Fig. 2

Examples of amica graphics, generated using the provided example dataset. a The number of identified proteins can be visualized in a bar plot. b The overlap of identified proteins between samples can be shown in interactive heatmaps such as the Jaccard coefficient shown here. Other visualization possibilities are the numbers of shared proteins or the overlap coefficients (not shown). c Scatter plots can be generated using different types of intensities and samples. Users can interactively highlight proteins and choose to draw a straight line, a linear regression line or no line in the scatter plot. d A PCA plot can help in identifying clusters