RCandyVis: Draw and annotate phylogenetic tree with taxon metadata, and...

In ChrispinChaguza/RCandy: RCandy: an R package for rapid visualisation of homologous recombination events in bacterial genomes

Draw and annotate phylogenetic tree with taxon metadata, and recombination events.

Description

This function reads a reference genome in GFF format and then plots the genetic features (coding sequences) on both forward and reverse strands.

Usage

RCandyVis(
  tree.file.name,
  taxon.metadata.file = NULL,
  taxon.metadata.columns = NULL,
  gubbins.gff.file = NULL,
  recom.input.type = "Gubbins",
  ref.genome.name = NULL,
  metadata.column.label.angle = 90,
  show.gene.label = FALSE,
  gene.label.angle = 45,
  show.metadata.columns = TRUE,
  subtree.tips = NULL,
  color.pallette = "inferno",
  taxon.metadata.columns.colors = NULL,
  taxon.id.column = NULL,
  show.genome.ticks = TRUE,
  show.genome.axis = TRUE,
  rec.heatmap.color = c("red", "blue"),
  tree.scale.length = NULL,
  show.rec.events = TRUE,
  show.metadata.label = TRUE,
  taxon.metadata.label.cex = 0.95,
  taxon.metadata.delimiter = "\t",
  ref.genome.length = NULL,
  show.rec.freq.per.base = FALSE,
  show.rec.freq.per.genome = TRUE,
  show.rec.per.genome.scale = FALSE,
  rec.events.per.base.as.heatmap = TRUE,
  ladderize.tree.right = NULL,
  midpoint.root = FALSE,
  rec.plot.bg.transparency = 0.1,
  show.genome.annot = TRUE,
  show.rec.plot.tracks = FALSE,
  show.rec.plot.border = FALSE,
  ace.model.name = "ER",
  trait.for.ancestral.reconstr = NULL,
  save.to.this.file = NULL,
  plot.width = 12,
  plot.height = 9.5,
  show.tip.label = FALSE,
  align.tip.label = FALSE,
  show.fig.legend = TRUE,
  genome.start = NULL,
  genome.end = NULL,
  color.tree.tips.by.column = NULL,
  tree.tip.node.cex = 0.35,
  tree.tip.label.cex = 0.35,
  tree.node.cex = 0.6
)

