xPrioritiserManhattan | R Documentation |
xPrioritiserManhattan
is supposed to visualise prioritised genes
using manhattan plot. Genes with the top priority are highlighed. It
returns an object of class "ggplot".
xPrioritiserManhattan(pNode, color = c("darkred", "darkgreen"), cex = 0.5, highlight.top = 20, highlight.col = "deepskyblue", highlight.label.size = 2, highlight.label.offset = 0.02, highlight.label.col = "darkblue", verbose = T, RData.location = "https://github.com/hfang-bristol/RDataCentre/blob/master/XGR/1.0.0")
pNode |
an object of class "pNode" |
color |
a character vector for point colors to alternate |
cex |
a numeric value for point size |
highlight.top |
the number of the top targets to be highlighted |
highlight.col |
the highlight colors |
highlight.label.size |
the highlight label size |
highlight.label.offset |
the highlight label offset |
highlight.label.col |
the highlight label color |
verbose |
logical to indicate whether the messages will be displayed in the screen. By default, it sets to false for no display |
RData.location |
the characters to tell the location of built-in
RData files. See |
an object of class "ggplot"
none
xRDataLoader
, xPrioritiser
,
xPrioritiserSNPs
, xPrioritiserGenes
,
xPrioritiserPathways
## Not run: # Load the library library(XGR) library(igraph) library(dnet) library(ggbio) # a) provide the SNPs with the significance info ## get lead SNPs reported in AS GWAS and their significance info (p-values) AS <- read.delim(file.path(path.package("XGR"),"AS.txt"), stringsAsFactors=FALSE) # b) perform priority analysis pNode <- xPrioritiserSNPs(data=AS, network="PCommonsUN_medium",restart=0.7) # c) manhattan plot mp <- xPrioritiserManhattan(pNode, highlight.top=10) #pdf(file="Gene_manhattan.pdf", height=6, width=12, compress=TRUE) print(mp) #dev.off() ## End(Not run)