The main window of ChipMonk contains 3 sections. At the top left is the Data Viewer which shows your data sets, data groups and any probe lists you've created. At the top right is the whole genome view which shows all of the chromosomes in your genome. At the bottom is the chromosome view which shows a detailed view of a region of chromosome and overlays both genome annotations and views of your data.
The data view is probably the simplest of the 3 views. It is in a tree structure and has 3 sections, Data Sets, Data Groups and Probe Sets.
From within the data view you can choose which data sets/groups are shown in the chromosome view. You can change which sets/groups are shown and their order by selecting View > Set Data Tracks. Alternatively, in the data view simply right click (or apple click) on the data set/group and check/uncheck the menu option which says "Show track in chromosome view".
As you select a data set/group in the data view, if it is visible in the chromosome view its track will be highlighted in yellow.
If you have selected a probe list in the data view then the chromosome view will show only the probes in that list, also all of the filters will use the currently selected probe list as a starting point for their analysis.
If you want to show all probes then either make sure nothing in the probe list tree is selected, or select the top level folder, which will have the same effect.
The genome view shows an overview of all the chromosomes in the genome.
You can click on any part of any chromosome in the genome view and the chromosome view will update to show that region.
One region of one chromsome in the genome view will have a red box around it. This represents the region currently being displayed in the chromosome view. This box will move as you scroll around the chromosome view.
The chromosome view is the most detailed view of your data. It consists of a series of horizontally arranged tracks of information.
At the top of the window are a series of blue tracks (which alternate light/dark). These show different classes of genome annotation (eg: cds, mrna, genes etc.). You can configure which types of annotation are shown by selecting View > Set Annotation Tracks. To save memory you can also configure which tracks of information are initially loaded under Edit > Preferences.
As you put your mouse over any feature it will become highlighted in yellow. If you would like to see more information about it then double click on it and a new window will open containing the details of the feature. A small label will appear over the feature as you put your mouse over it. If you want to you can make these labels appear permanently by selecting View > Show All Labels. Please note that this will clutter the display at all except the highest of zoom levels.
Under the blue annotation tracks are a set of red tracks which contain the data from a data set/group. The tracks are ordered simply by the order in which they were added. You can add/remove data tracks by right clicking (or apple clicking) on the data set you want to show and selecting "Show track in chromosome view". The data tracks show the log ratio (expt/control) for the data set. The faint grey line across the middle represents a log ratio of 0 (ratio of 1).
You can move around the chromosome view in a number of ways. Underneath the display is a scroll bar which you can use to scroll left and right through the whole of the chromosome.
You can also zoom in and out of the chromosome. One way to do this is by selecting View > Zoom in/out from the main menu. This will double or halve the size of the currently visible window.
A more flexible way to zoom in and out is to use the mouse in the chromosome view. If you hold down the left mouse button and drag over a region in the chromosome view, when you release the mouse the view will be reset to show just the region you have just selected. To zoom out again you can press the right mouse button (or apple click) anywhere in the chromosome window.
You can also change the scaling of the data tracks. By default the tracks set a cutoff of +/- 2-fold on the y-axis. This is normally OK for most Chip-on-chip data, but can cut off the top of some peaks. If you want to expand this scale you can select View>Set Data Zoom Level from the main menu and then adjust the cutoffs until you can see all of the data you want.
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