xCircos | R Documentation |
xCircos
is used to visualise the results of similarity analysis
as a circos plot.
xCircos(g, entity = c("SNP", "Gene"), top_num = 50, ideogram = T, chr.exclude = NULL, entity.label.cex = 0.8, verbose = T, RData.location = "https://github.com/hfang-bristol/RDataCentre/blob/master/XGR/1.0.0")
g |
an object of class "igraph". It stores semantic similarity results with nodes for genes/SNPs and edges for pair-wise semantic similarity between them |
entity |
the entity of similarity analysis for which results are being plotted. It can be either "SNP" or "Gene" |
top_num |
the top number of similarity edges to be plotted |
ideogram |
logical to indicate whether chromosome banding is plotted |
chr.exclude |
a character vector of chromosomes to exclude from the plot, e.g. c("chrX", "chrY"). Default is NULL |
entity.label.cex |
the font size of genes/SNPs labels. Default is 0.8 |
verbose |
logical to indicate whether the messages will be displayed in the screen. By default, it sets to true for display |
RData.location |
the characters to tell the location of built-in
RData files. See |
a circos plot with the semantic similarity between input snps/genes represented by the colour of the links
none
xSocialiserGenes
, xSocialiserSNPs
## Not run: # Load the library library(XGR) library(igraph) library(RCircos) library(GenomicRanges) # provide genes and SNPs reported in AS GWAS studies ImmunoBase <- xRDataLoader(RData.customised='ImmunoBase') # 1) SNP-based similarity analysis using GWAS Catalog traits (mapped to EF) ## Get lead SNPs reported in AS GWAS example.snps <- names(ImmunoBase$AS$variants) SNP.g <- xSocialiserSNPs(example.snps, include.LD=NA) # Circos plot of the EF-based SNP similarity network #out.file <- "SNP_Circos.pdf" #pdf(file=out.file, height=12, width=12, compress=TRUE) xCircos(g=SNP.g, entity="SNP") #dev.off() # 2) Gene-based similarity analysis using Disease Ontology (DO) ## Get genes within 10kb away from AS GWAS lead SNPs example.genes <- names(which(ImmunoBase$AS$genes_variants<=10000)) gene.g <- xSocialiserGenes(example.genes, ontology=c("DO") # Circos plot of the DO-based gene similarity network #out.file <- "Gene_Circos.pdf" #pdf(file=out.file, height=12, width=12, compress=TRUE) xCircos(g=gene.g, entity="Gene", chr.exclude="chrY") #dev.off() ## End(Not run)