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Create a Manhattan plot highlighting genome-wide significant and suggestive loci

Source: R/manhattan.R
manhattanExtra.Rd

manhattanExtra() displays association results for the entire genome on a Manhattan plot, highlighting genome-wide significant and suggestive loci. Required parameter is at least one dataset (dataframe) containing the association data (with columns CHROM,POS,P in upper or lowercase)

All other input parameters are optional

Usage

manhattanExtra(
  df,
  genome_wide_thresh = 5e-08,
  suggestive_thresh = 1e-06,
  flank_size = 1e+06,
  region_size = 1e+06,
  sign_thresh_color = NULL,
  sign_thresh_label_size = NULL,
  show_legend = TRUE,
  label_fontface = NULL,
  nudge_y = NULL,
  ymax = NULL,
  sign_thresh = NULL,
  label_color = NULL,
  color = NULL,
  legend_labels = NULL,
  annotate = NULL,
  ...
)

Arguments

df

Dataframe, GWAS summary statistics

genome_wide_thresh

A number. P-value threshold for genome wide significant loci (5e-08 by default)

suggestive_thresh

A number. P-value threshold for suggestive loci (1e-06 by default)

flank_size

A number (default = 1e6). The size of the flanking region for the significant and suggestitve snps.

region_size

A number (default = 1e6). The size of the region for gene annotation. Increase this number for sparser annotation and decrease for denser annotation.

sign_thresh_color

A string or vector of strings to set the color/s of the significance threshold/s

sign_thresh_label_size

A number setting the text size of the label for the significance thresholds (default text size is 3.5)

show_legend

A logical scalar, set to FALSE to hide the legend (default : TRUE)

label_fontface

A string or a vector of strings. Label font “plain”, “bold”, “italic”, “bold.italic” (ggrepel argument)

nudge_y

A number to horizontally adjust the starting position of each gene label (this is a ggrepel parameter)

ymax

Integer, max of the y-axis, (default value: ymax=(max(-log10(df$P)) + max(-log10(df$P)) * .2))

sign_thresh

A number or vector of numbers, setting the horizontal significance threshold (default: sign_thresh=5e-8). Set to NULL to hide the significance threshold.

label_color

A string or a vector of strings. To change the color of the gene or variant labels

color

A string or a vector of strings, for setting the color of the datapoints on the plot

legend_labels

A string or vector of strings representing legend labels for the input datasets

annotate

A number (p-value). Display annotation for variants with p-values below this threshold

...

Additional arguments passed to other plotting functions.

Value

ggplot object

Examples

if (FALSE) { # \dontrun{
manhattanExtra(df)
} # }