Since the X is always black, use a light color to encode these cells. To make blank and excluded values more apparent, check an option to place a black X through those cells. Of course, these choices are irrelevant if no values are off scale, blank or excluded. Instead do something like this - one rage for "1.0-1.99" and another for "2.0-2.99".Ĭhoose a color to use if the value is too large or too small to be part of the map you defined, or if the value is blank or excluded. You can't have one range "1-2" and another "2-3" because that would leave it ambiguous how to encode 2.0000. Enter a value or range of values, and what color you want it to show as. Then separately enter the maximum value (almost always positive) and color, and also enter the minimum value (almost always negative) and color. Usually correlation distance is used, but neither the clustering algorithm nor the distance need to be the same for rows and columns. First hierarchical clustering is done of both the rows and the columns of the expression matrix. You choose the baseline value (almost always 0.0) and color (usually white or black). Heat maps are ways to simultaneously visualize clusters of samples and features, in our case genes. If you select the Reverse Rainbow color map, the smallest values are encoded red. Using the Rainbow color map, the largest values are shown in red.
Prism chooses the range of colors by fixing the saturation and brightness to 100% and varying the hue from 0˚ to 300˚. You can choose whether black or white is for the lower value, and what the range of values is. Choose the range of values to convert to colors and the range of colors. You can even choose to make a heat map of variation, and base the heat map on the SD, %CV or SEM of replicate values. If you entered replicate values (side by side), you can later choose if you want the heat map to be based on the mean, median or geometric mean.
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