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

In Basic4Cseq: Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data

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

    ## S4 method for signature 'Data4Cseq'
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)
    ## S4 method for signature 'data.frame'
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

A multiscale intensity contact profile plot and a corresponding colour legend)

Note

PDF export and output as TIFF format are supported. The export format is chosen depending on the plot file name's ending. If no plot file name is provided, the result is plotted on screen.

Author(s)

Carolin Walter

Examples

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

Basic4Cseq documentation built on Nov. 8, 2020, 6:53 p.m.