CellexalVR features a settings menu that can be opened by pressing the escape key on your keyboard. Take off your headset first to more easily interact with your computer. In this menu you can find many changeable options. Almost every color used in CellexalVR's visualization can be changed in this menu. To change a color, click the color you want to change and a color picker will appear to the right. Use the hue slider and saturation/value box to choose your color. You may copy the chosen color using the RGB-code in the text box. This RGB-code can then be pasted in other colors' color pickers if needed. When changing colors that are interpolated by CellexalVR a gradient is shown to the right of the color's button that show the resulting interpolated colors.

In the top right corner of the screen when the settings are open, there is a quit button, press this to quit CellexalVR and return to the real world.

To save your settings, press "Save and close" below the menu, or press escape on your keyboard to close the menu, if there are unsaved changes you will be prompted to save or discard them. Settings are saved to your local Config/config.xml file in your CellexalVR installation (see below for how to find this file). This file is read when CellexalVR is started.

All the settings are listed below with accompanying descriptions.

General

Open manual in browser (Button) - Opens this manual in your favorite browser.

Username (String) - Enter a username and everything you do in this session will be saved under a folder Output/<username>. If you do not enter a username everything will still be saved in a folder Output/default_user.

Hardware

Require touchpad click to interact (Toggle) - Sets wether a click event is required to use the actions mapped to the touchpad/joystick. This should be toggled on/off depending on which brand your controllers are. If your controllers have a touchpad, it should likely be toggled on. If your controllers have a joystick, it should likely be toggled off.

Controller model (Mutliple choice) - Changes the controller models. Set automatically will make CellexalVR attempt to guess which brand of VR hardware you are running and set the models accordingly, the other options will set the models to that brand's controllers. More brands may be added in future versions of CellexalVR.

Controller colors (Multiple choice) - Changes the colors of the decals on the controllers. The available choices are:

• Static color - The touchpad decal will be colored green, the grip decal colored yellow and the trigger decal will be colored red. The other decals will be blue. Useful if you are explaining how to use CellexalVR to someone else.
• Animated pulse - All decals will have a multi-colored pulse moving along them.

Heatmaps

Heatmap colormap (Multiple choice) - Sets the heatmap colors to a predefined colormap.

High expression (Color) - The color that should be used for the highest expression on generated heatmaps.

Mid expression (Color) - The color that should be used for mid (50% of highest) expressions on generated heatmaps.

Low expression (Color) - The color that should be used for the lowest expressions on generated heatmaps.

Number of heatmap colors (Integer, minimum: 3) - CellexalVR will interpolate this many colors in total for heatmaps to use. Half of them will be colors between the chosen high expression color (see above) and mid expression, and the other half between mid expression and low expression.

Heatmap algorithm (Multiple choice) - Decides which algorithm should be used to generate heatmaps. This choice can drastically influence how long time it takes to generate heatmaps.

Graphs

Graph point quality (Multiple choice) - Lower graph point quality means less resolution for each point but significantly increases the number of cells that can be loaded at once. This needs to be changed before loading the data to take effect.

Graph point size (Multiple choice) - Changes the size of each individual point in the graphs. This can greatly enhance the quality of dense graphs as smaller points will obstruct visibility less. This needs to be changed before loading the data to take effect.

Graph colormap (Multiple choice) - Sets the gene expression colors to a predefined colormap.

High expression (Color) - The color that should be used for the highest expression on graphs.

Mid expression (Color) - The color that should be used for mid (50% of highest) expressions on graphs.

Low expression (Color) - The color that should be used for the lowest non-zero expressions on graphs.

Zero expression (Color) - The color that should be used for the zero expressions (no expression of that gene) on graphs.

Number of graph colors (Integer, minimum: 3) - CellexalVR will interpolate this many colors in total for graphs to use. Half of them will be colors between the chosen high expression color (see above) and mid expression, and the other half between mid expression and low expression.

Default color (Color) - The color that graphs should have by default when not colored by anything else.

