plotAmpliconView: plot ampliconView object with Gviz

In BIMSBbioinfo/AmpliconBiSeq: analyzing amplicon bisulfite sequencing data

Description

plot ampliconView object with Gviz

Usage

plotAmpliconView(obj, example.reads = FALSE, h.panel = NULL,
  sim.heat = TRUE, h.heat = 0.5, sim.col = colorRampPalette(c("blue",
  "yellow", "red"))(50), sim.na.threshold = 10, sim.measure = "similarity",
  newpage = TRUE, meta.exp = 80, ...)

Arguments

obj	AmpliconViews object with one amplicon. Use getAmplicon function to get one amplicon from one sample if necessary.
example.reads	if TRUE (default: FALSE), example reads sampled from actual reads will be displayed. Each AmpliconViews object will have a set of example reads that correspond to meta-methylation profiles.
h.panel	height of the panels, this should be a numeric vector with length equaling to the number of panels plotted
sim.heat	logical, if TRUE a similarity heatmap is drawn under the tracks, showing similarity of base methylation profiles
h.heat	relative height of the similarity heatmap, should be a numeric value between 0 and 0.5. Smaller the value, smaller the heatmap on the plot.
sim.col	colors for similarity heatmap default: colorRampPalette(c("black", "yellow","purple"))(50)
sim.na.threshold	number of pair-wise observation needed to calculate similarity scores from CpGs with low number of overlap may be unreliable
sim.measure	similarity measure, should be one of "similarity","tanay","msimilarity",
meta.exp	the meta-profiles explaining data set will be plotted
newpage	if TRUE the plot will start a fresh graphical device.
...	Other arguments to Gviz::plotTracks

Examples

data(ampViewEx) # load example data
      myAmp=getAmplicon(ampViewEx,"mock4","chr18_69674375_69674775")
      plotAmpliconView(myAmp)

BIMSBbioinfo/AmpliconBiSeq documentation built on May 5, 2019, 10:25 a.m.