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To input Eigenstrat files, click File -> New PCA or the New PCA button on the toolbar. On the screen that opens, click Import Data File and navigate to the PCA data file outputted by the Eigenstrat software. Then click Import Phenotype File and navigate to the phenotype data file.
To input Relate Data, click File -> New PCA or the New PCA button on the toolbar. On the screen that opens, click Import Data File and navigate to the PCA data file outputted by the Relate package. The relate package file includes the phenotype information in the data file.
In the drop-down menus, select the 2 or 3 PCAs to plot as the axes and select the column of the phenotype file that will be used to group the data. To draw the graph, click Finish or click Next to access the Appearance Options menu (See below...).
If a graph has already been plotted, and you wish to change the PCAs to be the axes or the column of the phenotype data to represent the data, you can access the initial menu by clicking the Data Options
button on the toolbar, or clicking Graph -> Data Options.
The Appearance Options menu can be accessed through the New PCA button by clicking Next after importing the files or by clicking the Appearance Options
button on the toolbar, or clicking Graph -> Appearance Options.
To set/change the heading, open the Appearance Options menu and type the heading into the text box that says “Set Heading.” To change the font of the heading, click Select Heading Font and select the font of choice.
To show/hide the border open the Appearance Options menu and (un)check the Show Border checkbox.
To show/hide the axes, axis labels, grid and scale, open the Appearance Options menu and (un)check the relevant checkboxes.
To set the position of the key, open the Appearance Options menu and select the key position from the drop down menu. To hide the key, select No Key from the drop down menu. To change the font of the key, click Select Key Font and select the font of choice.
Other settings and options can be changed by interacting with the graph. Certain elements can be clicked to view or modify their options.
To select an individual subject on the structure plot, click on the subject on the plot. This will bring up a subject menu where you can view the data about the subject (from the phenotype data file) and gives options to change the subject's icon as well as to delete the subject and hide or place the subject on top.
To change an individual subject's icon, click the subject on the graph and from the dialog that opens, select the icon shape and colour. Selecting the shape Default will set the shape of the icon to the group's shape and checking Clear all icon data specific to this individual will set the icon's shape and colour to the group's.
To place an individual subject on top, click the subject on the graph and from the dialog that opens, check the Place this individual on top checkbox and click Done.
To change a population group's name, click on the group in the key. This will bring up the Population Group dialog. From here you can set the group name and click Done.
To change a population group's icon, click on the group in the key. This will bring up the Population Group dialog. From here you can set the shape and colour of the icon and click Done.
To change a the order of the population groups in the key, click on the group in the key. This will bring up the Population Group dialog. From here you can click Shift Up or Shift Down shift the group's order in the key.
To create a label and annotate the graph, right click on the graph where the label is to be placed, and click Create Label at Mouse Pointer. Then enter the label's text and click OK to place the label.
To edit a label that has been created, click on the label to bring up the Label dialog. From this dialog you can edit the label's text, reposition the label or delete the label.
To hide a subject from the graph, click on the subject on the graph to bring up the subject dialog. From this menu you can choose to hide the subject from the graph.
To hide a population group from the graph, click on the group in the key to bring up the population group dialog and check the box labelled Hide this group from the graph.
To reshow a subject that has been hidden, click on the Select Hidden Individuals or Groups button and from the drop down menu that pops up, select the name of the subject or group that you wish to show. From the subject dialog you can now uncheck the Hide this Individual from the Graph or Hide this group from the Graph checkbox.
To search for a subject in the graph by name, click the Search for individual button in the toolbar. In the dialog, enter the Name (first, last or both) of the individual you wish to find and click Ok. If the individual was found in the data, it will be selected and the subject dialog for that individual will open. If the individual was not found, a message will display.
To rotate a 3D PCA plot, click the Show/Hide 3D PCA Rotate Panel button in the toolbar. This will bring up the rotate panel which contains a slider which can be dragged to rotate the graph about the z-axis.