Secondary Model View

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.

Options

Graph

Visualizes secondary model estimations and associated model parameters.

Mouse zoom: 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.

Context Menu (Right click in the graph):
Properties: 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.
Copy: Copies the graph to the clipboard enabling you to paste it in a graphical editor.
Save as...: 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.
Print: Print the graph directly from Knime PMM-Lab.
Zoom: Zoom in and out or auto range the view for one or both axes.

Display Options

Draw Lines: Connect data points with lines which helps to distinguish between different sets of data.
Display Highlighted Row: 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.
Show Legend: Display the parameter name together with symbol and color.
Add Info in Legend: 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.
Export as SVG: If checked, the graph outport contains a SVG file and not a PNG file after execution of the node.
Show Confidence Interval: Computes and displays confidence intervals.

Range

Check the box to set the minimum and maximum values for x and y axes.

Variables on Display

X and Y: Displays the heading of the displayed data column. Changing units automatically reformats the axes.
X/Y Transform: 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^).

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.

Filter

Filter the rows in the table to be displayed for the model status:
Ok = fitting successful.
No Covariance Matrix = Confidence intervals cannot be calculated. Editing the expert settings in the Model Fitting node or choosing a different formula may help.
Coeff out of limit = The fitting was successful, but only because the minimum/maximum values of the parameters given in the model formula were ignored.
Failed = Fitting was not successful. Editing the expert settings in the Model Fitting node or choosing a different formula may help.

Columns

Click on 'Customize' to select the columns to be displayed, e.g. model name, quality criteria (R², AIC) and assay conditions (temperature, pH, a_W).
'Set optimal width' changes the width of the columns such that the whole text is visible in each cell.

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.

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