Description Usage Arguments Value Note Author(s) See Also Examples
plotAttrExpl
plots density and/or box-plot of the analyzed attribute
at a feature level. These graphics could be displayed together using the
ggplot2 geom_violin method. If panel's pools are present, one facet for each
pool will be showed.
1 2 3 4 5 6 7 8 9 10 | plotAttrExpl(object, dens = FALSE, join = FALSE, log = TRUE,
pool = FALSE, ...)
## S4 method for signature 'TargetExperiment'
plotAttrExpl(object, level = "feature",
join = TRUE, log = TRUE, color = "blue")
## S4 method for signature 'TargetExperimentList'
plotAttrExpl(object, dens = FALSE,
join = FALSE, log = TRUE, pool = FALSE, attributeThres = NULL)
|
object |
TargetExperiment/TargetExperimentList class object. |
dens |
Logical indicating if density plot should be included |
join |
Logical indicating if boxplot and density function should be plotted together using the ggplot2 geom_violin method. |
log |
Logical indicating if the attribute should be considered in log10 scale. |
pool |
Logical indicating if plots should be displayed for each pool separately |
... |
necessary arguments |
level |
Character 'feature' or 'gene' indicating at which level should be analyzed the attribute. |
color |
A character indicating a valid name color. |
attributeThres |
Numeric indicating the attribute interval extreme values. It is not a mandatory parameter but if it is specified,then the plots will be colored according to the interval in which falls the attribute median values. |
ggplot2 graphics.
see full example in TargetExperiment-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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | ## Loading the TargetExperiment object
data(ampliPanel, package="TarSeqQC")
# Attribute boxplot and density plot exploration
g<-plotAttrExpl(ampliPanel,level="feature",join=TRUE, log=FALSE, color="blue")
# x11(type="cairo")
if(interactive()){
g
}
## Loading the TargetExperimentList object
data(TEList, package="TarSeqQC")
# Attribute boxplot and density plot exploration
g<-plotAttrExpl(TEList, log=FALSE, pool=FALSE)
# x11(type="cairo")
if(interactive()){
g
}
|
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