Usage
heatmapGenome(input, response = as.factor(rep("All", ncol(input))), chrominfo = chrominfo.Mb, cutoff = 1, lowCol = "blue", highCol = "yellow", midCol = "white", ncolors = 50, byclass = FALSE, showaber = FALSE, amplif = 1, homdel = -0.75, samplenames = colnames(input), vecchrom = 1:22, titles = "Image Plot", methodS = "ward", categoricalPheno = TRUE, CENTROMERE = FALSE)
Arguments
response
phenotype of interest. defaults to the same phenotype
assigned to all samples
chrominfo
a chromosomal information associated with the mapping
of the data
cutoff
maximum absolute value. all the values are floored to
+/-cutoff depending on whether they are positive of
negative. defaults to 1
ncolors
number of colors in the grid. input to
maPalette. defaults to 50 lowCol
color for the low (negative) values. input to
maPalette. defaults to "red" highCol
color for the high (positive) values. input to
maPalette. defaults to "green" midCol
color for the values close to 0. input to
maPalette. defaults to "black" byclass
logical indicating whether samples should be clustered within each level of the phenotype or overall. defaults to F
showaber
logical indicating whether high level amplifications and homozygous deletions should be indicated on the plot. defaults to F
amplif
positive value that all observations equal or exceeding it are marked by yellow dots indicating high-level changes. defaults to 1
homdel
negative value that all observations equal or below it are marked by light blue dots indicating homozygous deletions. defaults to -0.75
vecchrom
vector of chromosomal indeces to use for clustering and to display. defaults to 1:23
titles
plot title. defaults to "Image Plots"
methodS
clustering method to cluster samples. defaults to "ward"
categoricalPheno
logical indicating whether phenotype is
categorical. Continuous phenotypes are treated as "no groups" except
that their values are dispalyed.defaults to TRUE.
CENTROMERE
logical indicating whether to plot the centromere