plot_read_alignment: Plot Qualimap read alignment

In openanalytics/ggqualimap: Plots of Statistics Collected by Qualimap from RNASeq Data

Description

This function plots the read alignment stats of 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_read_alignment(..., interactive = TRUE, geom = c("jitter", "box"))

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) and "box". "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. "box" is only possible when the input contains only one qualimap object.
...	The set of qualimap 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

qualimap plot_bias_profile plot_coverage_profile plot_junction_analysis plot_genomic_origin

Examples

path = system.file("tests/qualimap-sample", package="ggqualimap")
obj = qualimap(sample_info = file.path(path, "annotation.txt"))

# interactive jitter
plot_read_alignment(sample = obj)

openanalytics/ggqualimap documentation built on May 24, 2019, 2:28 p.m.