Fig. 4

Examples of riboStreamR’s graphical output customization options. On the left side is a representation of the toolbar. (A) Filtering parameters are shown in blue, and allow plotting of distinct subsets of the input data; (A1) Read Length Distribution (RLD) plot where each line represents the alignments from 3 different samples; (A2) RLD plot where only alignments mapped to the CDS are included; (A3) RLD where only reads mapping to tRNA or rRNA regions are included. (B) Organizational parameters, shown in green, allow the user to adjust how the filtered data are grouped and positioned in the output; (B1) Same as A1; (B2) RLD plots where the two plots separate between alignments mapped within a CDS and those mapped to any other feature, and the lines separate between three different samples; (B3) RLD plots where each plot is a separate sample, and the two separate lines represent reads mapping to different feature types. (C) Examples of different plotting parameters, shown in orange, which change the aesthetics of the graphical output; (C1) same as A1 and B1; (C2) reduced bandwidth of line plot to simplify the comparisons between each separate read length; (C3) reduced range of x-axis range, as well as different color scheme of plots to highlight differences between samples