xQTLbiolinks (version 1.6.2)

xQTLvisual_eqtlExp: Boxplot of normalized expression stratified by genotypes for eQTL.

Description

Boxplot of normalized expression stratified by genotypes for eQTL.

Usage

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
)

Value

A list containing eQTL detail, expression profile and a ggplot object.

Arguments

variantName

(character) name of variant, dbsnp ID and variant id is supported, eg. "rs138420351" and "chr17_7796745_C_T_b38".

gene

(character) gene symbol or gencode id (versioned or unversioned are both supported).

variantType

(character) options: "auto", "snpId" or "variantId". Default: "auto".

geneType

(character) options: "auto","geneSymbol" or "gencodeId". Default: "auto".

tissueSiteDetail

(character) details of tissues in GTEx can be listed using tissueSiteDetailGTExv8 or tissueSiteDetailGTExv7

axis_text_size

(numberic) text size of the axis labels

axis_title_size

(numberic) text size of the axis title

title_size

(numberic) text size of the title of the plot

xlab_text

Lable for x-axis

ylab_text

for y-axis

ylim_v

Set scale limits

title_text

Title of the plot

jitter_color

(A character vector) Set the point color.

Examples

# \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") )
# }