Manhattan plot

manhattan() displays the association results for the entire genome 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

manhattan(
  df,
  ntop = 3,
  title = "",
  annotate = NULL,
  color = get_topr_colors(),
  sign_thresh = 5e-09,
  sign_thresh_color = "red",
  sign_thresh_label_size = 3.5,
  label_size = 3,
  size = 1,
  shape = 19,
  alpha = 1,
  highlight_genes_color = "green",
  highlight_genes_ypos = 1,
  axis_text_size = 11,
  axis_title_size = 12,
  title_text_size = 13,
  legend_title_size = 12,
  legend_text_size = 12,
  protein_coding_only = TRUE,
  angle = 0,
  legend_labels = NULL,
  gene = NULL,
  gene_padding = 1e+05,
  chr = NULL,
  annotate_with = "Gene_Symbol",
  region_size = 1e+06,
  legend_name = NULL,
  legend_position = "bottom",
  rect = NULL,
  nudge_x = 0.1,
  nudge_y = 0.2,
  xmin = NULL,
  xmax = NULL,
  ymin = NULL,
  ymax = NULL,
  highlight_genes = NULL,
  label_color = NULL
)

Arguments

df	Dataframe or a list of dataframes (required columns are CHROM,POS,P), in upper- or lowercase) of association results.
ntop	Number of datasets (GWASes) to show on the top plot
title	Plot title (optional
annotate	Display annotation for variants with p-values below this threshold
color	Optional parameter setting the color of the plot points (default: color="darkblue")
sign_thresh	Optional parameter setting the threshold of the dashed red horizontal line representing the significance threshold (default: sign_thresh=5.1e-9). Multiple thresholds can be provided in a vector, e.g sign_thresh=c(5.1e-9,1.0e-6)). Set this parameter to NULL if you dont want this line to appear at all sign_thresh=NULL
sign_thresh_color	set the color of the significance threshold line or lines
sign_thresh_label_size	Set the text size of the label for the signficance thresholdds (default text sizze is 3.5)
label_size	Optional parameter to set the size of the plot labels (default: label_size=3)
size	Optional parameter setting the size of the plot points (default: size=1.2)
shape	A number of vector of numers setting the shape of the plotted points
alpha	A number or vector of numbers setting the transparancy of the plotted points
highlight_genes_color	Colors for the hihglighted genes (default: green)
highlight_genes_ypos	Display the genes at this position on the y-axis (default value is 1)
axis_text_size	Text size of the x and y axes tick labels (default: 12)
axis_title_size	Text size of the x and y title labels (default: 12)
title_text_size	Text size of the plot title (default: 13)
legend_title_size	Text size of the legend title
legend_text_size	Text size of the legend text
protein_coding_only	Set this parameter to TRUE to only use protein coding genes for annotation
angle	The angle of the text label
legend_labels	Legend labels
chr	The chromosome to plot (i.e. chr15), only required if the input dataframe contains results from more than one chromosome
annotate_with	Annotate the variants with eiher Gene_Symbol or ID (default annotate_with="Gene_Symbol")
region_size	the size of the region used when annotating the top variant in a region (default value is 10000000 or 10 MB)
legend_name	Change the name of the legend (default: None)
legend_position	Top,bottom,left or right
rect	Rectangle to add to the plot
nudge_x	To vertically adjust the starting position of each gene label (this is a ggrepel parameter)
nudge_y	To horizontally adjust the starting position of each gene label (this is a ggrepel parameter)
xmin, xmax	Parameters setting the chromosomal range to display on the x-axis
ymin, ymax	Optional parameters, min and max of the y-axis, (default values: ymin=0, ymax=max(-log10(df$P)))
highlight_genes	A vector of genes or genes to highlight the datapoints for on the plot
label_color	Otpional parameter to change the color

Value

ggplot object

Examples

if (FALSE) {
data(gwas_CD)
manhattan(gwas_CD)
}