Area Range

The area range plot is automatically generated from FastQC output for inspecting read quality as a function of position along the sequence.

Example Data

An example table after parsing output from FastQC looks like:

Base	Mean	Lower Quartile	Upper Quartile
1	32.193	32.0	33.0
2	32.365	32.0	33.0
3	32.570	32.0	33.0

Plot Options

Option	Value
filename	supports either a single file path or list of lists with [plot tab name, file path] pairs (see Plot Tabs)
tab_name	left main menu entry
status	left main menu icon – supports ‘pass’, ‘fail’, ‘warn’, or alternatively, omitted (see Tab Status)
chart_properties	See table below

Chart Properties

Option	Value
type	the required entry is ‘arearange’
x_label	x-axis label
x_value	the header label defined in filename corresponding to x-values
y_label	y-axis label
lower_quartile	the header label defined in filename corresponding to lower quartile values
upper_quartile	the header label defined in filename corresponding to upper quartile values
mean	the header label defined in filename corresponding to mean values
zones	defined as ‘value’:’color’ with an initial ‘color’ as the base; see example below

Example JSON entry:

{
    "filename": "R1/Per_base_sequence_quality.csv",
    "tab_name": "Quality by Position",
    "status": "pass",
    "chart_properties": {
        "type": "arearange",
        "x_label": "Position",
        "x_value": "Base",
        "y_label": "Quality (Phred score)",
        "lower_quartile": "Lower Quartile",
        "upper_quartile": "Upper Quartile",
        "mean": "Mean"
    }
}

There is support for adding zones as well, if you’re going for the classic FastQC look and feel:

{
    "filename": [
        ["R1", "R1/Per_base_sequence_quality.csv"],
        ["R2", "R2/Per_base_sequence_quality.csv"]
    ],
    "tab_name": "Quality by Position",
    "status": "warn",
    "chart_properties": {
        "type": "arearange",
        "x_label": "Position",
        "x_value": "Base",
        "y_label": "Quality (Phred score)",
        "lower_quartile": "Lower Quartile",
        "upper_quartile": "Upper Quartile",
        "mean": "Mean",
        "zones": [
            {"value": 30, "color": "#e5afb0"},
            {"value": 34, "color": "#e6d6b1"},
            {"color": "#b0e5b1"}
        ]
    }
}