homeabout uscontact us


Creating a Color Matrix Plot



A color matrix plot is used to visualize the values in a dataset. The plot consists of a legend at the top and a grid of colored cells, with the genes in the columns and the samples in the rows. The legend consists of a color gradient above an expression value scale. The default range for the scale is from the minimum to the maximum value contained within the dataset.

Missing values are colored using the color value at the mid-point of the scale and have a white 'X' drawn through the colored tile (this is only visible if the dimensions of the colored tiles are large enough to display it).

Note: you cannot create a color matrix plot for an experiment (clustered dataset). For those, create a Matrix Tree Plot.



1. Double-click a dataset (raw, preprocessed, discretized, etc.) in the Experiments navigator. The item is highlighted and a color matrix plot of the dataset is displayed.


1. Click a dataset in the Experiments navigator. The dataset is highlighted.

2. Click the Color Matrix Plot toolbar icon , or select Color Matrix Plot from the Explore menu, or right-click the item and select Color Matrix Plot from the shortcut menu. A color matrix plot of the dataset is displayed.

Plot Indicators


Interacting With the Plot

Selecting Items

Displaying a Gene Expression Value


Plot Functions

Profile Matching

Color by Gene Lists or Variables

Exporting an Image


Customizing the Plot

Changing the Gradient Color and Scale

Resizing Cells in a Color Grid

Toggling the Color Grid On or Off


Related Topic:

 Displaying a Summary Statistics Chart