plot {pint} | R Documentation |
Plot the contribution of the samples and variables to the dependency model or dependency model fitting scores of chromosome or genome.
## S3 method for class 'GeneDependencyModel' plot(x, X, Y, ann.types = NULL, ann.cols = NULL, legend.x = 0, legend.y = 1, legend.xjust = 0, legend.yjust = 1, order = FALSE, cex.z = 0.6, cex.WX = 0.6, cex.WY = 0.6, ...) ## S3 method for class 'ChromosomeModels' plot(x, hilightGenes = NULL, showDensity = FALSE, showTop = 0, topName = FALSE, type = 'l', xlab = 'gene location', ylab = 'dependency score', main = NULL, pch = 20, cex = 0.75, tpch = 3, tcex = 1, xlim = NA, ylim = NA,...) ## S3 method for class 'GenomeModels' plot(x, hilightGenes = NULL, showDensity = FALSE, showTop = 0, topName = FALSE, onePlot = FALSE, type = 'l', ylab = "Dependency Scores", xlab = "Gene location (chromosome)", main = "Dependency Scores in All Chromosomes", pch = 20, cex = 0.75, tpch = 20, tcex = 0.7, mfrow = c(5,5), mar = c(3,2.5,1.3,0.5), ps = 5, mgp = c(1.5,0.5,0),ylim=NA,...)
x |
|
X, Y |
data sets used in dependency modeling. |
ann.types |
a factor for annotation types for samples. Each value corresponds one sample in datasets. Colors are used to indicate different types. |
ann.cols |
colors used to indicate different annotation types. Gray scale is used if 'NULL' given. |
legend.x, legend.y |
the x and y co-ordinates to be used to position the legend for annotation types. |
legend.xjust, legend.yjust |
how the legend is to be justified relative to the legend x and y location. A value of 0 means left or top justified, 0.5 means centered and 1 means right or bottom justified. |
order |
logical; if 'TRUE', values for sample contributions are ordered according to their values. |
cex.z, cex.WX, cex.WY |
Text size for variable names. |
hilightGenes |
vector of strings; Name of genes to be hilighted with dots. |
showDensity |
logical; if 'TRUE' small vertical lines are drwan in the bottom of the plot under each gene. |
showTop |
numeric; Number of models with highest dependencies to be
hilighted. A horizontal dashed line is drawn to show threshold
value. With |
topName |
logical; If |
type, xlab, ylab, main |
plot type and labels. See |
onePlot |
If |
pch, cex |
symbol type and size for hilightGenes. See |
tpch, tcex |
symbol type and size for genes with highest scores. See
|
ylim, xlim |
axis limits. Default values are calculated from
data. Lower limit for y is 0 and upper limit is either 1
or maximum score value. X limits are gene location
range. See |
mfrow, mar, ps, mgp |
chromosome plots' layout, marginals, text size and margin
line. See |
... |
optional plotting parameters |
Function plots scores of each dependency model of a gene for the whole
chromosome or genome according to used
method. plot(x, cancerGenes = NULL, showDensity = FALSE, ...)
is
also usable and chosen according to class of models
.
Olli-Pekka Huovilainen ohuovila@gmail.com
Dependency Detection with Similarity Constraints Lahti et al., MLSP'09. See http://www.cis.hut.fi/lmlahti/publications/mlsp09_preprint.pdf
DependencyModel-class
,
ChromosomeModels-class
,
GenomeModels-class
,
screen.cgh.mrna
,
screen.cgh.mir
data(chromosome17) ## pSimCCA model on chromosome 17p models17ppSimCCA <- screen.cgh.mrna(geneExp, geneCopyNum, 10, 17, 'p') plot(models17ppSimCCA, hilightGenes=c("ENSG00000108342", "ENSG00000108298"), showDensity = TRUE) ## Dependency model around 50th gene model <- models17ppSimCCA[[50]] ## example annnotation types ann.types <- factor(c(rep("Samples 1 - 10", 10), rep("Samples 11 - 51", 41))) plot(model, geneExp, geneCopyNum, ann.types, legend.x = 40, legend.y = -4, order = TRUE)