Perceptually, color attributes are the most powerful mapping and should be used for the strongest message you are trying to convey. This is clearly the most important entry in our legend. It should match our continuous mapping for the variable gal1RGexp in the Style menu. So adding a legend to show the quantitative measure of size tends not to add much to your drawing, and is optional or discouraged in many cases. We can tell big from small, but we can’t tell a 50 pixel diameter from 63 pixel diameter if they are not right next to each other and the same shape. Note: Although size is a useful attribute to map, showing it in a legend is often not too useful. This is a continuous mapping, meaning there is a function that calculates the size of the node and font from a numerical column in the node table. The first two are associated in that they both map measures of the nodes’ degree to the size of both the nodes and its label. But the easiest way to decide is to just make the full legend, look at the result, delete the legend and remake it with fewer boxes checked. So it will often make sense to only show a small number of the possible items. Third, a color gradient entry shows expression level of our protein of interest.ĭepending on the story you are trying to tell with your presentation, many mappings don’t add much information. The first two are called Ramp Functions that show both node size and font size get bigger for nodes of higher degree, i.e., those with more neighbors. In this example, we have color mapped to our variable called gal1Rexp, shape is mapped to a column called isLink, and the size of a node is mapped to the number of neighbors, or its degree.Ĭheck the Vertical Layout option, to position the legend along the right margin of the graph.Ĭheck the box Draw Bounding Box if you want to include a rectangle surrounding all the legend entries.Ĭlick Add Legend button on the bottom of the panel.Īs you see, we got four components because we had all four mappings checked. They show the name of the column in the node table followed by the name of the attribute to which it is mapped. Moving down the control panel, we see the list of mappings. You don’t have control over the font, size or alignment at this point, but I’ll show you how to edit those later. The name of the network goes into the default title, but you can enter whatever text you want. The title and subtitle are just text fields. The icon in the center column of the styles shows a double headed arrow for the right side of the icon for continuous mappings, and dots for discrete mappings.Ĭontinuous legends are made from numerical values, where the range is determined by looking at the node table, such as expression level. In addition to setting Default values, one can also set Mappings to assign values based on data in node or edge table columns. This is a common function in Cytoscape graphs and hard to recreate accurately if you use downstream programs (e.g., Adobe Illustrator) to annotate graphs for publication.įirst, let's review how Styles are used in Cytoscape. There is a variety of different features of the Legend Creator, but its primary function is to add a color gradient to quantify the mapping of fill color in a legend. It can generate a legend that illustrates the visual mapping used in your graphs. If you haven't already, install the Legend Creator app.
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