Arguments

tree.file.name	File name or ape phylo object containing the phylogenetic tree in Newick format.
taxon.metadata.file	File name or data frame containing taxon metadata.
taxon.metadata.columns	Vector containing metadata columns to plotted.
gubbins.gff.file	Gubbins output recombination file in GFF format.
recom.input.type	Type of input recombination data, either "Gubbins" GFF or "BRATNextGen" tabular data.
ref.genome.name	Reference genome file name in GFF format.
metadata.column.label.angle	Angle for the metadata column labels.
show.gene.label	A Boolean value indicating whether or not to show gene labels in the reference genome.
gene.label.angle	Angle for the gene labels.
show.metadata.columns	A Boolean indicating whether or not to show metadata in the figure.
subtree.tips	A vector containing a subset of taxons/taxa used to generate a subtree from the main phylogenetic tree.
color.pallette	A vector containing names of the viridis colour palletes for visualisation. Choose from "plasma", "cividis", "viridis", "magma" and "inferno".
taxon.metadata.columns.colors	A vector containing column names with custom colours (should be equal in size and same order as the vector specified for taxon.metadata.columns option)
taxon.id.column	Character or string for the column name containing the strain/taxon name in the metadata file.
show.genome.ticks	A Boolean indicating whether to show the xticks for the recombination events diagram/heatmap.
show.genome.axis	A Boolean indicating whether to show the axis for the recombination events diagram/heatmap.
rec.heatmap.color	A two-value vector containing colour names to use for the recombination event diagram/heatmap.
tree.scale.length	A positive number showing the length of the phylogenetic tree branches.
show.rec.events	A Boolean indicating whether to show the recombination event diagram/diagram.
show.metadata.label	A Boolean indicating whether to show labels for the selected metadata columns.
taxon.metadata.label.cex	A number for the size of the labels for the selected matadata columns
taxon.metadata.delimiter	A delimeter separating metadata columns.
ref.genome.length	An optional reference genome length, otherwise it's read from the reference genome GFF file or data frame.
show.rec.freq.per.base	A Boolean indicating whether to show the frequency of recombination per genomic position/base.
show.rec.freq.per.genome	A Boolean indicating whether to show the frequency of recombination events per genome/taxon.
show.rec.per.genome.scale	A boolean indicating whether to show the barplot scale for the number of recombination events per genome.
rec.events.per.base.as.heatmap	A Boolean indicating whether to show the frequency of recombination events per genome/taxon as a barchart or colour scale (heatmap).
ladderize.tree.right	A Boolean indicating whether to ladderize the phylogenetic tree to the right.
midpoint.root	A Boolean indicating whether to root the phylogenetic tree at midpoint.
rec.plot.bg.transparency	A value between 0 and 1 indicating the transparency level of the background for the recombination events diagram/heatmap.
show.genome.annot	A Boolean indicating whether to show genome annotation above the recombination events diagram/heatmap.
show.rec.plot.tracks	A Boolean indicating whether to plot genome tracks for each taxa.
show.rec.plot.border	A Boolean indicating whether to show the border for the recombination events diagram/heatmap.
ace.model.name	A character or string for the model name used for the discrete ancestral character reconstruction. Choose from "ARD", "ER" and "SYM".
trait.for.ancestral.reconstr	A character or string for the column in the metadata file or data frame used for discrete ancestral character reconstruction.
save.to.this.file	If speficified save the plot to this filename, otherwise show the plot in R.
plot.width	Width of the figure
plot.height	Height of the figure
show.tip.label	A Boolean indicating whether to show the phylogenetic tip labels.
align.tip.label	A Boolean indicating whether to align the phylogenetic tip labels.
show.fig.legend	A Boolean indicating whether to show the legend for the selected metadata columns.
genome.start	A positive number indicating start position in the genome to zoom in.
genome.end	A positive number indicating end position in the genome to zoom in.
color.tree.tips.by.column	Character or string for the column name in the metadata file for colouring the phylogenetic tree tips or terminal nodes.
tree.tip.node.cex	A number for the terminal node or tip size in the phylogenetic tree.
tree.tip.label.cex	A number for the tip label size in the phylogenetic tree.
tree.node.cex	A number for the size of the nodes phylogenetic tree.

Value

None

Author(s)

Chrispin Chaguza, [e-mail]

References

https://github.com/ChrispinChaguza/RCandy

Examples

## Not run: 
Read phylogenetic tree in Newick format, reference genome in GFF formatted file,
generated usign readseq, and Gubbins GFF file to plot the genomic features

metadata.file<-system.file("extdata", "ST320.tsv", package = "RCandy",
mustWork = TRUE)
tree.file<-system.file("extdata", "ST320.final_tree.tre", package = "RCandy",
mustWork = TRUE)
gubbins.gff<-system.file("extdata", "ST320.recombination_predictions.gff",
package = "RCandy",mustWork = TRUE)
ref.genome.gff<-system.file("extdata", "Hungary19A-6.gff", package = "RCandy",
mustWork = TRUE)

RCandyVis(tree.file.name = tree.file, taxon.metadata.file = metadata.file,
taxon.metadata.columns = c("Source","Country"),ref.genome.name = ref.genome.gff,
gubbins.gff.file = gubbins.gff,color.tree.tips.by.column = "Country",
show.rec.freq.per.base = FALSE,show.gene.label = FALSE,ladderize.tree.right = TRUE,
midpoint.root = TRUE)

RCandyVis(tree.file.name = tree.file, taxon.metadata.file = metadata.file,
taxon.metadata.columns = c("Source","Country"),ref.genome.name = ref.genome.gff,
gubbins.gff.file = gubbins.gff,color.tree.tips.by.column = "Country",
show.rec.freq.per.base = FALSE,show.gene.label = FALSE,ladderize.tree.right = TRUE,
midpoint.root = TRUE,genome.start = 30000, genome.end = 60000,show.gene.label=TRUE,
save.to.this.file = "RCandy.output.pdf",)

## End(Not run)

ChrispinChaguza/RCandy documentation built on June 23, 2022, 1:03 p.m.