R/visualize.R
xQTLvisual_eqtlExp.Rd
Boxplot of normalized expression stratified by genotypes for eQTL.
xQTLvisual_eqtlExp(
variantName = "",
gene = "",
variantType = "auto",
geneType = "auto",
tissueSiteDetail = "",
axis_text_size = 1.3,
axis_title_size = 1.3,
title_size = 1.4,
xlab_text = "Genotypes",
ylab_text = "Normalized expression",
ylim_v = NULL,
title_text = "",
jitter_color = NULL
)
(character) name of variant, dbsnp ID and variant id is supported, eg. "rs138420351" and "chr17_7796745_C_T_b38".
(character) gene symbol or gencode id (versioned or unversioned are both supported).
(character) options: "auto", "snpId" or "variantId". Default: "auto".
(character) options: "auto","geneSymbol" or "gencodeId". Default: "auto".
(character) details of tissues in GTEx can be listed using tissueSiteDetailGTExv8
or tissueSiteDetailGTExv7
(numberic) text size of the axis labels
(numberic) text size of the axis title
(numberic) text size of the title of the plot
Lable for x-axis
for y-axis
Set scale limits
Title of the plot
(A character vector) Set the point color.
A list containing eQTL detail, expression profile and a ggplot object.
# \donttest{
expEqtl<-xQTLvisual_eqtlExp(variantName="rs3778754", gene ="IRF5",
tissueSiteDetail="Whole Blood", xlab_text="Genotypes",
ylab_text="Expression", ylim_v=c(-2,2),
axis_text_size=1.3, axis_title_size=1.3, title_size=1.4,
title_text="Genotype-expression",
jitter_color=c("#83bea5", "#e09069","#8f9dc6") )
# }