Advanced Options

This page documents the use of the advanced options in samplot plot. This will include nearly all possible parameters to samplot plot that are not explained in the Basic Options page.

  --marker_size MARKER_SIZE
                        Size of marks on pairs and splits (default 3)
  -z Z, --z Z           Number of stdevs from the mean (default 4)
  -w WINDOW, --window WINDOW
                        Window size (count of bases to include in view),
                        default(0.5 * len)
  --minq MINQ           coverage from reads with MAPQ <= minq plotted in
                        lighter grey. To disable, pass in negative value
  --coverage_tracktype {stack,superimpose}
                        type of track to use for low MAPQ coverage plot.
  -a, --print_args      Print commandline arguments
  -H PLOT_HEIGHT, --plot_height PLOT_HEIGHT
                        Plot height
  -W PLOT_WIDTH, --plot_width PLOT_WIDTH
                        Plot width
  -q MIN_MQUAL, --min_mqual MIN_MQUAL
                        Min mapping quality of reads to be included in plot
  -j, --json_only       Create only the json file, not the image plot
  --start_ci START_CI   confidence intervals of SV first breakpoint (distance
                        from the breakpoint). Must be a comma-separated pair
                        of ints (i.e. 20,40)
  --end_ci END_CI       confidence intervals of SV end breakpoint (distance
                        from the breakpoint). Must be a comma-separated pair
                        of ints (i.e. 20,40)
  --long_read LONG_READ
                        Min length of a read to be treated as a long-read
                        (default 1000)
  --min_event_size MIN_EVENT_SIZE
                        Min size of an event in long-read CIGAR to include
                        (default 100)
  --xaxis_label_fontsize XAXIS_LABEL_FONTSIZE
                        Font size for X-axis labels (default 6)
  --yaxis_label_fontsize YAXIS_LABEL_FONTSIZE
                        Font size for Y-axis labels (default 6)
  --legend_fontsize LEGEND_FONTSIZE
                        Font size for legend labels (default 6)
  --annotation_fontsize ANNOTATION_FONTSIZE
                        Font size for annotation labels (default 6)
  --common_insert_size  Set common insert size for all plots
  --hide_annotation_labels
                        Hide the label (fourth column text) from annotation
                        files, useful for region with many annotations
  --coverage_only       Hide all reads and show only coverage
  --same_yaxis_scales   Set the scales of the Y axes to the max of all