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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).

Image
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) if(!require(gplots)){ install.packages("gplots", repos="http://ftp.heanet.ie/mirrors/cran.r-project.org/") } if(!require(gtools)){ install.packages("gtools", repos="http://ftp.heanet.ie/mirrors/cran.r-project.org/") } if(!require(gdata)){ install.packages("gdata", repos="http://ftp.heanet.ie/mirrors/cran.r-project.org/") } if(!require(caTools)){ 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")






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_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


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] - type: tracker_field ref: field_24 data: name: Expressions file Decimal separator (character) tracker: $tracker_2 options: dot,comma type: dropdown order: 55 flags: [searchable, public] - type: tracker_field ref: field_25 data: name: Type of file with Color names for columns tracker: $tracker_2 options: txt=txt - values separated with tabs,txt=txt separated with tab,csv=csv - values separated with commas,csv2=csv2 - values separated with semicolons type: dropdown order: 135 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


related

alias
HeatMaps | Heat Maps | r HeatMaps | r Heat Maps | HeatMap | Heat Map | r HeatMap | r Heat Map | r_HeatMap | r_Heat_Map
Category: 12.x
Category: 15.x
Category: 16.x
Category: 17.x