SiLeBAT/FSK-Lab

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<knimeNode icon="./ModelViewSecondary.png" type="Visualizer">
    <name>Secondary Model View</name>
    
    <shortDescription>
        View secondary estimations and the associated model parameters
    </shortDescription>

    <fullDescription>
        <intro>View the result of secondary model estimations: The change of model parameters with changing environmental conditions is visualized, e.g. an increasing bacterial growth rate with temperature.</intro>
        
        <option name="Graph">Visualizes secondary model estimations and associated model parameters.<br></br><br></br>
        <b>Mouse zoom:</b> To view a part of the graph in detail left click and simultaneously drag the mouse right and down. Another way is to use the zoom options in the context menu.<br></br><br></br>
        <b>Context Menu</b> (Right click in the graph):<br></br>
        <u>Properties:</u> Change font (type, size, color) and labels as well as the appearance of the graph. These changes are lost as soon as the options dialog is closed. To save a graph with changed properties (e.g. for a publication) use the "Save as..." option in the context menu.<br></br>
        <u>Copy:</u> Copies the graph to the clipboard enabling you to paste it in a graphical editor.<br></br>
        <u>Save as...:</u> Saves the graph as PNG (a bitmap image) or as SVG (a vector image). Compared to the PNG image in the outport (which has a resolution of 640x480 pixels) this PNG is saved with the same size as on the screen.<br></br>
        <u>Print:</u> Print the graph directly from Knime PMM-Lab.<br></br>
        <u>Zoom:</u> Zoom in and out or auto range the view for one or both axes.</option>
       
        <option name="Display Options">
        <u>Draw Lines:</u> Connect data points with lines which helps to distinguish between different sets of data.<br></br> 
        <u>Display Highlighted Row:</u> If checked, only the highlighted row in the table is displayed. A comfortable way to select sets of data is to highlight a row and then navigate with the arrow keys (up/down) through the table. Using the keyboard, the space bar can be used to select/unselect a set of data.<br></br>
        <u>Show Legend:</u> Display the parameter name together with symbol and color.<br></br>
        <u>Add Info in Legend:</u> Adds to the legend the name of the formula with which the secondary model was estimated. This option is only available when the legend is displayed.<br></br>
        <u>Export as SVG:</u> If checked, the graph outport contains a SVG file and not a PNG file after execution of the node.<br></br>
        <u>Show Confidence Interval:</u> Computes and displays confidence intervals.</option>
        
        <option name="Range">Check the box to set the minimum and maximum values for x and y axes.</option>
        
        <option name="Variables on Display"><u>X and Y:</u> Displays the heading of the displayed data column. Changing units automatically reformats the axes.<br></br>
        <u>X/Y Transform:</u> Transforms data on the X/Y axis (square root, ln, log10, basis e, basis 10). This is useful if a display of data other than the PMM-Lab default (log10) is wished for (e.g. as actual cell counts -> 10^).</option>
        
        <option name="Other Variables">If a parameter is dependent on more than one environmental condition (e.g. temperature and pH-value), the Secondary Model View displays one environmental condition on the x-axis and summarizes all additional environmental conditions in the Other Variables section. By clicking on one variable name, the values to be displayed in the graph can be selected in a popup window. By default, all values are displayed.</option>
        
        <option name="Filter">Filter the rows in the table to be displayed for the model status:<br></br>
        <u>Ok</u> = fitting successful.<br></br>
        <u>No Covariance Matrix</u> = Confidence intervals cannot be calculated. Editing the expert settings in the Model Fitting node or choosing a different formula may help.<br></br>
        <u>Coeff out of limit</u> = The fitting was successful, but only because the minimum/maximum values of the parameters given in the model formula were ignored.<br></br>
        <u>Failed</u> = Fitting was not successful. Editing the expert settings in the Model Fitting node or choosing a different formula may help.</option>
        
        <option name="Columns">Click on <u>'Customize'</u> to select the columns to be displayed, e.g. model name, quality criteria (R<sup>2</sup>, AIC) and assay conditions (temperature, pH, a<sub>W</sub>).<br></br>
        <u>'Set optimal width'</u> changes the width of the columns such that the whole text is visible in each cell.</option>
        
        <option name="Table"> The table shows the estimated models, whether they are currently being displayed (selected), the color and shape of the symbol and other information (see "Columns"). Clicking on a column header sorts the rows. To change the order of the columns drag the column headline. This is temporarily and not saved when the node dialog is closed.</option>
    </fullDescription>    
    
    <ports>
        <inPort index="0" name="Secondary model and parameters">Secondary model and parameters (e.g. from the Model Fitting node or the Fitted Model Reader node)</inPort>
        <outPort index="0" name="Selected models graph">Graph containing selected secondary models; the image is a PNG file (default) or a SVG file (see section 'Display Options')</outPort>
    </ports>    

</knimeNode>