R_demo demonstrates common uses of R to produce advanced and/or interactive graphs and reports in web pages within a full Wiki CMS/Groupware site, through the usage of
PluginR (
https://doc.tiki.org/PluginR).
There are a few
sets of pages already created to show off some possibilities, as well as to allow quick starting new users into customizing their more complex interfaces to run their R scripts and packages through a nice
Web 2.0 GUI:
- Demo1_simple_test. Testing simple R commands to test that the installation went fine
- Simple Text output
- Simple graphical output
- Demo2_params. Testing several other commands
- Tiki Dynamic variable usage
- Parsing html code
- Wikisyntax param
- Demo3_interface. Testing the process of working with datasets for a script to use them as parameters. The interface is organized in 4 tabas:
- Listing raw datasets
- This first tab uses the standard output of Plugin TrackerList to display the data stored in the database of datasets ("Tracker" or items, in Tiki terms).
- Showing the results after the dataset is run
- This part uses a Pretty Tracker with the (smarty) template in a wiki page, instead of just the standard output of Plugin TrackerList used in the first tab. Thus, the display is controlled by the (smarty) template "r_test3_template01", and it can be much more customized with the Wysiwyg editor in Tiki.
- Dataset edition (provided that a dataset is selected in the first tab)
- This third tab allows the user to edit the parameters for the graph generated by the R script, by means of using Plugin Tracker to preload a previous item when requested (itemId value must be assigned in the url).
- Inserting new datasets
- This last tab allows to insert new items, by means of using Plugin Tracker, despite the fact that the page has already loaded a previous item or not.
- Demo4_export. Testing the production of a basic image with svg and pdf export. (in the future, extended with the help of other R packages)
- Demo5_wordcloud. Testing some nice graphs from R. You might need some extra packages for R:
- Demo6_googleVis. Testing some nice interactive graphs
- Created through the googleVis package. You might need some extra R packages.
- Demo7_plot.ly. Testing Plot.ly (see https://plot.ly/ ). The Plotly R graphing library allows you to create and share interactive, publication-quality plots in your browser. Plotly is also built for working together, and makes it easy to post graphs and data publicly with a URL or privately to collaborators.
- Demo8_customoutput. Testing the customoutput parameter.
- Introduced in PluginR v0.87, customoutput produces no hardcoded graphical output from PluginR, but leaves the R script inside the plugin to manage chart generation. In a later step, image is displayed with either img for images, or mediaplayer for pdf's, videos, etc.
- Demo9_rcharts. Testing a series of examples of nice charts using
rCharts and the corresponding javascript library used in each case. rCharts is an R package to create, customize and publish interactive javascript visualizations from R using a familiar lattice style plotting interface.
- Demo10_clickme. Testing the
clickme package from Nacho Caballero. Clickme is an R package that lets you create interactive visualizations in the browser directly from your R session.
- Demo11_animation. Showing a way to produce a self-moving chart with data from different decades using the
ggplot2 and animation packages.
- Demo12_ecoengine. Testing the
ecoengine package from rOpenSci, which is a collaborative effort to develop R-based tools for facilitating Open Science. Some distribution maps is generated for a species using LeafletJS, as well as a photo gallery created from a queried species for demostration purposes.
- Demo13_parse_body. Testing the
parse_body param from PluginR v 0.81.2+, which facilitates a better communication between data collected in trackers andits usage in R
- Demo14_webshot. Testing the
webshot package. Webshot makes it easy to take screenshots of web pages (all or sections defined by css selectors) from R, and save them as png or pdf. (requires PhantomJS, installable from within the webshot R package).
- Demo15_pivottables. Testing the
rpivotTable package, which is an R htmlwidget built around the pivottable library. PivotTable.js is a Javascript Pivot Table library with drag'n'drop functionality built on top of jQuery/jQueryUI and written in CoffeeScript by Nicolas Kruchten at Datacratic. It is available under an MIT license.
