CAPS (Combined Analysis of Psychiatric Studies)

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Kelviz Basics - Creating, Saving, and Exporting A Figure

Importing Data Into Kelviz

  • Data need to be imported to be used in Kelviz. Click on the Import Data toolbar button, or select Import Data From File from the File menu.
  • Select the data file you wish to import. Kelviz will then prompt you for additional information needed to import the data file and turn it into a lineset.
  • In many cases, Kelviz can guess which columns you'll want for the position and PPL (or other Y-value). Review these and verify that they are correct.
  • If you already have one or more plots in your figure, or have an existing lineset you want to replace, those options are also provided.
  • You can also give a name to the line set, or add a prefix and/or suffix to each chromosome number.
  • If your datafile has any extra data you wish to include in annotations, you can specify those and Kelviz will import those data as well.
  • You can also change the color of the lineset.
  • When everything is ready to go, click the OK button. The lineset will be imported and added to your figure - creating a new plot within your figure if necessary.
  • Overlapping your existing data with another dataset is done the same way.

Saving And Reopening Your Figure

  • To save a figure for later reuse and/or modification, select Save As GRX from the File menu.
  • Give your GRX file a name, then click the Save button.
  • When you want to view or edit one of your figures again, or view or edit a figure from someone else, select Open GRX File from the File menu or click the Open GRX File toolbar button.
  • Select the figure file you want and click the Open button.
  • The figure will be opened and displayed in Kelviz.

Exporting An Image Of Your Figure

  • Kelviz offers the option to export your figure as an image file at any time. To begin, select one of Export To Color Image or Export To Grayscale Image from the File menu, or click the Export Color Image toolbar button.
  • Several image formats are provided. Pick one, give your image file a name, then click the Save button.
  • The image file, once created, is automatically opened so that you may see the result.

Changing Your Figure - Zooms and Views

Basic Zoom and Panning

  • Your plot can be changed so as to zoom in on one area of interest. To do this, click on the Zoom toolbar button to activate Zoom mode.
  • While in this mode, you can click and drag to select an area you wish to zoom in on.
  • Once you've zoomed in, you can adjust the area by panning around. To do this, click on the Pan toolbar button.
  • While in Pan mode, you can click and drag to move your view of the graph around.

View Navigation

  • Whenever a zoom or pan occurs, Kelviz saves the end result as a "view". You can navigate between these views in order with the Back and Forward toolbar buttons.
  • The Back button takes you to a previous view. The Forward button takes you to a next view (if any).
  • Alternatively, you can reset to Kelviz's "default" view (showing all data in the figure) by clicking the Home toolbar button.

Additional Zoom Options

  • Kelviz has a few additional options to zoom in on your plot.
  • Zoom X-Axis - Click on the Zoom X-Axis button to use this mode, then click and drag to select a region along the X-axis to zoom into.
  • Zoom Y-Axis - Click on the Zoom Y-Axis button to use this mode, then click and drag to select a region along the Y-axis to zoom into.
  • Zoom To Chromosome - Select a chromosome from the toolbar dropdown and click the Zoom To Chromosome button. The chromosome you selected will be displayed.

Set Specific Zoom Limits

  • If necessary, you can precisely specify what the upper and lower visible limits for each axis should be in your plot. To do this, select Set x-axis, y-axis limits from the Options menu.
  • Enter in your starting and ending chromosomes and positions for the X-axis, and any values desired for the Y-axis.
  • When your desired limits are entered, click the OK button.

Changing Your Figure - Lines

Changing Linesets

  • You can change the appearance and presentation of your data after importing. To get started, select Configure Line Sets from the Options menu.
  • From here, you can change each lineset's color, thickness, and style, add discrete symbols for each data point, change the order in which lines are drawn, and so forth.
  • Linesets can also be deleted if they are no longer needed in your figure.
  • When you are done making changes, click the OK button. Any changes you made will be immediately applied and shown in your plot.

