Description Usage Arguments Value Author(s) See Also Examples
Plots an overview of the genomic locations of the identified regions (see calculatePvalues) in a karyotype view. The coloring can be done either by significant regions according to their p-values, significant by adjusted p-values, or by annotated region if using matchGenes.
1 2 3 4 5 6 7 | plotOverview(
regions,
annotation = NULL,
type = "pval",
significantCut = c(0.05, 0.1),
...
)
|
regions |
The |
annotation |
The output from running matchGenes
on the output from calculatePvalues. It is only required
if |
type |
Must be either |
significantCut |
A vector of length two specifiying the cutoffs used to determine significance. The first element is used to determine significance for the p-values and the second element is used for the q-values. |
... |
Arguments passed to other methods and/or advanced arguments. Advanced arguments:
Passed to extendedMapSeqlevels. |
A ggplot2 plot that is ready to be printed out. Tecnically it is a ggbio object.
Leonardo Collado-Torres
calculatePvalues, matchGenes
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 | ## Construct toy data
chrs <- paste0('chr', c(1:22, 'X', 'Y'))
chrs <- factor(chrs, levels=chrs)
library('GenomicRanges')
regs <- GRanges(rep(chrs, 10), ranges=IRanges(runif(240, 1, 4e7),
width=1e3), significant=sample(c(TRUE, FALSE), 240, TRUE, p=c(0.05,
0.95)), significantQval=sample(c(TRUE, FALSE), 240, TRUE, p=c(0.1,
0.9)), area=rnorm(240))
annotation <- data.frame(region=sample(c("upstream", "promoter",
"overlaps 5'", "inside", "overlaps 3'", "close to 3'", "downstream"),
240, TRUE))
## Type pval
plotOverview(regs)
## Not run:
## Type qval
plotOverview(regs, type='qval')
## Annotation
plotOverview(regs, annotation, type='annotation')
## Resize the plots if needed.
## You might prefer to leave the legend at ggplot2's default option: right
plotOverview(regs, legend.position='right')
## Although the legend looks better on the bottom
plotOverview(regs, legend.position='bottom')
## Example knitr chunk for higher res plot using the CairoPNG device
```{r overview, message=FALSE, fig.width=7, fig.height=9, dev='CairoPNG', dpi=300}
plotOverview(regs, base_size=30, areaRel=10, legend.position=c(0.95, 0.12))
```
## For more custom plots, take a look at the ggplot2 and ggbio packages
## and feel free to look at the code of this function:
plotOverview
## End(Not run)
|
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