From the menubar at the top left corner of the plot 2D window, various features of the plot 2D window can be controlled. Table 2.1 shows the different options available.
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A red border around the render window indicates that this window is active. To activate a render window, you can either click on the render window or select the tab corresponding to the correct render window in the window controller. When a render window is active it means that you can add and remove plots to the window and change settings for the render window and the plots it contains. Only one render windows can be in the active state simultaneously.
A window controller tab consists of two main groups of controllers. The control options for the entire render window is placed to the left, and the control options for each plot in the render window is placed to the right in the window controller.
The left side of the window controller contains a list of all plots in the current render window. It also contains options for adding and deleting plots from the render window. Push the ``Add'' button to add a new plot to the window. From the ``Add plot'' dialog box, select which plot type to add to the render window. For a detailed description of the different plot types, see 2.5.2. The new plot will appear in the plot list. To delete a plot from the plot window, highlight the correct plot in the plot list and push the ``Delete'' button.
You can highlight one of the plots in the plot-list, and the plot setup dialog will appear to the right in the window controller. The plot setup dialog makes it possible to set the name of the selected plot. Default name is the name of the plot type. To specify which port x- and y- axis data comes from, select the correct ports from the ``X-axis data'' and ``Y-axis data'' drop down lists. Which column or row in the dataset to plot, is specified in a similar way. Default is to plot column 1 at both x- and y- axis. For a more detailed description of plot settings, see 2.5.5.
There are two ways to perform picking: Picking a single element, and picking a group of elements. To pick a single element, place the cursor over the object and push the left mouse button. To pick a group of elements, push the left mouse button and drag the mouse. A rectangle will now appear in the render window. When the left mouse button is released, all objects within the rectangle will be marked.
To unmark the marked objects simply place the cursor in the render window and push the left mouse button. If a new point or area is selected, the old selection will be unmarked. To make a new selection without unmark the old selection, push the ``Shift'' button. When the ``Shift'' button is used, marked objects will be unmarked if the user tries to mark them again.
In the File menu there are four options that allow the user to export or print the plots:
Table 2.1 says that it is possible to save a custom plot to a file. This saves a fully set up plot window, with all its settings including input ports, the plots and all the properties of the different plots. The one thing that is not saved is the data on the input ports, so that it is possible to reuse the configured plot windows with different data on the input ports.
When the Save Custom Plot As... option from the File menu is chosen the dialog of Figure 2.23 shows up.
In this dialog the name of the new Custom Plot is written and will be saved to disk as this name. When Ok has been pressed the Custom Plot is saved to disk and shows up in the tree view in the SciCraft main window as shown in Figure 2.24. Now the Custom Plot may be used in a Module Diagram as any other plot node.
This section describes on a general level the different plot types that is included in SciCraft. For a more thorough description of how to set the settings on the different plots, see section 2.5.5.
Figure 2.25 shows a sample Scatter Plot. A Scatter Plot takes a set of coordinates and sets markers on each coordinate's location in a coordinate system. The coordinate sets can be configured by selecting rows and/or columns from one of the input data matrices. The appearance of the markers are highly configurable, as it is possible to change the colour, size, and shape of all markers.
Figure 2.26 shows a sample Line Plot. Just as a Scatter Plot, a Line Plot takes a set of coordinates and sets markers on each coordinate's location in a coordinate system. In addition, lines are drawn between the markers in the same order as the coordinates are ordered. An additional option on the Line Plot is that it is possible to use the order in which the Y-coordinates are ordered as the X-coordinate of each coordinate pair. The appearance of the markers and lines between the markers are highly configurable, as it is possible to change the colour, size, and shape of all markers, and the colour, width, and style of the lines.
matrix = 1.00000 -2.00000 -3.00000 0.50000 2.00000 -6.00000 -4.00000 0.70000 3.00000 1.00000 -7.00000 1.00000 4.00000 -1.00000 -5.00000 1.30000 5.00000 3.00000 2.00000 1.50000 6.00000 5.00000 4.00000 2.00000 order = 2 3 7 6 4 1 5The matrix data set tell us how the clusters relates to each other and the order set tells us in which order the objects appear in. In later edition we hope to support other data formats as well.
