locuszoom: Locuszoom plot

In wuxi-nextcode/topR: Create custom plots for viewing genetic association results using ggplot

Description

locuszoom() 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)

Usage

locuszoom(
  df,
  ntop = 3,
  xmin = 0,
  size = 2,
  shape = 19,
  alpha = 1,
  label_size = 4,
  annotate_with = "ID",
  color = NULL,
  axis_text_size = 11,
  axis_title_size = 12,
  title_text_size = 13,
  show_genes = FALSE,
  show_overview = F,
  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 = "gray40",
  legend_name = "Data:",
  legend_position = "right",
  chr = NULL,
  vline = NULL,
  show_gene_names = NULL,
  legend_labels = NULL,
  gene = NULL,
  title = NULL,
  label_color = "gray40",
  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
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

## Not run: 
locuszoom(df)

## End(Not run)

wuxi-nextcode/topR documentation built on Dec. 23, 2021, 6:13 p.m.