PathVisio supports two different types of color sets: (1) color gradients and (2) color rules.
Users can choose predefined color-gradients (figure 1) and specify min and max values (figure 2). For three color gradients also the mean value can be specified.
Figure 1: predefined gradients
Figure 2: min and max values
With color rules, you can define categories and assign different colors to different categories. These rules can be based on numeric values (like p-value cutoffs) or non-numeric values (like experiment types).
Basic Visualization Options
Basic visualizations allow users to color datanodes in the pathway based on the loaded dataset. Simple visualization allow only one color set to be used. If more than one measurement per datanode (multiple rows) is in the dataset, then the datanode is split into multiple rows.
Advanced Visualization Options
Advanced visualization can be used when a user wants to use different color sets for different columns in the dataset. More than two color sets can be used – the datanode will be split into equal-sized columns. If more than one measurement per datanode (multiple rows) is in the dataset, then the datanode is split into multiple rows.