plot {TarSeqQC} | R Documentation |
plot
allows a fast and simple representation of one feature panel
using a polar histogram plot. Histogram bar reflects the percentage of
features that have shown the analyzed attribute in a user set interval.
The resulting graph can be busy and might be better off saved.
For TargetExperimentList objects, plot
allows a fast and simple
representation of several feature panels using a heatmap plot. Along the
x-axis, the features are represented and patients/samples along the y-axis.
Finally, each cell is colored according to the attribute interval.
## S3 method for class 'TargetExperiment' plot(x, y, attributeThres = c(0, 1, 50, 200, 500, Inf), binSize = 1, spaceGene = 0.2, spaceChr = 1.2, innerRadius = 0.3, outerRadius = 1, guides = c(20, 40, 60, 80), alphaStart = -0.3, circleProportion = 0.95, direction = "inwards", chrLabels = FALSE, ...) ## S3 method for class 'TargetExperimentList' plot(x, y, attributeThres = c(0, 1, 50, 200, 500, Inf), pool = FALSE, sampleLabs = TRUE, featureLabs = FALSE,...)
x |
TargetExperiment/TargetExperimentList class object. |
y |
not used but necessary for redefining the generic function. |
attributeThres |
Numeric indicating the interval extreme values. |
binSize |
Numeric indicating bin width. Should probably be left as 1, as other parameters are relative to it. |
spaceGene |
Numeric. Space between bins. |
spaceChr |
Numeric. Space between chromosomes. |
innerRadius |
Numeric. Radius of the inner circle. |
outerRadius |
Numeric. Radius of the outer circle. |
guides |
A vector with percentages to use for the white guide lines. |
alphaStart |
Numeric offset from 12 o'clock in radians. |
circleProportion |
Numeric proportion of the circle to cover. |
direction |
Character indicating if the increasing count goes from or to the center. |
chrLabels |
Logical. Chromosome names must be plotted?. |
pool |
Logical indicating if the plots should be performed for each pool separately |
sampleLabs |
Logical. Sample names must be plotted?. |
featureLabs |
Logical. Feature names must be plotted?. |
... |
not used but necessary for redefining the generic function. |
a ggplot2 graph.
see full example in TargetExperiment-class
see full example in TargetExperimentList-class
Gabriela A. Merino gmerino@bdmg.com.ar, Cristobal Fresno cfresno@bdmg.com.ar, Yanina Murua ymurua@leloir.org.ar, Andrea S. Llera allera@leloir.org.ar and Elmer A. Fernandez efernandez@bdmg.com.ar
http://www.r-bloggers.com/polar-histogram-pretty-and-useful/
## Loading the TargetExperiment object data(ampliPanel, package="TarSeqQC") # Definition of the interval extreme values attributeThres<-c(0,1,50,200,500, Inf) ## Plot panel overview g<-plot(ampliPanel, attributeThres, chrLabels =TRUE) if(interactive()){ g } ## Loading the TargetExperimentList object data(TEList, package="TarSeqQC") # Definition of the interval extreme values attributeThres<-c(0,1,50,200,500, Inf) ## Plot panel overview g<-plot(TEList, attributeThres=attributeThres, featureLabs =TRUE) if(interactive()){ g }