Region plot

regionplot() displays the association results for a smaler region within one chromosome Required parameter is at least one dataset (dataframe) containing the association data (with columns CHROM,POS,P in upper or lowercase), and either gene, variant or region (represented by chr, xmin and xmax)

All other input parameters are optional

regionplot(
  df,
  ntop = 3,
  annotate = NULL,
  xmin = 0,
  size = 2,
  shape = 19,
  alpha = 1,
  label_size = 4,
  annotate_with = "ID",
  color = get_topr_colors(),
  axis_text_size = 11,
  axis_title_size = 12,
  title_text_size = 13,
  show_genes = FALSE,
  show_overview = TRUE,
  show_exons = FALSE,
  max_genes = 200,
  sign_thresh = 5e-09,
  sign_thresh_color = "red",
  sign_thresh_label_size = 3.5,
  xmax = NULL,
  ymin = NULL,
  ymax = NULL,
  protein_coding_only = FALSE,
  region_size = 1e+06,
  gene_padding = 1e+05,
  angle = 0,
  legend_title_size = 12,
  legend_text_size = 12,
  nudge_x = 0.01,
  nudge_y = 0.01,
  rsids = NULL,
  variant = NULL,
  rsids_color = NULL,
  legend_name = "Data:",
  legend_position = "right",
  chr = NULL,
  vline = NULL,
  show_gene_names = NULL,
  legend_labels = NULL,
  gene = NULL,
  title = NULL,
  label_color = NULL,
  locuszoomplot = F,
  region = 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
annotate	Display annotation for variants with p-values below this threshold
xmin	Parameters setting the chromosomal range to display on the x-axis
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
label_size	Optional parameter to set the size of the plot labels (default: label_size=3)
annotate_with	Annotate the variants with eiher Gene_Symbol or ID (default annotate_with="Gene_Symbol")
color	Optional parameter setting the color of the plot points (default: color="darkblue")
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)
show_genes	Show genes instead of exons (default show_genes=FALSE)
show_overview	Show the overview plot (default show_overview=TRUE)
show_exons	Show exons instead of genees (default show_exons=FALSE)
max_genes	Only label the genes if they are fewer than max_genes (default values is 200).
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)
xmax	Parameters setting the chromosomal range to display on the x-axis
ymin	Optional parameters, min and max of the y-axis, (default values: ymin=0, ymax=max(-log10(df$P)))
ymax	Optional parameters, min and max of the y-axis, (default values: ymin=0, ymax=max(-log10(df$P)))
protein_coding_only	Set this parameter to TRUE to only use protein coding genes for annotation
region_size	the size of the region used when annotating the top variant in a region (default value is 10000000 or 10 MB)
gene_padding	The size of the region around the gene, if the gene argument was used (default: gene_padding=100000)
angle	The angle of the text label
legend_title_size	Text size of the legend title
legend_text_size	Text size of the legend text
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)
rsids	A vector of rs ids to highlight on the plot, e.g. rsids=c("rs1234, rs45898")
variant	Zoom in on this variant. Can be either an rsid, or a dataframe (like returned from get_best_hit())
rsids_color	The color of the variants in variants_id (default color is red)
legend_name	Change the name of the legend (default: None)
legend_position	Top,bottom,left or right
chr	The chromosome to plot (i.e. chr15), only required if the input dataframe contains results from more than one chromosome
vline	Parameter (optional) to add a vertical line to the plot at a specific chromosomal position, e.g vline=204000066. Multiple values can be provided in a vector, e.g vline=c(204000066,100500188)
show_gene_names	Show the gene names even though they exceed the max_genes count
legend_labels	Legend labels
gene	Zoom in on this gene (e.g. gene=FTO)
title	Plot title (optional
label_color	Otpional parameter to change the color
region	genetic region, e.g. chr1:67038906-67359979

Value

plots using egg (https://cran.r-project.org/web/packages/egg/vignettes/Ecosystem.html)

Examples

if (FALSE) {
regionplot(df,gene="FTO")
}