Histogram

This plot is useful in the context of 16S amplicon sequencing after we’ve quality trimmed reads then joined paired-end reads. Tabulating observed read lengths and their respective counts can give insights into the quality of the sequence ends.

Example Data

Length
153
179
177
191
198

Usage to Add

Given the example data for read length counts:

$ fqc add -x Length -Y "Read Count" --step 10 \
      plot_data/2016/160912_M03018/config.json \
      "Joined Read Lengths" \
      histogram \
      data/tables/histogram_example.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 ‘histogram’
subtitle an optional subtitle for the plot
x_label x-axis label
x_value the header label defined in filename corresponding to values
y_label y-axis label
step histogram bin size

Example JSON entry:

{
    "filename": "histogram_example.csv",
    "tab_name": "Joined Read Lengths",
    "chart_properties": {
        "type": "histogram",
        "x_value": "Length",
        "x_label": "Length",
        "y_label": "Read Count",
        "step": 10
    }
}
../_images/histogram_example.png