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Fitted Parameter View

Node extensions for KNIME Workbench version 1.0.0.202102171221 by BfR

View parameters of fitted models and environmental conditions. This is helpful for the selection of suitable parameters for the fitting of secondary models.

Options

Conditions to use
First, add one or more environmental conditions (e.g. temperature, pH, aw, sodium concentration) to be able to estimate, which parameters might be suited best for the fitting of secondary models. Now select one of the parameters in the table. The first condition will be shown on the x-axis in the graph and the others can be defined in the section 'Other Variables'.
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). 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: This check box has no function.
Export as SVG: If checked, the graph outport contains a SVG file and not a PNG file after execution of the node.
Display Options
Draw Lines: Connect data points with lines which helps to distinguish between different sets of data.
Show Legend: Display the model ID and the data set ID together with symbol and color.
Export as SVG: If this option is chosen, the outport will contain a SVG file and not a PNG file.
Display Highlighted Row: If checked, only the row currently highlighted in the table is displayed in the graph. This option is the default view in the Fitted Parameter View and cannot be changed.
Add Info in Legend: No additional information available.
Export as SVG: If checked, the graph outport contains a SVG file and not a PNG file after execution of the node.
Range
Set the minimum and maximum values for the x and y axes.
Variables on Display
X: If more than one environmental condition was added via the Conditions menu the one to be displayed on the x-axis can be defined here.
Y: The parameter to be displayed on the y-axis is set in the table and cannot be changed here.
X Unit: If the condition is 'temperature', the unit can be changed (°C, K or °F).
Y Unit: Units for parameters cannot be changed.
X and Y Transform: Transforms the data on the X and 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^).
Conditions: Add environmental conditions to the variables in the display menu. Which condition is currently displayed can be changed in the 'Variables on Display' and 'Other Variables' sections.
Other Variables
Is more than one condition selected (the one that is on the x-axis) the other conditions can be configured here. Example: The inactivation of a bacterial agent was estimated for different temperatures, pH values and water activities. The change of the inactivation parameter k due to different temperature values is displayed in the graph. Now choose from the 'Other Variables' for which pH and aw this change should be displayed.
Columns
Click on 'Customize' to select the columns to be displayed, e.g. model name, quality criteria (R2, AIC) and assay conditions (temperature, pH, aW).
'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.

Input Ports

Icon
Primary and/or secondary models (e.g. from the nodes Model Fitting or Primary Model Selection)

Output Ports

Icon
Graph displaying fitted parameters; the image is a PNG file (default) or a SVG file (see section 'Display Options')

Installation

To use this node in KNIME, install PMM Nodes from the following update site:

KNIME 4.3

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Developers

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