Description Usage Arguments Examples
plot ampliconView object with Gviz
1 2 3 4 | 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, ...)
|
obj |
|
example.reads |
if TRUE (default: FALSE), example
reads sampled from actual reads will be displayed. Each
|
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 |
1 2 3 | data(ampViewEx) # load example data
myAmp=getAmplicon(ampViewEx,"mock4","chr18_69674375_69674775")
plotAmpliconView(myAmp)
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