This menu will be created also:
Profile_r_demo_menupage
Requirements:
:
These pages will be created:
(listed properly only when shown here: http://profiles.tiki.org/R_demo , not when you are at profile installation in your remote tiki site)
Trackers
YAML
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preferences:
feature_trackers: y
trackerfield_file: y
trackerfield_files: y
trackerfield_dropdownother: y
feature_user_watches: y
feature_view_tpl: n
feature_edit_templates: y
feature_wiki_templates: y
feature_jquery_media: y
wikiplugin_r: y
wikiplugin_rr: y
wikiplugin_aname: y
feature_smileys: y
feature_search_fulltext: y
feature_wiki_argvariable: y
feature_syntax_highlighter: y
feature_syntax_highlighter_theme: default
wiki_dynvar_style: double
wikiplugin_div: y
wikiplugin_group: y
wikiplugin_iframe: y
wikiplugin_img: y
wikiplugin_pluginmanager: y
wikiplugin_list: y
wikiplugin_listpages: y
wikiplugin_titlesearch: y
wikiplugininline_div: y
wikiplugininline_group: y
wikiplugininline_iframe: y
wikiplugininline_img: y
wikiplugininline_fade: y
wikiplugininline_remarksbox: y
wikiplugininline_pluginmanager: y
wikiplugininline_list: y
wikiplugininline_listpages: y
wikiplugininline_titlesearch: y
feature_multilingual: y
lang_use_db: y
instructions: Welcome to Plugin R
objects:
-
type: tracker
ref: r_test_tracker1
data:
name: Datasets
description: Files with data (like csv) to be processed by R scripts through tracker plugin calls
default_status: open
show: [ status, creation_date, modification_date, list_modification_date ]
allow: [ comments, one_item_per_user, attachments ]
-
type: tracker_field
ref: r_test_summary
data:
name: Summary
tracker: $r_test_tracker1
type: text_field
flags: [ searchable, public, list, mandatory, link ]
order: 10
-
type: tracker_field
ref: r_test_description
data:
name: Description
tracker: $r_test_tracker1
type: text_area
options: 1
flags: [ public ]
order: 20
-
type: tracker_field
ref: r_test_from
data:
name: From user
tracker: $r_test_tracker1
type: user
options: 1
flags: [ searchable, public, list ]
order: 30
-
type: tracker_field
ref: r_test_attachment
data:
name: Dataset file
tracker: $r_test_tracker1
type: attachment
flags: [ searchable, public, list ]
order: 40
-
type: tracker_field
ref: r_test_xmin
data:
name: Minimum value for axis X
tracker: $r_test_tracker1
type: text_field
flags: [ searchable, public, list ]
order: 50
-
type: tracker_field
ref: r_test_xmax
data:
name: Maximum value for axis X
tracker: $r_test_tracker1
type: text_field
flags: [ searchable, public, list ]
order: 60
Groups & Permissions
YAML
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permissions:
Anonymous:
allow: view
deny: [ ]
Registered:
description: Will be ignored because group is already created
allow:
- create_tracker_items
- list_trackers
- view_trackers
- watch_trackers
deny: [ ]
objects:
-
type: wiki_page
id: r_test3_template01
allow: use_as_template
-
type: wiki_page
id: r_test13_template01
allow: use_as_template
Editors:
description: Trusted users
allow:
- modify_tracker_items
- trust_input
- view_templates
- edit_templates
- use_content_templates
- edit_content_templates
- admin_content_templates
- use_as_template
Admins:
description: Have all rights
allow:
- admin
- trust_input
Sample data
YAML
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objects:
-
type: tracker_item
ref: dataset_001
data:
tracker: $r_test_tracker1
status: open
values:
- [ $r_test_summary, Sample dataset ]
- [ $r_test_from, admin ]
- [ $r_test_description, "This dataset was created as part of the sample data for r_test." ]
- [ $r_test_attachment, '']
- [ $r_test_xmin, 1]
- [ $r_test_xmax, 10]
-
type: tracker_item
ref: dataset_002
data:
tracker: $r_test_tracker1
status: pending
values:
- [ $r_test_summary, We are working on this dataset ]
- [ $r_test_from, admin ]
- [ $r_test_description, "This will soon be changed" ]
