gwaRs (version 0.3.0)

mirrored_man_plot: Mirrored Manhattan Plot

Description

Creates a Mirrored Manhattan Plot for two traits

Usage

mirrored_man_plot(
  data,
  trait1 = NULL,
  trait2 = NULL,
  trait1_chromCols = c("gray66", "grey36"),
  trait2_chromCols = c("steelblue1", "steelblue4"),
  xlab = "Genomic Position (chromosome)",
  title = "Manhattan Plot",
  annotate_trait1_pval = FALSE,
  annotate_trait1_color = "red",
  annotate_trait2_pval = FALSE,
  annotate_trait2_color = "red",
  annotateSNP = NULL,
  annotateSNPcolor = "red",
  highlight = NULL,
  highlightcolor = "green3",
  genomewideline_trait1 = NULL,
  genomewideline_trait2 = NULL,
  genomewideline_type = "dashed",
  genomewideline_color = "red",
  suggestiveline_trait1 = NULL,
  suggestiveline_trait2 = NULL,
  suggestiveline_type = "dashed",
  suggestiveline_color = "blue"
)

Arguments

data

A tab-delimited or data frame with the compulsory columns: "CHR", "SNP", "BP", "P", "Trait".

trait1

A character string of the trait1 as it appears in the input data.

trait2

A character string of the trait2 as it appears in the input data.

trait1_chromCols

A character vector indicating which colors to alternate for trait1 chromosomes.

trait2_chromCols

A character vector indicating which colors to alternate for trait2 chromosomes.

xlab

A character string to be used as the x-axis label.

title

A character string to be used as the plot title

annotate_trait1_pval

If set, trait1 SNPs with p-value less than or equal to this p-value will be annotated on the plot.

annotate_trait1_color

A character string indicating the color to be used for annotating trait1 SNPs by p-value

annotate_trait2_pval

If set, trait2 SNPs with p-value less than or equal to this p-value will be annotated on the plot.

annotate_trait2_color

A character string indicating the color to be used for annotating trait2 SNPs by p-value

annotateSNP

A character vector of SNPs in your dataset to annotate. If some of the SNPs are not in your dataset, gwaRs will throw a warning message.

annotateSNPcolor

A character string denoting the color to use for the annotations.

highlight

A character vector of SNPs in the dataset to highlight. If some of the SNPs are not in your dataset, gwaRs will throw a warning message. Default is NULL.

highlightcolor

A character string denoting the color to use to highlight the SNPs.

genomewideline_trait1

Where to draw the "genome-wide significant" line for trait1

genomewideline_trait2

Where to draw the "genome-wide significant" line for trait2

genomewideline_type

A character string denoting the type of line to be used for the "genome-wide significant" line. This is the same for both traits. Default is dashed.

genomewideline_color

A character string denoting the color to be used for the "genome-wide significant" line. This is the same for both traits. Default is red.

suggestiveline_trait1

Where to draw the "suggestive" line for trait1.

suggestiveline_trait2

Where to draw the "suggestive" line for trait2.

suggestiveline_type

A character string denoting the type of line to be used for the "suggestive" line. This is the same for both traits. Default is dashed

suggestiveline_color

A character string denoting the color to be used for the "suggestive" line. This is the same for both traits. Default is blue.

Value

A Mirrored Manhattan plot for two traits.

Details

Create a Mirrored Manhattan Plot from a tab-delimited file or data frame with the compulsory columns: "CHR", "SNP", "BP", "P", "Trait" .

Examples

# NOT RUN {
mirrored_man_plot(inputData)
# }
# NOT RUN {
# }