plotBlocks {DepLogo}

Plots blocks of data

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,
  ...
)

## S3 method for class 'DLData'
plotBlocks(
  data,
  show.number = TRUE,
  block.fun = deprects,
  ic.scale = TRUE,
  add = FALSE,
  ...
)

## S3 method for class 'list'
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)