mmheatmap: Heatmap of the most abundant bins

In KasperSkytte/mmgenome2: Tools for extracting individual genomes from metagenomes

Description

Generates a heatmap of the coverage profiles for the bins.

Usage

mmheatmap(mm, CLASSIFICATION = NULL, BIN_COL, TOPN = 20, tax_add = NULL)

Arguments

mm	(required) A dataframe loaded with mmload.
CLASSIFICATION	Name of the variable in mm with taxonomic classification. The format must resemble that of the following: d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Sedimentibacteraceae;g__Sedimentibacter;s__. (Default: NULL)
BIN_COL	(required) Group the scaffolds by a variable in mm.
TOPN	Number of the most abundant bins to display. (Default: 20)
tax_add	Taxonomic levels to show from the taxonomy variable, one of c("Kingdom","Phylum","Class","Order","Family","Genus","Species"). (Default: NULL)

Value

A ggplot object. Note that mmgenome2 hides all warnings produced by ggplot objects.

Author(s)

Kasper Skytte Andersen [e-mail]

Rasmus Kirkegaard [e-mail]

Examples

library(mmgenome2)
data("mmgenome2")
mmgenome2
mmheatmap(
  mmgenome2,
  BIN_COL = "taxonomy",
  TOPN = 20
)

KasperSkytte/mmgenome2 documentation built on Dec. 14, 2021, 12:11 a.m.