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
}
}