Description
The PCL plotter enables you to visualize tabular data from PCL files in a scatter plot by specifying
any two experiments (i.e., hybridizations) on the X and Y axes. You can select points (genes) interactively and
save collections as genelists. This plotter is based on the
ICanPlot
software which is freely distributed and is described in the paper:
Sinha AU , Armstrong SA (2012)
iCanPlot: Visual Exploration of High-Throughput Omics Data Using Interactive Canvas Plotting.
PLoS ONE 7(2): e31690. doi:10.1371/journal.pone.0031690.
The plotter requires a browser which supports features of HTML5. These browsers include:
How to access the PCL plotter
The PCL plotter takes a PCL file as input, and it can be accessed wherever a PCL file is stored
(your repository) or created (in the clustering pipeline) by
clicking on this icon:
.
How to select experiments
By default, the experiment in the first column is used for the X-axis, the the second is used for the Y-axis. These
can be changed on the fly, and all the experiments in the PCL file are available to plot. In addition to the X and
Y axes, you can optionally use color and/or size to represent the data in other experiments.
Figure 1
How to select genes
You can select genes in one of four ways: The first is double clicking on a point (or a cluster of points). The second is by outlining a set of points (Figure 3). This is discussed below. The third is by
searching for a unique identifier (which must be in the leftmost column of the PCL file). The fourth is by choosing a genelist in the dropdown menu from your files in your genelists directory. When a gene is selected a small circle is drawn around the point (Figure 4). (Obviously
this is more useful in areas not dense with points.)
Figure 2
Lastly, you can select genes by drawing a polygon with the mouse around specific points. The polygon will turn purple and when you double-click, all the points inside are selected. The selected genes (as with those selected by name or genelist) are both circled (Figure 4) in the plot and appear in a table below the plot (Figure 5). To unselect, use Shift + double-click.
Figure 3
Figure 4
The table of data contains the values for each experiment, and will change if you change the X or Y axis. The magnifying glass fills in the accompanying circle so you can match the gene to the point. The
removes the gene from the list. If the annotations from your PCL file are long and make the table too wide, you can hide them by checking "Hide Annotations". The "Clear All" button unselects all the genes. If you want to save the list, you can create a gene list (see below).
Figure 5
How to save a genelist
You can save all the genes in the table into a genelist which is placed in your genelists directory. The name goes into the text field in Figure 5. If you specify the name of an existing genelist, you are allowed to overwrite it or append to it.
How to create a new PCL file.
You can create a new PCL file with the selected gene by pressing the button. Once it is created you can download and/or add it to your repository.
