plotPerPositionQuality

Class: BioReadQualityStatistics

Plot Phred score distributions

Syntax

plotPerPositionQuality(QSObj)
H = plotPerPositionQuality(QSObj)

Description

plotPerPositionQuality(QSObj) displays a series of box plots showing the Phred quality score distribution at each base position for the BioReadQualityStatistics object QSObj. Each box plot shows the median Phred score, the 25th and 75th percentiles, and the most extreme scores that are not considered outliers. An outlier is defined as a point that is more than 1.5 times the interquartile distance from the median.

H = plotPerPositionQuality(QSObj) returns the handle H to the axes object containing the generated plot.

Input Arguments

QSObj

BioReadQualityStatistics object.

Output Arguments

H

Handle to axes object containing generated plot.

Examples

expand all

Plot Phred score distributions

Create a BioReadQualityStatistics object from a FASTQ file using only the first 40 characters of each read with a minimum average quality score of 5.

QSObj = BioReadQualityStatistics('SRR005164_1_50.fastq', ...
                                  'FilterLength', 40, ...
                                  'QualityScoreThreshold', 5);

Plot Phred quality scores at given base positions.

plotPerPositionQuality(QSObj)
ans = 

  Axes (Quality Scores) with properties:

             XLim: [0.1000 41]
             YLim: [0 40]
           XScale: 'linear'
           YScale: 'linear'
    GridLineStyle: '-'
         Position: [0.1300 0.1100 0.7750 0.8150]
            Units: 'normalized'

  Use GET to show all properties

Was this topic helpful?