Plate Heatmap Viewer
The Plate Heatmap Viewer allows to visualize an entire screen using heatmaps corresponding to the spacial arrangement of the [microtiter plate](http://en.wikipedia.org/wiki/Microtiter_plate microtiter)s. Furthermore the UI provides controls to quickly browse the readout parameter and work with overlays (e.g. layout, nominal values). I allows access on the three different data levels (screen-plate-well), with corresponding levels of detail.
The Screen Viewer represents the main view showing the first level (screen). The menu provides beside the standard KNIME functionality also View controls and Trellis controls. The Trellis menu contains also view related functionality with the difference, that it concerns the plate matrix. The toolbar allows to control the data input selection (readout, overlay and plate filtering).
The Plate Viewer represents the second data level (plate). A plate view is opened by right-clicking on the corresponding plate in the heatmap trellis (ScreenViewer).
The Well views is the third and final level ind the (screen-plate-well) hierarchy. The view can be opened for a particular well by right-clicking on it. It gives a detailed view of the wells readouts and image data.
For quick data navigation the mouse has a lot of contextual functionality.
The view of the next level is opened by right clicking the corresponding item. Right click on a plate, to open the Plate Viewer. Right click on a well to open the Well viewer.
In the Screen Viewer plates can be selected (including all wells). The plate Viewer allows to select a subset of the plate wells. If at least one well is selected the entire plate is marked selected.
- single item selection
- drag selection (keep the left mouse button pressed to draw a selection rectangle)
- the "Command Key" allows to keep/edit the previous selection
The basic functions are:
- Adding a thumb: right click on the gradient slider.
- Removing a thumb: right click on the gradient slider and drag it away.
- Editing the color of a thumb: double click on the corresponding thumb. Choose the color in the dialog and press the OK-button.
A key feature is that it also allows to work with reference populations. Say you want to gray out the part of the scale that is occupied by your negative control. If in the configuration dialog of the node you specified "Reference Groups" in the "Control" tab, you will see them in the Colormap Dialog. The blue square indicates mean +- 3 standard deviations. Then you can produce the popup-menu by a right click on a reference group and add thumbs to the colormap. Double-click on the thumb opens the color selection dialog.
The Plate Heatmap Viewer supports tables containing image data. All the images from one or more columns are displayed in the Well Viewer. KNIME supports PNG image cells but a more efficient and better integrated way of handling images can be found in the Image Processing Extension. So far the best performance is achieved by using the "Image File Linker" node. But be careful! if handling a screen, you might quickly end up with a lot of disk space taken up by images (stored in the nodes) on your desktop machine.