FunciSNPplot: FunciSNPplot to visualize YAFSNP summary.
In FunciSNP: Integrating Functional Non-coding Datasets with Genetic Association Studies to Identify Candidate Regulatory SNPs

Description Usage Arguments Details Value Note Author(s) References See Also Examples

FunciSNPplot is a function developed to plot various types of plots to summarize and assist end-user in making informed discoveries of FunciSNP results. Plots can be stored in a folder for future reference.

FunciSNPplot(dat, rsq = 0, split = FALSE, splitbysnp = FALSE, tagSummary = FALSE, heatmap = FALSE, heatmap.key = FALSE,genomicSum = FALSE, save = FALSE, pathplot=getwd(), text.size=10, save.width=7, save.height=7)

`dat`	FunciSNP data.frame: `dat` is a data.frame object from FunciSNPAnnotateSummary. Need to run `FunciSNPAnnotateSummary` first.
`rsq`	an interger (0-1): `rsq` is the Rsquared cutoff used to subset.
`split`	logical: `split` will generate distribution plot of all Correlated SNPs by Rsquare values.
`splitbysnp`	logical: `splitbysnp` is similar to `split` but instead split the distribution by tagSNP.
`tagSummary`	logical: `tagSummary` Will output two plots per biofeature. The first one is a scatter plot showing the relationship between Rsquare and Distance to tagSNP for each YAFSNP. The second plot is a histogram distribution of number of correlated SNPs at each Rsquare value. Each set of plot is further divided by tagSNP. Best if used with `rsq` value.
`heatmap`	logical: `heatmap` correlation heatmap to visualize the number of correlated SNPs at each tagSNP overlapping each biological feature. Most informative if used with a `rsq` value.
`heatmap.key`	logical: `heatmap.key` Places the count of each cell on the heatmap.
`genomicSum`	logical: `genomicSum` Stacked bar chart summarizing all correlated SNPs for each of the identified genomie features (exon, intron, 5'UTR, 3'UTR, promoter, lincRNA or in gene desert (intergentic)). Most informative if used with a `rsq` value.
`save`	logical: `save` to save outputs to folder. Set at getwd(), in folder 'FunciSNP.VERSION/plots
`pathplot`	a character: `pathplot` is the path to the folder where to save the plots. Default to getwd() or current working directory.
`text.size`	Text size passed to graphing functions
`save.width`	Width of saved images in inches
`save.height`	Height of saved images in inches

Plots are generated either in X11 or in specified folder.

Simon G. Coetzee (maintainer: scoetzee@gmail.com); Houtan Noushmehr, PhD (houtan@usp.br)

SG. Coetzee, SK. Rhie, BP. Berman, GA. Coetzee and H. Noushmehr, FunciSNP: An R/Bioconductor Tool Integrating Functional Non-coding Datasets with Genetic Association Studies to Identify Candidate Regulatory SNPs., Nucleic Acids Research, In press, 2012 (doi:10.1093/nar/gks542).

getFSNPs, FunciSNPplot, FunciSNPAnnotateSummary, FunciSNPtable, FunciSNPbed

data(glioma)
gl <- FunciSNPAnnotateSummary(glioma)
FunciSNPplot(gl)
FunciSNPplot(gl, rsq=0, genomicSum=TRUE, save=FALSE)
FunciSNPplot(gl, rsq=0.5, genomicSum=TRUE, save=FALSE)
# DO NOT RUN
#FunciSNPplot(gl, tagSummary=TRUE, rsq=0.5)
#