vis_boxplot: Visually appealing boxplots

In TYMichaelsen/mmtravis: Tools for analysing (meta)transcriptomics data

Description

Boxplot

Usage

vis_boxplot(obj,group_by)

Arguments

obj	(required) A data object of class 'ampvis2' (see amp_load) or class 'mmt' (see mt_load).
group_by	(required) Group the samples by a variable in the metadata.
boxgroup_by	Group the samples within each boxplot by a variable in the metadata.
sort_by	Sort the boxplots by "median", "mean" or "total". (default: "median")
normalise	Can take one of following arguments: (default: "libsize") "total": Normalise the read counts to be in percent per sample. "libsize": Normalise the read counts to adjust for gene dispersion and total read counts per sample. See estimateSizeFactorsForMatrix for details. "none": No normalisation.
plot_type	Plot type. "boxplot" or "point". (default: "boxplot")
point_size	The size of points. (default: 1)
row_show	The number of variables to show, or a vector of gene/OTU names. (default: 20)
order_group	A vector to order the groups by.
order_boxgroup	A vector to order the box-groups by.
title_newline	Split the facet headers by newline. (default: FALSE)
title_size	Size of text in facet headers. (default: 5)
plot_flip	(logical) Flip the axes of the plot axis. (default: FALSE)
plot_log	(logical) Log10-scale the plot. (default: FALSE)
adjust_zero	Keep values of 0 in calculations by adding this value. (default: NULL)
detailed_output	(logical) Return additional details or not. If TRUE, it is recommended to save to an object and then access the additional data by View(object$data). (default: FALSE)
row_labels	(mmtravis only) Additional variables in genedata to plot (mmt).
tax_class	(ampvis2 only) Converts a specific phylum to class level instead, e.g. "p__Proteobacteria".
tax_empty	(ampvis2 only) How to show OTUs without taxonomic information. One of the following: "remove": Remove OTUs without taxonomic information. "best": (default) Use the best classification possible. "OTU": Display the OTU name.
tax_aggregate	(ampvis2 only) The taxonomic level to aggregate the OTUs. (default: "Genus")

Details

The plot is ordered as one would read a book, from left to right and top to bottom.

Value

A ggplot2 object. If detailed_output = TRUE a list with a ggplot2 object and additional data.

Author(s)

Thomas Yssing Michaelsen [e-mail]

Examples

## Not run: 
data("example_mmt")

vis_boxplot(example_mmt,
  group_by    = "Type",
  boxgroup_by = "Organism",
  row_show    = 10,
  row_labels  = "product",
  title_newline = T)

## End(Not run)

TYMichaelsen/mmtravis documentation built on Aug. 5, 2019, 10:48 a.m.