History: r_HeatMaps

Source of version: 1

! Profile R_HeatMaps

^This is a configuration profile to add a web interface for an [http://r-project.org|R package] called __EasyHeatMap__ (provided here as attachment also, while it's publicly unavailable elsewhere). 

{DIV(float="right")}{img src=http://www.r-project.org/Rlogo.jpg }{DIV}This R package allows the creation and edition of HeatMap graphics (as used in Bioinformatics) through a simple web interface. %%% %%% 

__Requirements__:
* A Tiki site on a server :-). See ((doc:Requirements)) and ((doc:Installation)) if needed. 
* ((doc:PluginR)), 
+ downloadable as a Mod from [http://mods.tiki.org/details.php?type=wikiplugins&mod=r|http://mods.tiki.org]
+ or installable as a mod from the tiki mods interface: tiki-mods.php
* [http://r-project.org|R project] installed in the same server as Tiki
** a few R packages which are dependencies or the EasyHeatMap package.

__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.
^

{maketoc title=""}

!! Preferences

{CODE(caption=>YAML,wrap=>0)}
preferences:
 auth_method: openid
 browsertitle: My Tiki
 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: Current Stable Branch
 sitetitle: Tiki 7.x
 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
{CODE}

!! Trackers

{CODE(caption=>YAML,wrap=>0)}
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]
{CODE}


!!# Wiki Pages


!!# Permissions



-=related=-
* http://doc.tiki.org/PluginR
* http://profiles.tiki.org/r_test
* http://www.r-project.org

-=alias=-
(alias(HeatMaps)) | (alias(Heat Maps)) | (alias(r HeatMaps)) | (alias(r Heat Maps)) | (alias(HeatMap)) | (alias(Heat Map)) | (alias(r HeatMap)) | (alias(r Heat Map)) | (alias(r_HeatMap)) | (alias(r_Heat_Map))

History

Enable pagination rows per page

Information	Version
Fri 19 of Aug, 2011 15:48 GMT-0000 Xavier de Pedro wrap added	3	Actions View Source
Fri 19 of Aug, 2011 15:47 GMT-0000 Xavier de Pedro perms added as well as pages, modules, etc.	2	Actions View Source
Fri 19 of Aug, 2011 15:15 GMT-0000 Xavier de Pedro first version	1	Actions View Source

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History: r_HeatMaps

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History: r_HeatMaps

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