Type: Package
Title: Manhattan, Q-Q, and PCA Plots using 'ggplot2'
Version: 0.3.0
Description: Generate Manhattan, Q-Q, and PCA plots from GWAS and PCA results using 'ggplot2'.
License: MIT + file LICENCE
Encoding: UTF-8
LazyData: true
Imports: RColorBrewer (≥ 1.1.2), ggplot2, ggrepel, dplyr, tidyr, data.table, scales, stats, grDevices
RoxygenNote: 7.1.1
Depends: R (≥ 2.10)
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
URL: https://github.com/LindoNkambule/gwaRs
BugReports: https://github.com/LindoNkambule/gwaRs/issues
NeedsCompilation: no
Packaged: 2021-04-19 17:05:40 UTC; lindokuhle
Author: Lindokuhle Nkambule ORCID iD [aut, cre]
Maintainer: Lindokuhle Nkambule <lindonkambule116@gmail.com>
Repository: CRAN
Date/Publication: 2021-04-19 17:30:06 UTC

Create Manhattan, Q-Q, and PCA plots for GWAS data.

Description

A package for creating Manhattan, Q-Q, and PCA plots for GWAS data.

Author(s)

Lindokuhle Nkambule lindonkambule116@gmail.com

See Also

Useful links:

GWAS results

Description

Example GWAS data.

Highlight SNPs

Description

A couple of SNPs to be annotated

Karyotype Plot

Description

Creates a Karyotype plot

Usage

karyotype_plot(
  data,
  density.col = c("darkgreen", "yellow", "red"),
  window.size = 1e+06,
  title = NULL
)

Arguments

data

A data.frame with "CHR" and "BP"columns.

density.col

A character vector with colors to use for gradients.

window.size

A double precision numeric value indicating the window size.

title

A string denoting the title to use for the plot. Default is 'Manhattan Plot'

Details

Creates a SNP Karyotype or Density plot from an R dataframe with "CHR" and "BP" columns.

Value

A SNP Karyotype plot.

Author(s)

Lindokuhle Nkambule

Examples

karyotype_plot(gwasData)

Manhattan Plot

Description

Creates a Manhattan plot

Usage

man_plot(
  data,
  chromCol = c("gray44", "black"),
  genomewideline = -log10(5e-08),
  suggestiveline = -log10(1e-05),
  chromosome = "ALL",
  annotatePval = FALSE,
  annotateSNP = NULL,
  annotateCol = "red",
  highlight = NULL,
  highlightCol = "green3",
  title = NULL
)

Arguments

data

PLINK assoc output, tab-delimited, or a data.frame with "SNP", "CHR", "BP", and "P" columns.

chromCol

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

genomewideline

Where to draw the "genome-wide significant" line. Default -log10(5e-8). Set to FALSE or F to disable

suggestiveline

Where to draw the "suggestive" line. Default -log10(1e-5). Set to FALSE or F to disable.

chromosome

An integer indicating which chromosome to plot. Default is "ALL".

annotatePval

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

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.

annotateCol

A 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.

highlightCol

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

title

A string denoting the title to use for the plot. Default is 'Manhattan Plot'

Details

Creates a Manhattan plot from PLINK assoc output (or any tab-delimited file or data frame with "SNP", "CHR", "BP", and "P" columns).

Value

A Manhattan plot.

Author(s)

Lindokuhle Nkambule

Examples

man_plot(gwasData)

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.

Details

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

Value

A Mirrored Manhattan plot for two traits.

Author(s)

Lindokuhle Nkambule

Examples

## Not run: 
mirrored_man_plot(inputData)

## End(Not run)

PCA results

Description

Example PCA data.

PCA Plot

Description

Creates a PCA plot

Usage

pca_plot(
  data,
  xComponent = "PC1",
  yComponent = "PC2",
  legendPos = "right",
  soft = "PLINK",
  colPalette = "Accent",
  title = NULL
)

Arguments

data

PLINK pca or EIGENSTRAT smartpca output, (or any tab-delimited file or data.frame with the same format as PLINK pca or EIGENSTRAT smartpca output)

xComponent

A character vector indicating the principal component value to use for the x-axis. Default is "PC1"

yComponent

A character vector indicating the principal component value to use for the x-axis. Default is "PC2"

legendPos

A character vector indicating the legend position. Default is "right".

soft

A character vector indicating the software output format. Default is "PLINK". If you have a tab-delimited file or data.frame with the same format as EIGENSTRAT output, use "EIGENSTRAT"

colPalette

A character vector indicating the color palette to use. Default is "Accent".

title

A string denoting the title to use for the plot. Default is 'PCA Plot'

Details

Creates a PCA plot from PLINK pca output, EIGENSTRAT smartpca, (or any tab-delimited file or data.frame with the same format as PLINK pca or EIGENSTRAT smartpca output).

Value

A PCA plot.

Author(s)

Lindokuhle Nkambule

Examples

pca_plot(pcaData)

QQ Plot

Description

Creates a Q-Q plot

Usage

qq_plot(
  data,
  point_col = "black",
  diag_col = "red",
  diag_line = "solid",
  title = NULL
)

Arguments

data

PLINK assoc output, tab-delimited, or a data.frame with "P" column.

point_col

A character vector indicating the color to use for the SNP p-values. Default is "black".

diag_col

A character vector indicating the color to use for the diagonal line. Default is "red".

diag_line

A character vector indicating the line type to use for the diagonal line. Default is "solid".

title

A string denoting the title to use for the plot. Default is 'Q-Q Plot'

Details

Creates a Q-Q plot from PLINK assoc output (or any tab-delimited file or data frame with "P" column).

Value

A Q-Q plot.

Author(s)

Lindokuhle Nkambule

Examples

qq_plot(gwasData)