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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:
Recommendation:
Required R packages
Some screenshots of the profile after being applied to your tiki site:
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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
- 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.
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)
- Profile_r_heatmaps_test
- Profile_r_heatmaps_template
- Profile_r_heatmaps_menupage
- Profile_r_heatmaps_instructions
- Profile_r_heatmaps_edit
- Profile_r_heatmaps
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: y1.2. 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_input1.3. 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_test1.5. Useful navigational aid
1.5.1. Wiki Page for the Menu
This will add the page Profile_r_heatmaps_menupage as the menu contentYAML
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_menupage1.5.2. 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 RHeatMaps | Heat Maps | r HeatMaps | r Heat Maps | HeatMap | Heat Map | r HeatMap | r Heat Map | r_HeatMap | r_Heat_Map