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.

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")

Profile R_HeatMaps

These pages will be created:
(listed properly only when shown here: http://profiles.tiki.org/R_HeatMaps , not when you are at profile installation in your remote tiki site)

1.1. Preferences

YAML

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
 feature_user_watches: y
 feature_wiki_argvariable: y
 feature_wiki_ext_icon: n
 feature_wiki_templates: 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

1.2. Groups and Permissions

YAML

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

1.3. Trackers

YAML

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]

1.4. Wiki Pages

YAML

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

1.5. Useful navigational aid

1.5.1. Wiki Page for the Menu

This will add the page Profile_r_heatmaps_menupage as the menu content

YAML

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

1.5.2. Module wiki side menu

YAML

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

alias

Information	Version
Fri 14 of Oct, 2016 09:17 GMT-0000 Xavi (as xavidp - admin) Mass search and replace	28	View
Tue 11 of Jun, 2013 07:56 GMT-0000 Xavier de Pedro removed sef	27	View
Mon 03 of Jun, 2013 11:02 GMT-0000 Xavier de Pedro updated with new fields	26	View
Tue 10 of Jul, 2012 14:50 GMT-0000 Xavier de Pedro added check for preinstalled package	25	View
Sun 13 of Nov, 2011 20:25 GMT-0000 Xavier de Pedro added multilingual feature and save in db, to allow easy translation of missing strings by admins reviewing this profile from non-english-speaking countries	24	View
Sun 13 of Nov, 2011 17:16 GMT-0000 Xavier de Pedro fixed syntax for tracker fields in 8x	23	View
Sun 13 of Nov, 2011 15:59 GMT-0000 Xavier de Pedro added a few pref	22	View
Thu 10 of Nov, 2011 12:26 GMT-0000 Xavier de Pedro added a few screenshots	21	View
Sat 27 of Aug, 2011 11:26 GMT-0000 Xavier de Pedro updated title and subtitle	20	View
Sat 27 of Aug, 2011 11:25 GMT-0000 Xavier de Pedro absolute links	19	View
Sat 27 of Aug, 2011 11:19 GMT-0000 Xavier de Pedro changed title and subtitle	18	View
Sat 27 of Aug, 2011 11:18 GMT-0000 Xavier de Pedro moved instructions param to first level (removed one space)	17	View
Sat 27 of Aug, 2011 11:07 GMT-0000 Xavier de Pedro re-categorized	16	View
Mon 22 of Aug, 2011 12:56 GMT-0000 Xavier de Pedro update perms	15	View
Mon 22 of Aug, 2011 12:45 GMT-0000 Xavier de Pedro moved local perms to the right place?	14	View
Mon 22 of Aug, 2011 11:26 GMT-0000 Xavier de Pedro added missing and required perm for anons to view the tracker in order to allow them (R) to download item attachments	13	View
Mon 22 of Aug, 2011 11:10 GMT-0000 Xavier de Pedro added local perm for tracker2 so that anons (R) can download item attachments	12	View
Mon 22 of Aug, 2011 11:02 GMT-0000 Xavier de Pedro added test page	11	View
Mon 22 of Aug, 2011 07:43 GMT-0000 Xavier de Pedro added link and correected info on link to package	10	View
Sat 20 of Aug, 2011 23:21 GMT-0000 Xavier de Pedro renamed template	9	View
Sat 20 of Aug, 2011 23:18 GMT-0000 Xavier de Pedro improved names of wiki pages	8	View
Sat 20 of Aug, 2011 23:15 GMT-0000 Xavier de Pedro more info on dependencies of R packages	7	View
Fri 19 of Aug, 2011 16:29 GMT-0000 Xavier de Pedro more	6	View
Fri 19 of Aug, 2011 16:10 GMT-0000 Xavier de Pedro info on how to use profiles	5	View
Fri 19 of Aug, 2011 16:03 GMT-0000 Xavier de Pedro foo	4	View

History: R_HeatMaps

Preview of version: 20

Profile R_HeatMaps

1.1. Preferences

1.2. Groups and Permissions

1.3. Trackers

1.4. Wiki Pages

1.5. Useful navigational aid

1.5.1. Wiki Page for the Menu

1.5.2. Module wiki side menu

History

Menu

Current Profiles

Latest Changes

Similar pages

Search

Most Popular Tags

About Tiki

Support

Community

Documentation

Development

Legal

Tiki Project Sites

Networks

History: R_HeatMaps

Preview of version: 20

Profile R_HeatMaps

1.1. Preferences

1.2. Groups and Permissions

1.3. Trackers

1.4. Wiki Pages

1.5. Useful navigational aid

1.5.1. Wiki Page for the Menu

1.5.2. Module wiki side menu

History

Menu

Current Profiles

Latest Changes

Similar pages

Search

Most Popular Tags

Tiki Newsletter

About Tiki

Support

Community

Documentation

Development

Legal

Tiki Project Sites

Networks