Changeset 11422:40b5a911f6c5 in orange


Ignore:
Timestamp:
03/22/13 11:15:09 (13 months ago)
Author:
Ales Erjavec <ales.erjavec@…>
Branch:
default
Message:

Fixed sphinx warnings.

Location:
docs
Files:
4 edited

Legend:

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Removed
  • docs/extend-widgets/rst/settings.rst

    r11408 r11422  
    176176state so that when the user changes a check box, the attribute changes 
    177177and vice-versa. Although you can create such a link manually, you 
    178 should always use the module :doc:`OWGUI <owgui.rst>` instead; 
     178should always use the module :doc:`OWGUI <owgui>` instead; 
    179179for instance, for a check box, use :obj:`OWGUI.checkBox` and not 
    180180simply the Qt's :obj:`QCheckBox`. 
     
    183183the data, while other are context-dependent. For the first to be saved 
    184184properly, you only need to list them in the :obj:`settingsList` 
    185 in the widget definition, as already described :doc:`elsewhere <settings.rst>` 
     185in the widget definition, as already described :doc:`elsewhere <settings>` 
    186186 
    187187************************** 
  • docs/widgets/rst/visualize/linearprojection.rst

    r11359 r11422  
    4444nicely characterizes mamals from the other organisms, and that laying eggs is 
    4545something that birds do. This specific visualization was obtained using FreeViz 
    46 ([Demsar2007]_), while the widget also implements an interface to supervised 
    47 principal component analysis ([Koren2003]_), partial least squares (for a nice 
    48 introduction, see [Boulesteix2007]_), and RadViz visualization and 
     46([1]_), while the widget also implements an interface to supervised 
     47principal component analysis ([2]_), partial least squares (for a nice 
     48introduction, see [3]_), and RadViz visualization and 
    4949associated intelligent data visualization technique called VizRank  
    50 ([Leban2006]_) 
     50([4]_) 
    5151 
    5252.. image:: images/LinearProjection-Zoo.png 
     
    7777order to understand how a change of one anchor affects the positions of the 
    7878data points. Controls in :obj:`Forces` box are used to set the parameters that 
    79 define the type of the forces between the data points (see [Demsar2007]_). 
     79define the type of the forces between the data points (see [1]_). 
    8080In any linear projection, projections of unit vector that are very short 
    8181compared to the others indicate that their associated attribute is not very 
     
    9393 
    9494The fourth projection search technique that can be accessed from this widget 
    95 is VizRank search algorithm with RadViz visualization ([Leban2006]_). This is 
     95is VizRank search algorithm with RadViz visualization ([4]_). This is 
    9696essentially the same visualization and projection search method as implemented 
    9797in :ref:`Radviz`. 
     
    107107---------- 
    108108 
    109 .. [Demsar2007] Demsar J, Leban G, Zupan B. FreeViz-An intelligent multivariate 
     109.. [1] Demsar J, Leban G, Zupan B. FreeViz-An intelligent multivariate 
    110110   visualization approach to explorative analysis of biomedical data. J Biomed 
    111111   Inform 40(6):661-71, 2007. 
    112112 
    113 .. [Koren2003] Koren Y, Carmel L. Visualization of labeled data using linear 
     113.. [2] Koren Y, Carmel L. Visualization of labeled data using linear 
    114114   transformations, in: Proceedings of IEEE Information Visualization 2003 
    115115   (InfoVis'03), 2003. `PDF <http://citeseerx.ist.psu.edu/viewdoc/download;jsessionid=3DDF0DB68D8AB9949820A19B0344C1F3?doi=10.1.1.13.8657&rep=rep1&type=pdf>`_ 
    116116 
    117 .. [Boulesteix2007] Boulesteix A-L, Strimmer K (2006) Partial least squares: 
     117.. [3] Boulesteix A-L, Strimmer K (2006) Partial least squares: 
    118118   a versatile tool for the analysis of high-dimensional genomic data, 
    119119   Briefings in Bioinformatics 8(1): 32-44.  
    120120   `Abstract <http://bib.oxfordjournals.org/cgi/content/abstract/8/1/32>`_ 
    121121 
    122 .. [Leban2006] Leban, G., B. Zupan, et al. (2006). "VizRank: Data Visualization 
     122.. [4] Leban, G., B. Zupan, et al. (2006). "VizRank: Data Visualization 
    123123   Guided by Machine Learning." Data Mining and Knowledge Discovery 13(2): 
    124124   119-136. 
  • docs/widgets/rst/visualize/radviz.rst

    r11359 r11422  
    3333----------- 
    3434 
    35 Radviz ([Hoffman1997]_) is a neat non-linear multi-dimensional visualization 
     35Radviz ([1]_) is a neat non-linear multi-dimensional visualization 
    3636technique that can display data on three or more attributes in a 2-dimensional 
    3737projection. The visualized attributes are presented as anchor points equally 
     
