Finally, a color scheme is applied for the visualization and the expression matrix is displayed. Then the branches of the dendrograms are rotated so that the blocks of 'high' and 'low' expression values are adjacent in the expression matrix.
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.
Introduce more structure to the graph by inserting gaps to the right of any column or below any row.Heat maps are ways to simultaneously visualize clusters of samples and features, in our case genes. Or base it on the SD, SEM or CV among replicates to make a heat map of variation. If you entered replicate values, base the heat map on the mean, median or geometric mean of the replicates. Specify special colors for values that are "off the map" or for excluded values. Color scales can encode continuous data with one scale, continuous data with two scales (perhaps one for positive numbers and another for negative numbers) or discrete categories (1=blue, 2=red. Reverse the direction of either axis, or transpose the X and Y axes. Each square in the graph is color coded to denote the value entered into that cell of the table. The columns corresponds to different data sets in your table, and the rows in the graph correspond to different rows in the data table. The plotting area is divided into squares. Heat maps are a new way to plot grouped data.
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