R_HeatMaps

Profile R_HeatMaps

This is a configuration profile to add a web interface for an R package called EasyHeatMap (link to package provided in this page, while it's publicly unavailable elsewhere).

This R package allows the creation and edition of HeatMap graphics (as used in Bioinformatics) through a simple web interface. A few other pages are created within this profile.

Some screenshots of the profile after being applied to your tiki site:

Requirements:

• A Tiki site on a server :-). See Requirements and Installation if needed.
• PluginR
  downloadable as a Mod from http://mods.tiki.org
  or installable as a mod from the tiki mods interface: tiki-mods.php
• Understand how to apply a profile into your own Tiki site :-)
  See the page Welcome to Tiki Profiles
• R project installed in the same server as Tiki
  • a few R packages which are dependencies or the EasyHeatMap package.
    See below

Recommendation:

• Play with profile r_test first
  Eventually, you might like to try first with profile r_test, since it might serve you as an entry point for the usage of R scripts through Tiki.

Required R packages

##################################################################
### Chunk 1: Installation of easyHeatMap package and dependencies
##################################################################

##### NOTE:
# * You need a few packages: install the ones you are missing in the central server location for R packages.
# * In this example we install them with this params: lib="/usr/lib/R/site-library", repos="http://ftp.heanet.ie/mirrors/cran.r-project.org/"
#   but adapt the server paths or urls to your specific case
# * Remember you can install packages:
#  * from the terminal with some command like:
#      R CMD INSTALL /home/foo/myPackage.tar.gz --library="/usr/lib/R/site-library"
#  * or from an R session with something like:
#      install.packages(pkgs="/home/foo/myPackage.tar.gz", lib="/usr/lib/R/site-library", repos="http://ftp.heanet.ie/mirrors/cran.r-project.org/")

##### Install the following required dependencies if needed in the central server location 
##### so that they can be reached by the webserver user (www-data, etc)
install.packages("gplots", repos="http://ftp.heanet.ie/mirrors/cran.r-project.org/")
install.packages("gtools", repos="http://ftp.heanet.ie/mirrors/cran.r-project.org/")
install.packages("gdata", repos="http://ftp.heanet.ie/mirrors/cran.r-project.org/")
install.packages("caTools", repos="http://ftp.heanet.ie/mirrors/cran.r-project.org/")


##### Install the package "easyHeatMap"
### for the time being you can fetch it from:
### https://ueb.ir.vhebron.net/files/easyHeatMap_1.18.tar.gz
### or 
### http://dl.dropbox.com/u/24830595/easyHeatMap_1.18.tar.gz
install.packages(pkgs="/home/user/easyHeatMap_1.18.tar.gz")

1. Preferences

instructions: Welcome to Easy Web HeatMaps using R and Tiki
preferences:
 browsertitle: My Easy Web HeatMaps with Tiki and R
 display_timezone: UTC
 error_reporting_adminonly: n
 error_reporting_level: 2047  
 feature_edit_templates: y
 feature_jquery_jqs5: y
 feature_jquery_reflection: y
 feature_jquery_tablesorter: y
 feature_left_column: user
 feature_right_column: user
 feature_search_fulltext: y
 feature_sefurl: y
 feature_show_stay_in_ssl_mode: n
 feature_slideshow: y
 feature_syntax_highlighter: y
 feature_trackers: y
 trackerfield_file: y
 trackerfield_files: y
 trackerfield_dropdownother: y
 feature_user_watches: y
 feature_wiki_argvariable: y
 feature_wiki_ext_icon: n
 feature_wiki_templates: y
 feature_multilingual: y
 lang_use_db: y
 fgal_root_user_id: 2
 fgal_root_wiki_attachments_id: 3
 gal_use_lib: gd
 https_login: disabled
 https_port:
 sitemycode: |
  {if $tiki_p_admin == "y"}
  {tr}Quick Admin{/tr}:
  {icon _id=database_refresh title="{tr}Clear all Tiki caches{/tr}" href="tiki-admin_system.php?do=all"}
  {icon _id=wrench title="{tr}Modify the look & feel (logo, theme, etc.){/tr}" href="tiki-admin.php?page=look&cookietab=2"}
  {if $prefs.lang_use_db eq "y"}{icon _id=world_edit title="{tr}Show interactive translation settings{/tr}" href="tiki-edit_languages.php?interactive_translation_mode=on"}{/if}
  {/if}
 sitesubtitle: With Tiki & Plugin R
 sitetitle: HeatMaps
 slide_style: clear.css
 wikiHomePage: HeatMaps
 wiki_dynvar_style: double
 wiki_edit_icons_toggle: y
 wiki_uses_slides: y
 wikiplugin_iframe: y
 wikiplugin_listpages: y
 wikiplugin_perspective: n
 wikiplugin_pluginmanager: y
 wikiplugin_r: y
 wikiplugin_rr: y
 wikiplugin_slideshow: y
 wikiplugin_titlesearch: y
 wikiplugininline_code: y
 wikiplugininline_div: y
 wikiplugininline_fade: y
 wikiplugininline_fancylist: y
 wikiplugininline_fancytable: y
 wikiplugininline_iframe: y
 wikiplugininline_img: y
 wikiplugininline_listpages: y
 wikiplugininline_perspective: n
 wikiplugininline_pluginmanager: y
 wikiplugininline_r: y
 wikiplugininline_remarksbox: y
 wikiplugininline_rr: y
 wikiplugininline_slideshow: y
 wikiplugininline_split: y
 wikiplugininline_titlesearch: y

