plotBlocks: Plots blocks of data

In Jstacs/DepLogo: Dependency Logo

Description

Plots the blocks of data in data by successive, vertically arranged sub-plots of the function provided as block.fun. If data is a single DLData object, one block is plotted. Further arguments are provided to block.fun.

Usage

plotBlocks(
  data,
  show.number = TRUE,
  block.fun = deprects,
  ic.scale = TRUE,
  add = FALSE,
  ...
)

Arguments

data	the data, a single DLData object or a list of DLData objects
show.number	if true, the number of sequences (in total) in data is displayed on the left side of the plot
block.fun	the function called for each of the blocks
ic.scale	if TRUE, output of block.fun may be scaled by "information content"
add	if TRUE, the plot is added to an existing plot
...	if add=FALSE forwarded to the internal call to plot

Author(s)

Jan Grau <[e-mail]>

See Also

deprects

logo

colorchart

Examples

# read data and create DLData object
seqs <- read.table(system.file("extdata", "cjun.txt", package = "DepLogo"), 
    stringsAsFactors = FALSE)
data <- DLData(sequences = seqs[, 1], weights = log1p(seqs[, 2]) )

# plot all data
plotBlocks(data)

# partition data
partitions <- partition(data, threshold = 0.3)
# and plot partitions
plotBlocks(partitions)

# or plot partitions as sequence logos
plotBlocks(partitions, block.fun = logo)

Jstacs/DepLogo documentation built on April 22, 2021, 1:21 a.m.