- [ $r_test_attachment, '']
- [ $r_test_xmin, 21]
- [ $r_test_xmax, 30]
-
type: tracker_item
ref: dataset_003
data:
tracker: $r_test_tracker1
status: closed
values:
- [ $r_test_summary, A really old dataset ]
- [ $r_test_from, admin ]
- [ $r_test_description, "This dataset is outdated." ]
- [ $r_test_attachment, '']
- [ $r_test_xmin, 100]
- [ $r_test_xmax, 110]
Modules
YAML
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objects:
-
type: module
ref: module_last_modif_tracker_items
data:
name: last_modif_tracker_items
groups: [ Anonymous, Registered ]
position: right
order: 5
params:
trackerId: $r_test_tracker1
name: Summary
Wiki pages
YAML
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preferences:
enable: [ feature_wiki ]
objects:
-
type: wiki_page
ref: r_test_instructions_page
data:
name: Welcome to Plugin R
description: Basic intructions of PluginR and this profile
lang: en
mode: create_or_update
content: wikicontent:Profile_r_test_instructions
-
type: wiki_page
ref: r_test1_page
data:
name: r_demo01_simple_test
description: Interface to send datasets
lang: en
mode: create_or_update
content: wikicontent:Profile_r_test1_simple_test
-
type: wiki_page
ref: r_test2_page
data:
name: r_demo02_params
description: Interface to test several things
lang: en
mode: create_or_update
content: wikicontent:Profile_r_test2_params
-
type: wiki_page
ref: r_test3_page
data:
name: r_demo03_interface
description: Interface to change graph params and display png
lang: en
mode: create_or_update
content: wikicontent:Profile_r_test3_interface
-
type: wiki_page
ref: r_test3_template01_page
data:
name: r_demo03_template01
description: Template for wiki page
lang: en
mode: create_or_update
content: wikicontent:Profile_r_test3_template01
-
type: wiki_page
ref: r_test4_page
data:
name: r_demo04_export
description: Interface to test some export options for figures
lang: en
mode: create_or_update
content: wikicontent:Profile_r_test4_export
-
type: wiki_page
ref: r_test5_page
data:
name: r_demo05_wordcloud
description: Some examples of neat Cloud-art graphs to dogfood Tiki information
lang: en
mode: create_or_update
content: wikicontent:Profile_r_test5_wordcloud
-
type: wiki_page
ref: r_test6_page
data:
name: r_demo06_googleVis
description: Some examples of neat usage of RGoogleVis package
lang: en
mode: create_or_update
content: wikicontent:Profile_r_test6_googleVis
-
type: wiki_page
ref: r_test7_page
data:
name: r_demo07_plot.ly
description: Some examples of using Plot.ly
lang: en
mode: create_or_update
content: wikicontent:Profile_r_test7_plot.ly
-
type: wiki_page
ref: r_test8_page
data:
name: r_demo08_customoutput
description: Some examples of the usage of parameter customoutput producing either custom png or custom pdf displayed embedded within the same wiki page
lang: en
mode: create_or_update
content: wikicontent:Profile_r_test8_customoutput
-
type: wiki_page
ref: r_test9_page0
data:
name: r_demo09_rcharts
description: series of examples of nice charts using the R package rCharts and the corresponding javascript library used in each case.
lang: en
mode: create_or_update
content: wikicontent:Profile_r_test9_rcharts
-
type: wiki_page
ref: r_test9_page1
data:
name: r_demo09_rcharts_highcharts
description: an example of nice charts using the R package rCharts and the corresponding javascript library HighCharts.
lang: en
mode: create_or_update
content: wikicontent:Profile_r_test9_rcharts_highcharts
-
type: wiki_page
ref: r_test9_page2
data:
name: r_demo09_rcharts_leaflet
description: an example of nice charts using the R package rCharts and the corresponding javascript library Leaflet.
lang: en
mode: create_or_update
content: wikicontent:Profile_r_test9_rcharts_leaflet
-
type: wiki_page
ref: r_test9_page3
data:
name: r_demo09_rcharts_morris
description: an example of nice charts using the R package rCharts and the corresponding javascript library MorrisJS.
