xCtree: Function to draw a tree-like circular plot

In hfang-bristol/XGR: Exploring Genomic Relations for Enhanced Interpretation Through Enrichment, Similarity, Network and Annotation Analysis

Function to draw a tree-like circular plot

Description

xCtree is supposed to draw a tree-like circular plot (dendrogram circular layout), with tips labelled (outwards or inwards). The tree is provided as an object of class "igraph".

Usage

xCtree(
ig,
leave.label.orientation = c("outwards", "inwards"),
leave.label.size = 2,
leave.label.color = "steelblue",
leave.label.alpha = 0.7,
leave.label.wrap = NULL,
leave.label.expansion = NULL,
leave.size = 0,
limit.expansion = 1.1,
edge.color = "grey",
edge.alpha = 0.5,
edge.width = 0.5
)

Arguments

ig	an object of class "igraph" with node attribute 'name'. It could be a 'phylo' object converted to. Note: the leave labels would be the node attribute 'name' unless the node attribute 'label' is explicitely provided
leave.label.orientation	the leave label orientation. It can be "outwards" and "inwards"
leave.label.size	the text size of the leave labelings. By default, it is 2
leave.label.color	the color of the leave labelings
leave.label.alpha	the alpha of the leave labelings
leave.label.wrap	the wrap width of the leave labelings
leave.label.expansion	the x- and y-expansion of the leave labelings. The value of 1 for the exact location of the leave, and the outwards (>1; by default 1.05 if NULL) and the inwards (<1; by default 0.98 if NULL)
leave.size	the size of the leave nodes. By default, it is 0
limit.expansion	the x- and y-limit expansion. By default, it is 1.1. Beware the orignial limit is [-1,1]
edge.color	the color of edges
edge.alpha	the alpha of edges
edge.width	the width of edges

Value

a ggplot2 object appended with 'ig' and 'data' which should contain columns 'x','y', 'leaf' (T/F), 'name' (the same as V(ig)$name), 'tipid' (tip id), 'label' (if not given in ig, a 'name' varient), 'angle' and 'hjust' (assist in leave label orientation).

Note

none

See Also

xCtree

Examples

## Not run: 
library(XGR)
RData.location <- "http://galahad.well.ox.ac.uk/bigdata"

AA.template <- xRDataLoader("AA.template",
RData.location=RData.location)
# consensus tree
ig <- AA.template$consensus$ig

# outwards
gp <- xCtree(ig, leave.label.orientation="outwards",
leave.label.wrap=50, limit.expansion=1.5, leave.size=2)
head(gp$data %>% dplyr::arrange(tipid))

# inwards
gp <- xCtree(ig, leave.label.orientation="inwards",
leave.label.wrap=30)

# obtain 'xcoord' and 'ycoord'
gp <- ggraph::ggraph(ig, layout='dendrogram', circular=TRUE)
data <- gp$data %>% dplyr::arrange(.ggraph.orig_index)
V(ig)$xcoord <- data[,'x']
V(ig)$ycoord <- data[,'y']

## End(Not run)

hfang-bristol/XGR documentation built on Feb. 4, 2023, 7:05 a.m.