Changing Lines In Bulk

  • Kelviz provides the ability to change line properties in bulk. To do this, select Configure All Lines from the Options menu.
  • In this dialog, one must select both the property or properties to be changed, and what it or they should be changed to.
  • Once this is done, click the OK button. All lines will be updated with the settings specified.

Changing Lines One At A Time

  • For more fine-grained control, individual chromosome lines can be changed one at a time. This can be done by selecting Configure Individual Lines from the Options menu.
  • From here, you can navigate through your choices of lines by chromosome until you find the ones you want to change.
  • For every line, you can change the same properties available when changing line sets - the color, the style, the symbol size, et cetera.
  • You can change any number of lines you like.
  • Once all the changes you have made are entered, click the OK button, and they will be applied to your figure.

Horizontal Lines

  • You can add - or remove - horizontal lines across a plot for display purposes. To do this, select Add Or Remove Horizontal Lines from the Edit menu, or click the Change Horizontal Lines toolbar button.
  • To add a new horizontal line, type in the Y-axis values in the space indicated.
  • You can also change the thickness of ALL horizontal lines in the plot.
  • To remove an existing horizontal line, select that line in the list of horizontal lines already in your plot.
  • When you've made all the choices you have in mind, click the OK button. Horizontal lines will be modified as indicated.

Changing Your Figure - Axes and Annotations

Axis and Figure Labels

  • Many parts of a Kelviz figure can be labelled for added clarity. To get started with this, select Configure Figure Labels from the Options menu.
  • You can add titles for your figure, and labels for the X and Y axes of your plot, and adjust all their font sizes.
  • The chromosome numbers added along the X-axis can also be changed here.
  • When you have made any adjustments you have in mind, click the OK button and they will be applied to your figure.

Creating Annotations One At A Time

  • Kelviz offers the option to annotate data points in your figure. There are three different methods by which you can select data points of interest.
  • Annotate Point - Click on the Annotate Point button to use this mode, then click anywhere on the figure. The data point nearest where you click is annotated.
  • Annotate Peak - Click on the Annotate Peak button, then drag to select an area on the figure. The highest peak in the area you select is annotated.
  • Annotate Valley - Click on the Annotate Valley button, then drag to select an area on the figure. The lowest valley in the area you select is annotated.

Creating Multiple Annotations At Once

  • The Annotate by Threshold function lets you create many annotations at once. To use it, begin by clicking the Annotate Threshold button.
  • Select an annotation creation mode. This determines which data points will be selected for annotation.
  • Enter in a threshold value. Data points above (or below) this value on the Y-axis will be annotated based on the mode you select.
  • If desired, you can also further limit the mass creation of annotations to a single lineset.
  • When you've made all your selections, click the OK button. The annotations will be created and displayed.

Annotation Layout - manual and automatic

  • Annotation labels normally have their location automatically picked, but they can be moved around. To do this, begin by clicking the Move Annotation button.
  • You can now relocate an annotation label anywhere you like by dragging and dropping that annotation.
  • Alternatively, Kelviz provides an automatic annotation layout feature. To use this, click on the Automatically Layout Annotations button.
  • You can either reset annotation locations back to their defaults, or have Kelviz attempt to place annotation labels optimally. When you've made your choice, click the OK button.
  • Note that the automatic layout option can take some time, particularly if there are a lot of annotations in your figure.

Individual Annotation Appearance

  • Annotation label text, color, and size can be configured on a per-annotation basis. To do this, right-click on an annotation you want to change and select Edit Annotation.
  • Annotation text is normally automatically generated. You can put in custom text, and control whether or not metadata is included.
  • Font size and color can either use the defaults for your figure, or they can be changed for each annotation.
  • When your changes have all been entered, click the OK button. The annotation's appearance will be changed accordingly.

Default Annotation Appearance

  • To change the default appearance for all annotations, select Configure Annotations from the Options menu.
  • Here, you can change the precision used in automatically generated annotation text, as well as the default color and font size.
  • When you've made the selections you want, click the OK button. All annotations that make use of the defaults will be updated.

