plot_sequence_quality: Plot FastQC per base sequence quality

In openanalytics/ggfastqc: Generate Summary Plots of FastQC Reports

Description

This function plots the per base sequence quality across samples. If info regarding the group each sample belongs to is also available, then the generated plot will take that into account to colour / facet accordingly.

Usage

plot_sequence_quality(..., interactive = TRUE, geom = c("line"))

Arguments

interactive	logical, default is TRUE, which returns an interactive plotly plot. If FALSE, it returns a static ggplot2 plot.
geom	Only possible value is "line".
...	The set of fastqc objects to plot, usually of the form sample_name_1 = obj1, sample_name_2 = obj2, etc. See examples. The names will be used as title for facets.

Value

The plot object

See Also

fastqc plot_dup_stats plot_total_sequence_stats plot_gc_stats

Examples

path <- system.file("tests/fastqc-sample", package="ggfastqc")
obj <- fastqc(sample_info = file.path(path, "annotation.txt"))

# interactive = TRUE (plotly)
plot_sequence_quality(sample = obj)

# interactive = FALSE (ggplot2)
plot_sequence_quality(sample = obj, interactive = FALSE)

openanalytics/ggfastqc documentation built on May 24, 2019, 2:27 p.m.