| 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
 [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)