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Genesis produces structure charts by taking input from the Structure, Admixture or CLUMPP tools, together with a PLINK-style fam and optionally a phenotype file which would contain population labels.
To input these files, click File -> New Admixture or the New Admixture button on the toolbar. On the screen that opens, click Import Data File and navigate to the admixture data file outputted by the Admixture/CLUMPP tools. Then click Import Fam File and navigate to the fam data file. Finally, click Import Pheno File and navigate to the phenotype data file.
You can import multiple data files into the same project by clicking Import Data File again. These files can be imported in any order relative to the importing of the fam and pheno file.
In the drop-down menu 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 column of the phenotype data used to group the data or import additional data files, 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 Admixture 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 population group labels, open the Appearance Options menu and (un)check the Show Population Group Labels checkbox. To change the font of the population group labels, click Select Population Group Label Font and select the font of choice.
To change the size and spacing of a structure plot, open the Appearance Options menu and select values for the Set Graph Height, Set Thickness of Each Subject and Set Distance Between Graphs boxes.
To set the orientation of the structure plot, and select Horizontal or Vertical from the bottom drop down menu.
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 the option to hide the subject from the plot.
To select a population group, click on the population group label for the group. This will bring up a menu where you can change the Name of the group and also shift the group left/right (or up/down) in the graph.
To change the colours and order of the colours in the graph, right click anywhere on the graph and select Population Group Options. From the next menu, click the button next to the colour you wish to change and from the next dialog, click the Select Colour button to change the colour or the Shift Up and Shift Down buttons (or the Shift Left and Shift Right buttons) to change the order of the colours.
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.