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Heat Maps

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12.11 Heat Maps

Heat Maps are two-dimensional intensity plots of spreadsheet data. Heat Maps are useful to find non-random patterns in the data, particularly for log ratios or segmentation covariates.

Heat Map Plot Modes

Heat Maps can be visualized with or without marker map data. When marker map data is available the Plot Viewer will present the Heat Map data in position scaled form and enable the Genome Browser with the genomic position on the X-axis regardless of whether marker names were column headers or row labels in the generating spreadsheet. See Figure 97

Otherwise, the data will be presented in a uniform scale, and without the Genome Browser and in the orientation consistent with the generating spreadsheet, i.e. rows will remain rows and columns will remain columns.

[Picture]

Figure 97: Heat Map of segmentation covariates results for Chromosome 22

The Y-axis corresponds to the Sample Index. When plotted in uniform scale the indices mean the first through nth active rows. When plotted in genomic position scale, the indices are either the active rows or the active columns depending on which dimension does not correspond to marker names. The 50th sample index corresponds to the 50th active row or column.

Graph Controls Specific to Heat Maps

The graph controls specific to Heat Maps are:

  • Data Aggregation Method
  • Color

The Data Aggregation Method selection allows for the specification of how pixels are aggregated if there are not enough pixels available to plot all of the data selected. The data needs to be aggregated because in all but a few cases there are more active cells in a spreadsheet than there are available pixels on a computer monitor for display. A decision needs to be made as to what value to show for each pixel. The options available are Mean, Min, Max and Extreme.

  • Mean: Computes the mean value and displays the color based on the overall mean value for the data shown.
  • Min: Displays the color for the pixel based on the minimum value of all data points competing for the pixel.
  • Max: Displays the color for the pixel based on the maximum value of all data points competing for the pixel.
  • Extreme (default): Displays the color for the pixel based on the value that is furthest away from the mean value.

The Color tab allows for selection of the colors used in the intensity gradient as well as the values used for assigning colors. There are three available modes, 2 Color Auto, 3 Color Auto and Manual.

In 2 Color Auto mode, two colors are used for the intensity gradient, and are based on the minimum and maximum values for all data in the current zoom. Changing the zoom will recalculate these values. Only the colors used can be changed in this mode. To change a color, click on the color box and select the desired color.

In 3 Color Auto mode, three colors are used for the intensity gradient, and are based on the minimum, mean and maximum values for all data in the current zoom. Changing the zoom will recalculate these values. Only the colors used can be changed in this mode. To change a color, click on the color box and select the desired color.

In Manual mode, additional color splits can be added or removed. The minimum number of colors allowed is two, and there is no maximum. To change the color, click on the color box and select the desired color. To change the split value, double click on the value and enter in the new value. The colors will be resorted with the smallest value on the top and the largest value on the bottom.

If the Heat Map is being used to look for regions of copy number variation, a helpful option, Set CNV Defaults, is available. This sets four splits with three colors. The split values can be changed to fit specific loss/gain thresholds.

To add a new split click on Add and a copy of the currently selected split will be added to the split list box.

To remove a split, select the split to remove and then click Remove.

To use the minimum, mean or maximum values for a particular zoom for all zooms, change the mode from an auto mode to Manual without changing the values used for splits. Now, no matter what the zoom, the same colors will be used for the same intensities.

The Full Domain View in Heat Maps

The Full Domain view for a Heat Map graph displays the same information as the heat map. It is not intended as an analytic resource. This view is useful to provide a sense of context while inspecting the graph more closely.

The Data Console in Heat Map Graphs

The Data Console provides a detailed text output including hyperlinks when left-clicking on graph elements.

Left-clicking a marker produces the marker name, it’s position (if it is position scaled), and several hyperlinks to various helpful websites.

Clicking a Heat Map value produces the row and column information, value, and (if available) chromosomal position information as well has hyperlinks to various helpful websites.

Adding Additional Graphs

In the case that data is marker mapped (and therefore position scaled) the Add Graphs control item will be visible when clicking on the User Graphs top-level node item. Selecting it will make the Add Graph control panel accessible. See Using the User Graphs Tree Window for more information on how to add graphs.

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