Removing Annotations

  • To remove an individual annotation, right-click on it and select Remove Annotation.
  • To remove all annotations at once, select Remove All Annotations from the Edit menu.
  • You will be prompted to confirm this action, as it cannot be undone.

Multiple Plots

Figure Layout And Adding Additional Plots

  • Until now, we have only used one plot in all our figures. Kelviz, however, can have multiple plots in a figure. To get started with this, select Configure Figure Layout from the Options menu.
  • To add another plot, click the Add New Plot button. Click Refresh Preview to see where it would be placed.
  • Kelviz uses a virtual "grid" of rows and columns for laying out plots. For example, you can put your new plot next to your existing one by putting it in a second "column".
  • Experiment with different layouts and how they would appear using the Refresh Preview button.
  • Even if you don't intend to use multiple plots, some helpful options are here, such as the figure size, padding, and how detailed any exported images should be (in DPI).
  • When you've added all the plots you want, click the OK button, and they will be added to your figure.

Displaying Data In Other Plots

  • Additional plots can display their own data. To make this happen, select Import Data From File from the File menu, or click on the Import Data toolbar button, and pick a file to import.
  • When importing data, select the plot you want to import into.
  • The Import Data procedure is otherwise unchanged.
  • Additional plots can also display the data from existing plots, allowing alternate zooms and annotations. To do this, select Configure Line Sets from the Options menu.
  • Select the plot you want to have displaying another plot's data, then turn on Use lines from another plot.
  • Repeat for any other plots you want to have showing another plot's data.
  • When you've made these changes for all your plots, click OK. Your figure will be updated.
  • Once this is done, you can adjust these plots as desired without affecting their "parent" plot - such as by zooming in on a particular chromosome, or adding annotations.
  • Annotations are tied to the plot they're in, not the plot data is coming from, so you can annotate different parts of the same data.

Per-Plot Titles

  • By default, plots are automatically labelled in order with the letters a-z. This can be changed by selecting Configure Figure Labels from the Options menu.
  • After turning off automatic plot titles, the option to change each plot's title individually will become available.
  • While here, you can also change the X-axis and Y-axis labels for each plot.
  • When you've made all the changes you like, click the OK button. Your figure will be updated.

Legends

  • By default, a plot's legend in Kelviz is automatically added when more than one lineset is present.
  • A single legend for all lines in the figure, however, can be created. To do this, select Configure Figure Legends from the Options menu.
  • There are three possible locations for the figure-wide legend. It can be placed on either side of the figure, for example.
  • Alternatively, you can give the figure-wide legend its own space in Kelviz's conceptual layout grid.
  • If you choose this option, you will then be able to more precisely position the figure-wide legend using the Configure Figure Layout dialog.

Collages

  • Collages are a very different form of multiple plots in Kelviz; they are generated from an existing plot, splitting up the data from that plot into multiple subplots.
  • To generate one of these, select Create Collage Table From Figure from the File menu.
  • There are two primary types of collages - chr (per-chromosome) and lineset (per-lineset). These create one new plot for every chromosome or every lineset in your plot respectively.
  • The number of columns in your collage table should also be specified. Kelviz takes this and adds as many rows as necessary to include every plot.
  • By default, plots are automatically labelled in order with the letters a-z, and only one legend is used. These can both be changed so that plots have no titles and each plot has its own legend.
  • Plots are also normally generated with their view limits partially based on the current view limits of your plot. You can change this so that it shows all data instead.
  • Collage size is in inches, and auto-determined by scaling down the current overall plot size. You can have this calculation done using a different plot size, or set a single size for the whole collage.
  • You can also change which chromosomes (or linesets) should be included.
  • When your options are all set, click the OK button.
  • You will be prompted for a filename and a format option. Kelviz can create a new figure (in its GRX format) with the plots created, or export it directly to one of its image formats.
  • The collage will be created where you specify.
NationWideChildrens Rutgers University Rutgers University USC Information Sciences Institute Washington University in St.Louis National Institute of Mental Health