2D Line Plot
Choose the data set in the Control panel, and which data file to plot either in the Control panel or in the drop-down list in the top of the main window. You can define which colors to represent the data within the Data maneger. Press the 2D plot button in the upper right part of the main window, or select it in the View menu (main window). The data points will be plotted against the column they belong to and therefore the x-axis will be on a categorical scale. The data points in one data row are represented with a line in the color defined in the Data manager under the Color & Symbols tab. In the status bar of the chart window, the project name, data set, and data file are given, and it is indicated if the data is transposed or not. By pressing the Edit button in the chart window, you can customize the plot by adding a title, changing background color and much more. The samples in the figure below have been colored according to the group they belong to.
Normally, samples are arranged in rows and genes in columns which results in each sample plotted against each gene. If the data is transposed, it is the other way around: genes plotted against each sample. The genes in the figure below have been colored so that one color represents one gene.
Scaling has large effect on the appearance of plots. Watch the Autoscaling tutorial at www.multid.se to learn more.