Most expressed cells marker (Toggle) - Determines if the red circles around the most expressed cells when coloring graphs by the expression of a gene should be shown.

Gene regulatory networks

Line coloring method (Multiple choice) - Determines which method should be used to color the lines between correlating genes in gene regulatory networks. The choices are:

• By correlation - Lines will be colored based on how much the genes are correlating. Correlation can be positive or negative. Choosing this will reveal four more options listed below.
  • High positive correlation (Color) - The color that should be used for the highest positive (strongest) correlation.
  • Low positive correlation (Color) - The color that should be used for the lowest positive (weakest) correlation.
  • Low negative correlation (Color) - The color that should be used for the lowest negative (weakest) correlation.
  • High negative correlation (Color) - The color that should be used for the highest negative (strongest) correlation.
• Random - The colors will be random.

Number of colors (Integer, minimum: 1 or 4) - Determines the number of colors that the networks will use for their lines between genes. If the line coloring method is set to 'By correlation' this number must be at least 4, if it is set to 'Random' it must be at least 1.

Line width (Decimal number, positive non-zero) - The width of the lines between genes in generated networks.

Selection

Generate colors (Integer and button) - Generate a set of colors by entering the number of colors you want and press either random for random colors or rainbow for a rainbow of colors. This will remove all your current colors and replace them with the specified amount of new colors.

Selection colors (Multiple colors) - These are the colors that the selection tool will have available when making a selection. To change a color, click it and use the color picker. To remove a color, press the red x. To add a new color, press the plus sign.

Velocity

High velocity (Color) - The color that should be used for the highest (longest) velocities. Only used if "Color mode: Gradient" is chosen in the velocity menu.

Low velocity (Color) - The color that should be used for the lowest (shortest) velocities. Only used if "Color mode: Gradient" is chosen in the velocity menu.

Folders and files

Open data folder (Button) - Opens the folder where your data is. Put your data (the files that the cellexalVR R-package outputs) in a folder inside this folder.

Open output folder (Button) - Opens the folder where the generated output is. Here you can find log files, output R-objects and html reports of your CellexalVR session.

Open config file (Button) - Opens the config file in your favorite text editor.

Open scripts folder (Button) - Opens the folder where you may put your own scripts for generating heatmaps, gene regulatory networks and more.

Open R log (Button) - Opens the log file where all output from R scripts is written.

Open CellexalVR log (Button) - Opens the log file where all output from CellexalVR is written.

Open Unity log folder (Button) - Opens the log file where all output from Unity is written. This file is probably only useful to you if you are a programmer.

Visual

Spawn notifications (Toggle) - Determines if notifications about R scripts and such should be displayed.

Skybox (Multiple choice) - Determines which skybox should be used.

Skybox tint color (Color) - Tints the skybox by some color. Can for example be used to darken the skybox by choosing a grey color.

Miscellaneous

Reset all settings (Button) - Resets all settings to their default value.

Profiles

Preamble - Profiles are a way to save a set of settings for later use or to share with others. Profiles are saved as xml-files in the Config folder where CellexalVR is installed, or in the same folder where your loaded data is, Data/<dataset name>, if the profile is marked as dataset specific (more on that below). To copy a profile from one machine to another, send the xml-file to the target machine and place it in the same folder it was on the original.
By default there is one profile, default, this profile can be edited but not deleted.

Current profile (Multiple choice) - Changes the current profile.

Create new profile (Text input and button) - Creates a new profile that can be modified with the specified name.

Dataset specific profile (Toggle) - Sets this profile to dataset specific. A dataset specific profile will be saved together with the loaded dataset, so both a dataset and a settings profile can be shared more easily. Ticking this means that this profile will only be visible in the "Current profile" drop down menu when this specific dataset is loaded. This can also be utilised to reduce clutter in the drop down.

Delete profile (Button) - Deletes the currently selected profile permanently. This action can not be undone. The default profile can not be deleted.