Heatmap¶

A heatmap is generated using tile quality data from FastQC, but a custom one can be generated using data with an x, a y, and value associated with the coordinate.

Example Data¶

Tile	Base	Mean
1101	1	0.4305
1101	2	0.1525
1101	3	0.0202

Usage to Add¶

Tile example data from FastQC can be added manually using:

$ fqc add --x-value Barcode --y-value Count --min-value -10 --max-value 10 \
      plot_data/2016/160912_M03018/config.json \
      "Barcode Counts" \
      bar \
      example/data/tables/160912_top50barcodes.csv

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 ‘heatmap’
subtitle	an optional subtitle for the plot
x_label	x-axis label
x_value	the header label defined in filename corresponding to x-values
y_label	y-axis label
y_value	the header label defined in filename corresponding to y-values
value	the header label defined in filename corresponding to heatmap values
min_color	the minimum color used in the heatmap color map
mid_color	the middle color used in the heatmap color map
max_color	the maximum color used in the heatmap color map
min	the minimum value defined for the heatmap color map
max	the maximum value defined for the heatmap color map

Example JSON entry:

{
    "filename": "R1/Per_tile_sequence_quality.csv",
    "tab_name": "Quality by Tile",
    "status": "pass",
    "chart_properties": {
        "type": "heatmap",
        "subtitle": "Per Tile Average Quality Deviation",
        "x_label": "Position",
        "x_value": "Base",
        "y_label": "Tile",
        "y_value": "Tile",
        "shape": "square",
        "value": "Mean",
        "min": "-10",
        "max": "10",
        "min_color": "#36c",
        "mid_color": "#ffffff",
        "max_color": "#dc3912"
    }
}