An example of a dendrogram plot can be seen in Figure .
Histogram plot is a statistical plot which is used to graphically summarise and display the distribution of a data set. The histogram plot needs two inputs, a vector containing the data that will be counted and segmented and a scalar that defines how many bins/buckets will be used.
An example can be seen in Figure 2.28.
The image plot displays a two dimensional matrix of values as a color mapped image. The values are mapped linearly from lowest to highest value against one of the color maps.
Density plot is a plot that illustrates the distribution of data inside a region. The plot will count the number of data objects found and show the population as a colour that grows more and more white as the density increases. The density plot has an option for blurring the plot--averaging the density values using a mask with customisable size. In a blurred density plot, the colour of one density is influenced by the densities of all its neighbours. The number of neighbours that influences a density colour, is specified by the size of the averaging mask.
This section describes how to set settings that applies to the entire plot node, eg. setting the input ports and choosing how many plot windows to use.
To display the settings dialog choose 'Settings' under the 'Edit' menu, or simply press 'Ctrl+S'.
Please notice that the new settings will not be valid until after you press the 'Apply' or the 'Ok' button. Pressing the 'Cancel' button at any time will discard the new settings and keep the old ones.
The 'Input ports' section of the main settings window is shown in figure 2.29.
The 'Render windows' section is shown in figure 2.30.
Select how many plot windows you would like to view in the Plot Node view.
The 'Plot Mappings' section is shown in figure 2.31.
Plot mapping works as follows: If two plots are mapped, selection in one of the two plots will also lead to a selection in the other plot. The mapping can be done automatically based on the dimension of the data set, or manually by simply selecting which two plots that should be mapped. Automatic mapping is switched off by default.
This section describes how to set settings that applies to one render window at a time.
The 'General' section of the render window settings window is shown in figure 2.33.
The 'Label' section of the render window settings window is shown in figure 2.34.
The 'Grid' section of the render window settings window is shown in figure 2.35.
The 'Axis' section of the render window settings window is shown in figure 2.36.
Figure 2.37 shows a Scatter Plot which is configured properly to plot column 1 and column 3 of the default input port against each other.
There are four main fields in the configuration dialog:
How to set marker labels and changing the layout of plot markers are described in the following two paragraphs.
Figure 2.38 shows the setup dialog, in which the marker label settings are set. Figure 2.38 will set labels on the plot markers from the data that is on the input port labels. It will retrieve the labels from row number 1 in the matrix in the input port data.
There are three main options for how to set marker labels:
First of all, start by clicking on the Marker Settings button in the Scatter Plot Setup window. A new window will now appear on the screen, as illustrated in Figure 2.39.
If you want to change the marker symbol, toggle the Marker symbol radiobutton and continue by choosing the desired symbol from the combobox. It is also possible to change the style of the marker. Set the colour by clicking on the colour button. A new window, where you can choose a colour from a colour map will appear on the screen. When you have picked a new colour and closed the window, the new colour will be set on the button. Size and thickness of the marker is changed by clicking on the vertical arrows or by typing the value directly.
Instead of using a marker symbol you have the opportunity to replace the marker symbol by a 'text' symbol. Start by toggling the radiobutton named Text marker. Continue by typing in your text in the line edit field. If you want to change the layout of the font, click on the button next to the line edit field. A new window will now appear on the screen where you can change the settings of the font. It is also possible to change the colour of the text. This is done in the same way as for marker symbols.
When all changes are done, click on the Apply button, and the new marker settings will be applied for the current plot. By clicking on the Ok button the new settings will be applied and the Marker settings window will be closed. A preview of the current marker will be shown at the buttom of the window.
SciCraft enables the user to look up gene annotation data. Simply select one or more points in the scatter plot and click the Databaseinfo button, as shown in Figure 2.37. This will cause the Database information window, as shown in Figure 2.40. Select a data source and click Apply to look up the gene annotation information. A description of a specific gene is shown by clicking on it.
