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main:expca [2016/11/10 14:32]
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main:expca [2016/11/10 14:35] (current)
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 +====== Workflow and Statistical Analysis catalogs ======
 +===== An example: PCA =====
 +
 +== Overview of the interaction mechanism of the different file types ==
 +{{pca_flow.png?​nolink|}}
 +
 +== PCA.def ==
 +This definition file serves to automatically build the GUI of input masks of the analysis parameters with some default values, and also the the header of R scripts taken into account the initialization of parameters with the values given by the user.
 +
 +{{pca_def.png?​direct&​800|}}
 +
 +
 +== GUI of input mask of the analysis parameters ​ (automatically generated) ==
 +
 +{{:​default:​pca_gui.png?​nolink|}}
 +
 +
 +== Header of the R code (automatically generated) ==
 +
 +{{pca_r_header.png?​direct|}}
 +
 +== PCA.R - R code written by the provider ==
 +
 +The R script written by the provider. It should not include the initialisation part of the parameters, given that the header of each script, automatically generated, takes into account this part. See above.
 +
 +{{pca_r_core.png?​direct|}}
 +
 +**...**
 +
 +== PCA.xml ==
 +This documentation file describes the analysis parameters within the input mask.
 +
 +<code xml>
 +
 +<?xml version="​1.0"​ encoding="​UTF-8"?>​
 +<​!DOCTYPE analysis>​
 +<​analysis name="​PCA">​
 + <​description>​
 +Principal component analysis (PCA) is a mathematical procedure _NL_
 +that uses an orthogonal transformation to convert a set of observations _NL_
 +of possibly correlated variables into a set of values of linearly_NL_
 +uncorrelated variables called principal components. ​
 +See [PCA|http://​en.wikipedia.org/​wiki/​Principal_component_analysis]
 +        </​description>​
 + <​helptable>​
 + <​setting>​
 + <​field>​Launch</​field>​
 + <​desc>​
 +                              Field indicating whether you want to execute this 
 +                              analysis in the workflow (checked) or not (unchecked).
 +                         </​desc>​
 + <​example></​example>​
 + </​setting>​
 + <​setting>​
 + <​field>​Scale</​field>​
 + <​desc>​
 +                              Indicates whether the variables should be scaled to have unit variance ​
 +                              before the analysis takes place.
 +                        </​desc>​
 + <​example>​No by default (done in a previous step)</​example>​
 + </​setting>​
 + <​setting>​
 + <​field>​ Labels on Score graphs:</​field>​
 + <​desc>​
 +                              Indicates whether the samples labels should be put in the Score plot.
 +                        </​desc>​
 + <​example>​Yes (by default)</​example>​
 + </​setting>​
 + <​setting>​
 + <​field>​Samples within ellipses</​field>​
 + <​desc>​
 +                              Indicates whether ellipses should be drawn in the Scores plot around ​
 +                              samples from the same factorial group.
 +                        </​desc>​
 + <​example>​No (by default)</​example>​
 + </​setting>​
 + </​helptable>​
 +</​analysis>​
 +
 +</​code>​
  
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