2. Groups and Permissions

permissions:
 Anonymous:
  allow: view
  deny: [ ]
  objects:
   -
    type: tracker
    id: $tracker_2
    allow: [tracker_view_attachments, view_trackers]
 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_heatmaps_template_page
    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

3. Trackers

objects:
 -
  type: tracker
  ref: tracker_2
  data:
   name: HeatMap Generation
   description: Tracker to manage the data for the generation and edition of HeatMaps
   sort_default_field: modification
   allow: [attachments, creator_modification]
   show: [list_modification_date, modification_date, creation_date]
 -
  type: tracker_field
  ref: field_7
  data:
   name: Name
   tracker: $tracker_2
   type: text_field
   order: 10
   description: Some name to identify (and potentially recall in a later stage) this Heatmap from others in this site
   flags: [link, searchable, public, mandatory]
 -
  type: tracker_field
  ref: field_8
  data:
   name: Description
   tracker: $tracker_2
   type: text_area
   order: 20
   flags: [public]
 -
  type: tracker_field
  ref: field_9
  data:
   name: Added by
   tracker: $tracker_2
   options: 1
   type: user
   order: 30
   flags: [searchable, public]
 -
  type: tracker_field
  ref: field_10
  data:
   name: Expressions file name
   tracker: $tracker_2
   options: ntsu
   type: attachment
   order: 40
   flags: [link, searchable, public]
 -
  type: tracker_field
  ref: field_11
  data:
   name: Expressions file type
   tracker: $tracker_2
   options: txt,txt,csv,csv2
   type: dropdown
   order: 50
   flags: [searchable, public]
 -
  type: tracker_field
  ref: field_12
  data:
   name: Name for this plot
   tracker: $tracker_2
   options: My Plot,My Plot
   type: dropdown_other
   order: 60
   flags: [searchable, public]
 -
  type: tracker_field
  ref: field_13
  data:
   name: Title to show in plot
   tracker: $tracker_2
   options: Heatmap,Heatmap
   type: dropdown_other
   order: 70
   flags: [searchable, public]
 -
  type: tracker_field
  ref: field_14
  data:
   name: Distance function to group rows
   tracker: $tracker_2
   options: cor,cor,euclidean,manhattan,maximum,canberra,binary,minkowski
   type: dropdown
   order: 80
   flags: [searchable, public]
 -
  type: tracker_field
  ref: field_15
  data:
   name: Distance function to group columns
   tracker: $tracker_2
   options: euclidean,euclidean,manhattan,maximum,canberra,binary,minkowski,cor
   type: dropdown
   order: 90
   flags: [searchable, public]
 -
  type: tracker_field
  ref: field_16
  data:
   name: Group rows and plot dendrogram?
   tracker: $tracker_2
   options: TRUE,TRUE,FALSE
   type: radio
   order: 100
   flags: [searchable, public]
 -
  type: tracker_field
  ref: field_17
  data:
   name: Group columns and plot dendrogram?
   tracker: $tracker_2
   options: TRUE,TRUE,FALSE
   type: radio
   order: 110
   flags: [searchable, public]
 -
  type: tracker_field
  ref: field_18
  data:
   name: Scale data by
   tracker: $tracker_2
   options: row,row,column,none
   type: dropdown
   order: 120
   flags: [searchable, public]
 -
  type: tracker_field
  ref: field_19
  data:
   name: Color palette to use
   tracker: $tracker_2
   options: redblue(64),redblue(64),heat.colors(64),topo.colors(64),rainbow(36)
   type: dropdown
   order: 120
   flags: [searchable, public]
 -
  type: tracker_field
  ref: field_20
  data:
   name: File with color names for columns
   tracker: $tracker_2
   options: ntsu
   type: attachment
   order: 130
   flags: [searchable, public]
 -
  type: tracker_field
  ref: field_21
  data:
   name: Type of information about density
   tracker: $tracker_2
   options: density,density,histogram,none
   type: dropdown
   order: 140
   flags: [searchable, public]
 -
  type: tracker_field
  ref: field_22
  data:
   name: Expansion coeficient for fonts in columns
   tracker: $tracker_2
   options: 0.7,0.8,0.8,0.9,1.0,1.1,1.2,1.3
   type: dropdown_other
   order: 150
   flags: [searchable, public]
 -
  type: tracker_field
  ref: field_23
  data:
   name: Expansion coeficient for fonts in rows
   tracker: $tracker_2
   options: 0.7,0.7,0.8,0.9,1.0,1.1,1.2,1.3
   type: dropdown_other
   order: 160
   flags: [searchable, public]