Brief descriptions of the variuos fields in the window are shown below:
The tooltips can be assigned to the different markers in the same way as one assign labels to the different markers. By pressing the Tooltip labels button that is located below the combo boxes in which one assigns the data to the markers, a dialog similar to the one in Figure 2.38 pops up. In the dialog it is possible to choose from the following three options:
When one of the last two options is chosen, the labels will pop up as tooltips when the mouse is over a marker.
Figure 2.42 shows a Line Plot which is configured properly to plot column 2 of the default input port with increasing indexes.
There are three main fields in the configuration dialog:
How to change the layout of plot markers is described in the following paragraph.
Start by clicking on the Line Settings button in Line Plot Setup window. A new window will then appear on the screen, as illustrated in figure 2.43.
If you want to change the current marker symbol a line plot, choose the Marker Settings tab and then follow the procedure as described in 2.5.5, ScatterPlot.
Otherwise, continue by clicking on the Line Settings tab. Change the the line type by choosing the desired one from the combobox. The line colour is set by clicking on the colour button. A new window will then appear, where you have the possibility to choose the desired colour. Pick the new colour from the map, and close the window. The new colour will then be set on the colour button. The width of the line is set by clicking on the vertical arrows or by typing the value directly. A preview of the line will be shown at the buttom of the window.
When all changes to the line is done, continue by clicking on the Apply button and the new settings for the line will be applied. If you click the Ok button the changes will be applied and the window will be closed.
SciCraft enables its users to set tooltip labels on a line plot. The
tooltip labels will be set on each of the markers of the line in a
plot. The tooltip labels are set in the same way as they are set on a
scatter plot (see the corresponding paragraph,
page , in the previous section for
details).
SciCraft enables its users to set tooltip labels on a dendrogram plot.
The tooltip labels will be set on the leaf nodes of the dendrogram
plot, in the order according to the order list on the input port. The
tooltip labels are set in the same way as they are set on a scatter
plot (see the corresponding paragraph,
page , in the section before the
previous section for details).
Labels can be set on the leaf nodes in the same way as tooltip labels by pressing the Label Settings button and choosing the desired settings. When choosing Use order indices, the leaf's order is printed, while these indices are used for lookup in the specified datasource when the From data radio button is set.
It's possible to read meta data from any port defined in the plot node and map these data to colours and sizes of plot markers. This mapping possibility applies to both line and scatter plots. One may use either colour or size mapping, or both.
In both the Marker and Line Settings dialogs there is a Meta Data tab which is used to configure both the colour and size mapping from an input port. Figure 2.45 shows the settings window when the Meta Data tab has been chosen.
The data to use for mapping is chosen by selecting an input port on the desired type(s) of mapping and then choosing how to read the data, i.e. selecting column or row. The number of the column or row to use is then chosen by clicking the up/down arrows on the spin box or by typing the value directly. Note: If the module diagram has not yet been run, no data is available on any input ports, and the index or column/row number chosen may be out of bounds because no check can be made on the data. In addition, if the data set read from the selected port has a different size than that of the plot, the largest data set is stripped (end elements are removed) before mapping to achieve equal size on the two data sets.
If you want to map the meta data read from the chosen input port to marker colours, just check the checkbox named Map to Marker Colour. Then choose a min and a max colour. The min colour is the colour associated with the minimum value in the data set read from the input port, and similarly the max colour is the colour associated with the maximum value. This mapping is linear. To choose these colours, just click the corresponding colour buttons. A new dialog will appear. Select the desired colour and then press Ok. The new colour will then be set on the colour button.
Mapping meta data to marker sizes is quite similar to that of mapping data to colours. Just check the checkbox named Map to Marker Size. The min size is the marker size associated with the minimum value in the data set, and similarly the max size corresponds to the maximum value. This mapping is also linear. Use the up/down arrows on the spin boxes or type the values directly.