xMEplot | R Documentation |
xMEplot
is supposed to visualise eQTL analysis using violin
plot.
xMEplot(gene = 580484, snp = "rs13182119", summary, expression, genotype, contexts = c("CD14", "LPS2", "LPS24", "IFN", "Bcell", "NK", "Neutrophil", "Monocyte", "shared_CD14", "shared_IFN", "shared_LPS2", "shared_LPS24"), colormap = "sci_jco", ncolumns = NULL)
gene |
an integer specifying ArrayAddress or a character specifying a gene symbol (possibly several ArrayAddress queried returning a list of ggplot objects) |
snp |
a dbSNP |
summary |
a data frame storing eQTL summary statistics. It must contain columns 'context', 'gene', 'snps', 'FDR', 'statistic' |
expression |
a data matrix/frame with genes in rows and samples in columns |
genotype |
a data (sparse) matrix/frame with SNPs in rows and samples in columns |
contexts |
a vector specifying contexts included |
colormap |
the colormap ("sci_jco") |
ncolumns |
an integer specifying the number of columns for contexts. By defaul, it is NULL (decided on according to the number of contexts that will be visualised) |
a ggplot object (or a list of ggplot objects)
none
xME
## Not run: # Load the library library(XGR) library(ggpubr) summary <- xRDataLoader('JK_cohort_xMEdb', RData.location=RData.location) genotype <- xRDataLoader('JK_cohort_genotype', RData.location=RData.location) expression <- xRDataLoader('JK_cohort_expression_cis', RData.location=RData.location) gp <- xMEplot(gene="MED7", snp='rs13182119', summary, expression, genotype, contexts=c("CD14","LPS2","LPS24","IFN","Bcell","NK","Neutrophil","Monocyte")) ## End(Not run)