4. Wiki Pages

preferences:
  enable: [ feature_wiki ]
objects:
  -
    type: wiki_page
    ref:  r_heatmaps_instructions_page
    data:
      name: Welcome to Easy Web HeatMaps using R and Tiki
      description: Basic intructions of PluginR and this profile
      lang: en
      mode: create_or_update
      content: wikicontent:Profile_r_heatmaps_instructions
  -
    type: wiki_page
    ref:  r_heatmaps_page
    data:
      name: HeatMaps
      description: Interface to list and create heatmaps
      lang: en
      mode: create_or_update
      content: wikicontent:Profile_r_heatmaps
  -
    type: wiki_page
    ref:  r_heatmaps_edit_page
    data:
      name: HeatMaps Edition
      description: Interface to show the results from the analysis and eventually allows editing and resubmitting again as much as needed.
      lang: en
      mode: create_or_update
      content: wikicontent:Profile_r_heatmaps_edit
  -
    type: wiki_page
    ref:  r_heatmaps_template_page
    data:
      name: HeatMaps_template
      description: Template for smarty content on a wiki page which will not be parsed as wiki syntax
      lang: en
      mode: create_or_update
      content: wikicontent:Profile_r_heatmaps_template
  -
    type: wiki_page
    ref:  r_heatmaps_test_page
    data:
      name: HeatMaps Test
      description: Test page to check whether everything is installed properly in Tiki, R and their required packages for the Easy Web HeatMap generation.
      lang: en
      mode: create_or_update
      content: wikicontent:Profile_r_heatmaps_test

5. Useful navigational aid

5.1. Wiki Page for the Menu

objects:
  -
    type: wiki_page
    ref: r_heatmaps_menupage_include
    data:
      name: Menu for Easy Web HeatMaps with Tiki and R
      description: Menu for Easy Web HeatMaps with Tiki and R in a collaborative way
      lang: en
      mode: create_or_update
      content: wikicontent:Profile_r_heatmaps_menupage

5.2. Module wiki side menu

objects:
 -
  type: module
  ref: module_menupage
  data:
   name: menupage
   position: right
   groups: [ Anonymous, Registered ]
   order: 1
   params:
    pagemenu: Menu for Easy Web HeatMaps with Tiki and R

• http://doc.tiki.org/PluginR
• http://profiles.tiki.org/r_test
• http://www.r-project.org