plotHapNet: plotHapNet

Description

plotHapNet

Usage

plotHapNet(
  hapNet,
  size = "freq",
  scale = 1,
  cex = 0.8,
  cex.legend = 0.6,
  col.link = 1,
  link.width = 1,
  show.mutation = 2,
  backGround = backGround,
  hapGroup = hapGroup,
  legend = FALSE,
  show_size_legend = TRUE,
  show_color_legend = TRUE,
  pie.lim = c(0.5, 2),
  main = main,
  labels = TRUE,
  legend_version = 0,
  labels.cex = 0.8,
  labels.col = "blue",
  labels.adj = NULL,
  labels.font = 2,
  ...
)

Value

No return value

Arguments

hapNet

an object of class "haploNet"

size

a numeric vector giving the diameter of the circles representing the haplotypes: this is in the same unit than the links and eventually recycled.

scale

a numeric indicate the ratio of the scale of the links representing the number of steps on the scale of the circles representing the haplotypes or a character one of c('log10', 'log2') indicate the scale method by log10(size) or log2(size), respectively. Default as 1

cex

character expansion factor relative to current par("cex")

cex.legend

same as cex, but for text in legend

col.link

a character vector specifying the colours of the links; eventually recycled.

link.width

a numeric vector giving the width of the links; eventually recycled.

show.mutation

an integer value:

if 0, nothing is drawn on the links;

if 1, the mutations are shown with small segments on the links;

if 2, they are shown with small dots;

if 3, the number of mutations are printed on the links.

backGround

a color vector with length equal to number of Accession types

hapGroup

a matrix used to draw pie charts for each haplotype; its number of rows must be equal to the number of haplotypes

legend

a logical specifying whether to draw the legend, or a vector of length two giving the coordinates where to draw the legend; FALSE by default. If TRUE, the user is asked to click where to draw the legend.

show_size_legend, show_color_legend

wether show size or color legend

pie.lim

A numeric vector define the maximum and minmum pie size, which will be avoid the pie to samll or too large

main

The main title (on top) using font, size (character expansion) and color par(c("font.main", "cex.main", "col.main")).

labels

a logical specifying whether to identify the haplotypes with their labels (default as TRUE)

legend_version

the size legened style, default as 0

labels.cex

the size of labels

labels.col

the labels color

labels.adj

a named list contains two length vectors defining the adjustment of labels. The names should be exactly matched with the haplotype names. default as NULL.

labels.font

the font of labels, default as 2

...

other parameters will pass to plot function

Details

Additional parameters control the network features: labels.cex = 1, labels.font = 2, link.color = "black", link.type = 1, link.type.alt = 2, link.width = 1, link.width.alt = 1, altlinks = TRUE, threshold = c(1,2), haplotype.inner.color = "white", haplotype.outer.color = "black", mutations.cex = 1, mutations.font = 1, mutations.frame.background = "#0000FF4D", mutations.frame.border = "black", mutations.text.color = 1, mutations.arrow.color = "black", mutations.arrow.type = "triangle", mutations.sequence.color = "#BFBFBF4D", mutations.sequence.end = "round", mutations.sequence.length = 0.3, mutations.sequence.width = 5, pie.inner.segments.color = "black", pie.colors.function = rainbow, scale.ratio = 1, show.mutation = 2

The alter links could be eliminated by set the 'threshold' to 0 or set 'altlinks' as FALSE.

Examples

Run this code


# \donttest{
data("geneHapR_test")
hapSummary <- hap_summary(hapResult)

# calculate haploNet
hapNet <- get_hapNet(hapSummary,
                     AccINFO = AccINFO, # accession types
                     groupName = colnames(AccINFO)[2])

# plot haploNet
plot(hapNet)

# plot haploNet
plotHapNet(hapNet,
           size = "freq",   # circle size
           scale = "log10", # scale circle with 'log10(size + 1)'
           cex = 1, # size of hap symbol
           col.link = 2, # link colors
           link.width = 2, # link widths
           show.mutation = 2, # mutation types one of c(0,1,2,3)
           legend = FALSE) # legend position
# }