plotVmat.default {VplotR} | R Documentation |
The default plotVmat method generates a ggplot representing a heatmap of fragment density.
## Default S3 method: plotVmat( x, hm = 90, colors = COLORSCALE_VMAT, breaks = NULL, xlim = c(-250, 250), ylim = c(50, 300), main = "", xlab = "Distance from center of elements", ylab = "Fragment length", key = "Score", ... )
x |
A computed Vmat (ideally, should be normalized) |
hm |
Integer, should be between 0 and 100. Used to automatically scale the range of colors (best to keep between 90 and 100) |
colors |
a vector of colors |
breaks |
a vector of breaks. length(breaks) == length(colors) + 1 |
xlim |
vector of two integers, x limits |
ylim |
vector of two integers, y limits |
main |
character, title of the plot |
xlab |
character, x-axis label |
ylab |
character, y-axis label |
key |
character, legend label |
... |
additional parameters |
A Vmat ggplot
data(bam_test) data(ce11_proms) V <- plotVmat( bam_test, ce11_proms, normFun = 'libdepth+nloci', return_Vmat = TRUE ) plotVmat(V)