MissingStreambar: Assess Data Coverage Across All Loci and Taxa

In carolinafishes/toast: Transcriptome Ortholog Alignment Sequence Tools

Assess Data Coverage Across All Loci and Taxa

Description

Compare missing data between loci and taxa at different hierarchical levels

Usage

MissingStreambar(tsv, taxonomy, taxonomy_level, threshold, type)

Arguments

tsv	A data frame of missing data coverage such as the generated “parsed_busco_results.tsv”
taxonomy	User made data.frame of taxonomy levels following the format of cetacean_taxonomy
taxonomy_level	Target column name to define level
threshold	Cutoff value for minimum number of sequences allowed per taxon
type	Type of plot to generate, either “bar” or “stream”

Value

Generate either stacked barplots or stream plots to look at missing data patterns between loci and taxa at user defined hierarchical levels

Author(s)

Dustin J Wcisel, [e-mail]

James Thomas Howard, [e-mail]

Jeffrey A Yoder, [e-mail]

Alex Dornburg, [e-mail]

Examples

MissingStreambar(tsv, taxonomy, taxonomy_level, threshold, type="bar")

carolinafishes/toast documentation built on Dec. 19, 2024, 12:47 a.m.