plot_total_sequence_stats: Plot FastQC total sequences stats

In openanalytics/ggfastqc: Generate Summary Plots of FastQC Reports

Description

This function plots the total sequences 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_total_sequence_stats(..., interactive = TRUE, geom = c("jitter",
  "point", "bar"))

Arguments

interactive	logical, default is TRUE, which returns an interactive plotly plot. If FALSE, it returns a static ggplot2 plot.
geom	Possible values are "jitter" (default), "point" and "bar". "jitter" is only possible for interactive = TRUE, and is usually the preferred option since it provides the lowest ink ratio, and contains the least amount of clutter.
...	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_sequence_quality 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_total_sequence_stats(sample = obj) # geom = "jitter" (default)
plot_total_sequence_stats(sample = obj, geom = "point")
plot_total_sequence_stats(sample = obj, geom = "bar")

# interactive = FALSE (ggplot2)
plot_total_sequence_stats(sample = obj, interactive = FALSE) # jitter
plot_total_sequence_stats(sample = obj, interactive = FALSE, geom = "point")
plot_total_sequence_stats(sample = obj, interactive = FALSE, geom = "bar")

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