Package 'heattree'

Isolate metadata from Bansal et al. 2021

Description

Isolate metadata from Bansal et al. 2021 (doi:10.1016/j.ygeno.2021.09.021) included for use as an example data set. This is the parsed version of the included "bansal_2021_metadata.tsv" file.

Format

data.frame

Source

Bansal, K., Kumar, S., Kaur, A., Singh, A. and Patil, P.B., 2021. Deep phylo-taxono genomics reveals Xylella as a variant lineage of plant associated Xanthomonas and supports their taxonomic reunification along with Stenotrophomonas and Pseudoxanthomonas. Genomics, 113(6), pp.3989-4003.

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A phylogeny from Bansal et al. 2021

Description

A core gene phylogeny from Bansal et al. 2021 (doi:10.1016/j.ygeno.2021.09.021) included for use as an example data set. This is the parsed version of the included "bansal_2021_tree.nwk" file.

Format

ape::phylo

Source

Bansal, K., Kumar, S., Kaur, A., Singh, A. and Patil, P.B., 2021. Deep phylo-taxono genomics reveals Xylella as a variant lineage of plant associated Xanthomonas and supports their taxonomic reunification along with Stenotrophomonas and Pseudoxanthomonas. Genomics, 113(6), pp.3989-4003.

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Create an interactive phylogenetic tree

Description

Create an interactive phylogenetic tree using the javascript heat-tree package

Usage

heat_tree(
  tree = NULL,
  metadata = NULL,
  aesthetics = NULL,
  width = NULL,
  height = NULL,
  elementId = NULL,
  ...
)

Arguments

tree	One or more trees to plot. Can be a raw newick-formatted string, a phylo object, or a list of such inputs. If a list is provided, its names will be used to name trees.
metadata	Metadata associated with tree. Can be a data.frame or tibble with a column containing IDs matching the tree labels. The ID column is detected automatically. If there are multiple trees (a list), then a list of tables of equal length is required. If a list is provided, its names will be used to name metadata tables.
aesthetics	A named character vector defining which metadata columns are initially used to color/size tree parts. If there are multiple trees (a list), then a list of equal length is required.
width	Width of the widget (CSS units or number).
height	Height of the widget (CSS units or number).
elementId	Optional element ID for the widget.
...	Options passed to options parameter of the underlying HeatTree.heatTree() javascript function to modify the initial state of the widget.

Value

An htmlwidget object of class heat_tree that renders an interactive phylogenetic tree visualization. The object contains:

• x: A list with tree data and options passed to JavaScript

• width, height: Dimensions of the widget

• elementId: Optional DOM element ID

The widget can be displayed in R Markdown, Quarto, or using and IDE like RStudio.

Examples

# Create an empty tree viewer for loading data interactively
heat_tree()

# Create a tree viewer with example data included with the package
data(weisberg_2020_metadata)
data(weisberg_2020_mlsa)
heat_tree(
  tree = weisberg_2020_mlsa,
  metadata = weisberg_2020_metadata,
  aesthetics = c(tipLabelColor = 'host_type')
)

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Shiny bindings for heat_tree

Description

Output and render functions for using heat_tree within Shiny applications and interactive Rmd documents.

Usage

heat_treeOutput(outputId, width = "100%", height = "400px")

renderheat_tree(expr, env = parent.frame(), quoted = FALSE)

Arguments

outputId	output variable to read from
width, height	Must be a valid CSS unit (like '100%', '400px', 'auto') or a number, which will be coerced to a string and have 'px' appended.
expr	An expression that generates a heat_tree
env	The environment in which to evaluate expr.
quoted	Is expr a quoted expression (with quote())? This is useful if you want to save an expression in a variable.

Value

heat_treeOutput() returns an output function that creates a Shiny UI element for displaying a heat_tree widget. Used in the UI definition of a Shiny app.

renderheat_tree() returns a render function that can be assigned to an output element in the server function of a Shiny app. It returns a Shiny render binding.

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A BEAST phylogeny from Weisberg et al. 2020

Description

A BEAST phylogeny from Weisberg et al. 2020 (doi:10.1126/science.aba5256) included for use as an example data set. This is the parsed version of the included "weisberg_2020_beast.tre" file.

Format

ape::phylo

Source

Alexandra J. Weisberg et al., Unexpected conservation and global transmission of agrobacterial virulence plasmids.Science368,eaba5256(2020)

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Isolate metadata from Weisberg et al. 2020

Description

Isolate metadata from Weisberg et al. 2020 (doi:10.1126/science.aba5256) included for use as an example data set. This is the parsed version of the included "weisberg_2020_metadata.tsv" file.

Format

data.frame

Source

Alexandra J. Weisberg et al., Unexpected conservation and global transmission of agrobacterial virulence plasmids.Science368,eaba5256(2020)

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A MLSA phylogeny from Weisberg et al. 2020

Description

A MLSA phylogeny from Weisberg et al. 2020 (doi:10.1126/science.aba5256) included for use as an example data set. This is the parsed version of the included "weisberg_2020_mlsa.tre" file.

Format

ape::phylo

Source

Alexandra J. Weisberg et al., Unexpected conservation and global transmission of agrobacterial virulence plasmids.Science368,eaba5256(2020)

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