plot_merged_assignment: Generates a single column ggplot for a taxonomic assignment...

In MetaComp: EDGE Taxonomy Assignments Visualization

Description

This implementation...

Usage

plot_merged_assignment(assignment, taxonomy_level,
  sorting_order = "abundance", row_limit = 60, min_row_abundance = 0,
  plot_title, filename)

Arguments

assignment	The gottcha-like merged assignment table.
taxonomy_level	The level which need to be plotted.
sorting_order	the order in which rows shall be sorted, "abundance" is defult, "alphabetical" is an alternative.
row_limit	the max amount of rows to plot (default is 60).
min_row_abundance	the minimal sum of abundances in a row required to plot. Rows whose sum is less than this value are dropped even if row_limit is specified. Ignored for "alphabetical" order. (default 0.0).
plot_title	The plot title.
filename	The output file mask, PDF and SVG files will be produced with Cairo device.

Examples

## Not run: 
hmp_even_fp <- system.file("extdata", "HMP_even", package="MetaComp")
hmp_stagger_fp <- system.file("extdata", "HMP_stagger", package="MetaComp")
data_files <- data.frame(V1 = c("HMP_even", "HMP_stagger"),
                         V2 = c(file.path(hmp_even_fp, "allReads-gottcha2-speDB-b.list.txt"),
                                file.path(hmp_stagger_fp, "allReads-gottcha2-speDB-b.list.txt")))
write.table(data_files, file.path(tempdir(), "assignments.txt"),
                                                 row.names = FALSE, col.names = FALSE)
gottcha2_assignments = merge_edge_assignments(
                         load_edge_assignments(
                           file.path(tempdir(), "assignments.txt"), type = "gottcha2"))
plot_merged_assignment(gottcha2_assignments, "family", 'alphabetical', 100, 0,
                                       "HMP side-to-side", file.path(tempdir(), "assignment.pdf"))

## End(Not run)

MetaComp documentation built on May 2, 2019, 9:25 a.m.