    4747 
    4848The snapshot shown below shows a Radviz widget with a visualization of the 
    49 data set from functional genomics ([Brown2000]_). In this particular 
     49data set from functional genomics ([2]_). In this particular 
    5050visualization the data instances are colored according to the corresponding 
    5151class, and the visualization space is colored according to the computed class 
     
    6464"spo mid") is quite characteristic for instance of class Ribo, which at the 
    6565same time have comparable lower value of other attributes. High values of 
    66 heat 20 and diau f are characteristic for Resp class. See [Leban2006]_ and 
    67 [Mramor2007]_ for further illustrations of utility of Radviz in analysis of 
     66heat 20 and diau f are characteristic for Resp class. See [3]_ and 
     67[5]_ for further illustrations of utility of Radviz in analysis of 
    6868this and similar data set from functional genomics. Other options in the 
    6969:obj:`Settings` tab are quite standard. The :obj:`Point size` controls the size 
     
    8686 
    8787Just like all point-based visualizations, this widget includes tools for 
    88 intelligent data visualization (VizRank and FreeViz, see [Leban2006]_) and 
    89 [Demsar2007]_) and interface for explorative data analysis - selection of data 
     88intelligent data visualization (VizRank and FreeViz, see [3]_) and 
     89[4]_) and interface for explorative data analysis - selection of data 
    9090points in visualization. Just like in :ref:`Scatter Plot` widget, intelligent 
    9191visualization can be used to find a set of attributes that would result in an 
     
    103103---------- 
    104104 
    105 .. [Hoffman1997] Hoffman,P.E. et al. (1997) DNA visual and analytic data mining. 
     105.. [1] Hoffman,P.E. et al. (1997) DNA visual and analytic data mining. 
    106106   In the Proceedings of the IEEE Visualization. Phoenix, AZ, pp. 437-441. 
    107107 
    108 .. [Brown2000] Brown, M. P., W. N. Grundy, et al. (2000). 
     108.. [2] Brown, M. P., W. N. Grundy, et al. (2000). 
    109109   "Knowledge-based analysis of microarray gene expression data by using 
    110110   support vector machines." Proc Natl Acad Sci U S A 97(1): 262-7. 
    111111 
    112 .. [Leban2006] Leban, G., B. Zupan, et al. (2006). "VizRank: Data Visualization 
     112.. [3] Leban, G., B. Zupan, et al. (2006). "VizRank: Data Visualization 
    113113   Guided by Machine Learning." Data Mining and Knowledge Discovery 13(2): 
    114114   119-136. 
    115115 
    116 .. [Demsar2007] Demsar J, Leban G, Zupan B. FreeViz-An intelligent multivariate 
     116.. [4] Demsar J, Leban G, Zupan B. FreeViz-An intelligent multivariate 
    117117   visualization approach to explorative analysis of biomedical data. J Biomed 
    118118   Inform 40(6):661-71, 2007. 
    119119 
    120 .. [Mramor2007] Mramor M, Leban G, Demsar J, Zupan B. Visualization-based 
     120.. [5] Mramor M, Leban G, Demsar J, Zupan B. Visualization-based 
    121121   cancer microarray data classification analysis. Bioinformatics 23(16): 
    122122   2147-2154, 2007. 
  • docs/widgets/rst/visualize/scatterplot.rst

    r11359 r11422  
    6868all the pairs of attributes to find interesting scatterplots. Intelligent data 
    6969visualizations techniques are about finding such visualizations automatically. 
    70 Orange's Scatterplot includes one such tool called VizRank ([Leban2006]_), that 
     70Orange's Scatterplot includes one such tool called VizRank ([1]_), that 
    7171can be in current implementation used only with classification data sets, that 
    7272is, data sets where instances are labeled with a discrete class. The task of 
     
    9898learning it would be best to leave them at their defaults. The options are 
    9999grouped according to the different aspects of the methods as described in 
    100 [Leban2006]_. The projections are evaluated through testing a selected 
     100[1]_. The projections are evaluated through testing a selected 
    101101classifier (:obj:`Projection evaluation method` default is k-nearest neighbor 
    102102classification) using some standard evaluation technique 
     
    202202---------- 
    203203 
    204 .. [Leban2006] Leban G, Zupan B, Vidmar G, Bratko I. VizRank: Data 
     204.. [1] Leban G, Zupan B, Vidmar G, Bratko I. VizRank: Data 
    205205   Visualization Guided by Machine Learning. Data Mining and Knowledge 
    206206   Discovery 13(2): 119-136, 2006. 
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