing the opacity changes how we interpret the colors, so for these geoms, show selection by changing the stroke instead. 2014.3.13 scale_size_animint 2014.2.24 vervet data. 2014.01.27 allow specifying guide="none" in ggplot2 scales that would generate a legend. 2013.11.22 Test for warnings. Warn when 0-sized geoms are produced, since they will be invisible. Do not sort NULL during check for animation values, to avoid warning. 2013.11.19 draw colored, sized "a" in legend for geom_text. geom_text(aes(size)) is resized using e.g. 2013.11.15 Bugfix: filter NaN before passing data to lineThing to avoid hiding an entire line if only one element is NA. 2013.10.23 Include 1 animint in a knitr Rmd document when processed in the same directory. Generate documentation example web site. Bugfix for geom_point(colour=constant). 2013.10.15 Hide only y axis and not x axis if axis.text.y=element_blank(), etc. 2013.10.4 Bugfixes for geom_ribbon(aes(fill=variable)) and geom_text(aes(color=variable)). 2013.9.26 Update R/JS comments from emails to Susan. gg2animint examples are animated and interactive. 2013.8.29 Implementation of geom_hex with relevant examples and documentation. 2013.8.15 Updated package requirements (MASS, reshape2, maps) Updated documentation to include warnings about using google chrome with animint 2013.7.29 Fix for significant digits issue with clickSelects - fixed by exporting as character into JSON file, then importing and converting to numerals. Axes can now be removed for maps 2013.7.26 bugfix for animations: before, we assumed that the animation variable takes values in 1..n, but now this is treated properly by looking at the actual values. make_text for quick labels. make_*(data, ...) WARNING when stat_bin is used to put several clickSelects or showSelected values in the same bin!