lang: en
mode: create_or_update
content: wikicontent:Profile_r_test9_rcharts_morris
-
type: wiki_page
ref: r_test9_page4
data:
name: r_demo09_rcharts_nvd3
description: an example of nice charts using the R package rCharts and the corresponding javascript library NVD3.
lang: en
mode: create_or_update
content: wikicontent:Profile_r_test9_rcharts_nvd3
-
type: wiki_page
ref: r_test9_page5
data:
name: r_demo09_rcharts_polychart
description: an example of nice charts using the R package rCharts and the corresponding javascript library Polychart.
lang: en
mode: create_or_update
content: wikicontent:Profile_r_test9_rcharts_polychart
-
type: wiki_page
ref: r_test9_page6
data:
name: r_demo09_rcharts_rickshaw
description: an example of nice charts using the R package rCharts and the corresponding javascript library RickShaw.
lang: en
mode: create_or_update
content: wikicontent:Profile_r_test9_rcharts_rickshaw
-
type: wiki_page
ref: r_test9_page7
data:
name: r_demo09_rcharts_xcharts
description: an example of nice charts using the R package rCharts and the corresponding javascript library XCharts.
lang: en
mode: create_or_update
content: wikicontent:Profile_r_test9_rcharts_xcharts
-
type: wiki_page
ref: r_test9_page8
data:
name: r_demo09_rcharts_512paths
description: an example of nice charts using the R package rCharts and some js functions to produce an awesome chart from NY Times 512 Paths to the White House.
lang: en
mode: create_or_update
content: wikicontent:Profile_r_test9_rcharts_512paths
-
type: wiki_page
ref: r_test10_page
data:
name: r_demo10_clickme
description: Some examples with the Clickme R package that lets you create interactive visualizations in the browser directly from your R session
lang: en
mode: create_or_update
content: wikicontent:Profile_r_test10_clickme
-
type: wiki_page
ref: r_test11_page
data:
name: r_demo11_animation
description: An example of chart showing choropleths of different decades using R packages ggplot2 and animation
lang: en
mode: create_or_update
content: wikicontent:Profile_r_test11_animation
-
type: wiki_page
ref: r_test12_page
data:
name: r_demo12_ecoengine
description: Some distribution maps is generated for a species using LeafletJS, as well as a photo gallery created from a queried species for demostration purposes.
lang: en
mode: create_or_update
content: wikicontent:Profile_r_test12_ecoengine
-
type: wiki_page
ref: r_test13_page
data:
name: r_demo13_parse_body
description: Demostration of the usage of parameter parse_body
lang: en
mode: create_or_update
content: wikicontent:Profile_r_test13_parse_body
-
type: wiki_page
ref: r_test13_template01_page
data:
name: r_demo13_template01
description: Template for wiki page
lang: en
mode: create_or_update
content: wikicontent:Profile_r_test3_template
-
type: wiki_page
ref: r_test14_page
data:
name: r_demo14_webshot
description: Demostration of the usage of the Webshot R package
lang: en
mode: create_or_update
content: wikicontent:Profile_r_test14_webshot
-
type: wiki_page
ref: r_test15_page
data:
name: r_demo15_pivottables
description: Demostration of the usage of the rpivotTable R package (which uses PivotTable.js - a Javascript Pivot Table library with drag and drop functionality built on top of jQuery/jQueryUI and written in CoffeeScript by Nicolas Kruchten at Datacratic)
lang: en
mode: create_or_update
content: wikicontent:Profile_r_test15_pivottables
Content Templates for pre-defined reports
YAML
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objects:
-
type: template
ref: content_template_report_01
data:
name: Report 01
content: wikicontent:Profile_r_test_ContentTemplate_Report_01
sections: [ wiki ]
Useful navigational aid
This will add the page
Profile_r_test_menupage as the menu content
YAML
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objects:
-
type: wiki_page
ref: r_test_menupage_include
data:
name: Menu for R demo
description: Collaborative simple menu
lang: en
mode: create_or_update
content: wikicontent:Profile_r_demo_menupage
YAML
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objects:
-
type: module
ref: module_menupage
data:
name: menupage
position: right
groups: [ Anonymous, Registered ]
order: 2
params:
pagemenu: Menu for R demo
Links