Change Project Properties and MOG Properties

12 Change Project Properties and MOG Properties

A user can change the behaviour and appearance of MOG and tweak parameters according to her/his requirements. Two types of properties can be altered: project properties and MOG properties. Each can be accessed from the parent window's upper menubar: "Edit ->Properties" (Figure 28).

Figure 28: Properties Window.

12.1 Project properties

Project properties are specific for a given project and are saved with that project file.

From the Properties Window (Figure 28) a user can change text on visualizations, and calculation parameters.

1. "Default X-Axis label" is the default label of the X-Axis in visualizations (line chart, box plot, and histogram).
2. "Default Y-Axis label is the default label of the X-Axis in visualizations (like line chart, box plot, and histogram.)
3. "Default Chart Title" is the default title displayed in line charts.
4. "Project parameters" lets a user set the numbers of permutations and threads used in the calculations, rather than use the default values. It opens a small dialog box.

Number of Permutations are the number of permutations used in computing the p-values (see 1. A higher setting will take a longer time to compute p values but give more accurate estimates. A lower setting will have a higher error in p value estimation but compute more quickly. The precision of the permutation tests also depend on the number of samples in each group. Setting the permutations to 100 allows a minimum p-value of 0.001.
Number of Threads: The number of threads used in multi-threading operations. To utilize maximum CPU, enter a higher value. The maximum value depends on the processor, we recommend a number equal to the number of cores in your processor, e.g., for a quad-core processor choose 4.
Default Replicate Group: Chooses the default replicate column using information in the sample describing the samples. The user can override the default and select the parameters to designate the replicate groups (see Replicate Column).

12.2 MOG properties

MOG properties are central to MOG and are saved in a binary file named "metaomgraph.prefs". This file is created when MOG is executed for the first time, and is updated when modified by the MOG user. If this file is deleted, a new file is created with default settings. The following MOG properties can be changed from the Properties Window (Figure 28).

1. "R path" lets the user set a path to R which can be used with MOG (see Section 11). This opens a new dialog where user can enter the Path to R. If an R path is not defined by the user, MOG automatically detects the default path based on the operating system.
   
   Path to Rscript.exe is the path to R executable which is used to execute R scripts.
   Path to folder containing R Scripts is the path to a directory which contains scripts to be used with MOG. This parameter is optional; it is not required to execute R scripts.
2. MOG colors: Changes the appearance of MOG, MOG visualizations and MOG output. All table and background colors can be set via the "Change colors" dialog.
   
   Load Preset loads saved color profiles. Light, sky and dark profiles are provided with MOG by default.
   A user can customize and create new color themes by choosing the colors. CLICKing "Apply" will apply the new theme by default to all subsequent MOG projects. If the user-customized theme isn't saved, the user will be prompted to save it. Any saved theme can be applied to a project from the "Load Preset" pull-down menu.