The Main Window 2D Button Panel

  • To learn more on the A part click here
  • To learn more on the B part click here
  • To learn more on the C part click here
  • To learn more on the D part click here

The A Part

  • The "Heat Mode" button switches the window to the "Heat" mode
  • The "2D Mode" button switches the window to the "2D" mode
  • The "3D Mode" button switches the window to the "3D" mode

The B Part

    These buttons allow you to select the axes that are used for drawing the 2D projection of the data. The middle button shows the data attribute that is taken for the axis. Clicking the middle button brings up a menu of all the attributes to let you choose the one desired. The triangle buttons on the left and right allow for an easy cycling among the attributes. The graphic of the data is always updated immediately to reflect the change of the axes.

The C Part

  • The "Best View" shows the data in the most significant axes.
  • The "Fit color" button shows the profiles in the Profile Panel in colors that depend on the value of the fit of the gene within its cluster (for Fit, see the List Panel).
  • The "PCA axes" button allows you to switch to the PCA display mode. In this mode, the axes are no longer gene columns, but the eigenvectors of the data. The PCA mode amplifies the amount of information shown.
  • The "Unclass'd" checkbox allows you to show / hide genes that are not assigned to any of the clusters (i.e., they are assigned to the noise cluster, gaussian model only). These genes are represented by red crosses.
  • The "Points" button shows/hides the points.
  • The button on the right of Points (showing "3D" in the screenshot) lets you choose the display mode of the genes. As in 3D mode, five options available:
    • "3D" represents genes as 3D spheres. This is visually the most appealing and gives a good sense of the perspective, but may be rather slow with thousands of genes to display (note that in 2D mode, 3D points and Flat points are the same)
    • "Flt" represents genes as flat circles. This is much faster to draw than 3D spheres (useful on slow machines), but conveys less visual information (note that in 2D mode, 3D points and Flat points are the same)
    • "Dn", "Dl" and "Dv" yield a density graph, respectively normal, light or very light.
  • The "Show hulls" button shows/hides the convex hull of clusters
  • The "T" button changes the hull mode to translucent, giving you an additional feeling of the respective positions of the clusters
  • The "Names" button shows/hides the centers of the clusters, as well as their names (labels) if present
  • The "Variances" button shows/hides the variance of the clusters by drawing an ellipsoid centered on the average of the cluster with a radius equal to the variance (this button is disabled in PCA mode)