Basic4Cseq (version 1.8.0)

drawHeatmap: Draw a heatmap-like multi-scale contact profile

Description

This method draws a fragment-based heatmap-like plot for 4C-seq data around a given viewpoint. For a given number of bands, color-coded running medians or running means of signal intensity (normalized and log-scaled) in different fragments are displayed; the window size of the running medians or running means increases from top to bottom. A corresponding colour legend is added in an extra plot.

Usage

"drawHeatmap"(expData, plotFileName = "", smoothingType = "median", picDim = c(9, 2.2), bands = 5, cutoffLog = -7.0, xAxisIntervalLength = 50000, legendLabels = expression(2^-7, 2^0), useFragEnds = TRUE) "drawHeatmap"(expData, plotFileName = "", smoothingType = "median", picDim = c(9, 2.2), bands = 5, cutoffLog = -7.0, xAxisIntervalLength = 50000, legendLabels = expression(2^-7, 2^0), useFragEnds = TRUE)

Arguments

expData

Experiment data from a given 4C-seq experiment for visualization; can be a Data4Cseq object or a data frame

plotFileName

Name for the heatmap plot

smoothingType

Type of interpolation (running mean or running median). Default value is "median" (i.e. running median)

picDim

Dimensions of the plot. Default value is c(9, 2.2), to fit a small heatmap plot below the main 4C-seq plot that is created by visualizeViewpoint

bands

Number of coloured "bands" (rows) to visualize. The first band contains the raw data (running median or running mean with window size 1), the following bands increase in window size (+2 per band)

cutoffLog

Cut off value for the logarithmic scale

xAxisIntervalLength

Length of the x axis intervals in the plot

legendLabels

Labels for a heat colour legend plot; labels should correspond to the logarithmic cut offs

useFragEnds

Indicates whether fragment end data is used directly or interpolated on fragment level

Value

Examples

  if(interactive()) {
    data(liverData)
    drawHeatmap(liverData)
  }