iqqunif: iqqunif

Description Usage Arguments Value Examples

View source: R/iqqunif.R

Description

Create interactive qqplots with an assumed uniform distribution

Usage

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iqqunif(d, CI = 0.95, opacity = 1, groupcolors, splitby = NULL,
  moreinfo = TRUE, db, highlight_p, highlight_name, annotate_p, annotate_name,
  highlighter = "red", line, background, title, bigrender = FALSE,
  file = "iqqunif", wi = 7, hgt = 7, res = 300)

Arguments

d

dataframe with at least two columns, p-value and Name; Color, Shape, Info optional

CI

two-sided confidence interval, default 0.95

opacity

point opacity, default 1

groupcolors

named vector of colors corresponding to data in Group column

splitby

if data contains Color and/or Shape, indicate variable(s) by which the data should be subsetted for calculating CIs

moreinfo

includes more information on hover, refers to Info column

db

choose database to connect to ("dbSNP", "GWASCatalog", or enter your own search address)

highlight_p

p-value threshold to highlight

highlight_name

vector of names to highlight, dataframe must include a Name column

annotate_p

p-value threshold to annotate, dataframe must include a Name column

annotate_name

vector of names to annotate, dataframe must include a Name column

highlighter

highlighter color

line

draw a red line at pvalue threshold (observed)

background

can change to "white"

title

plot title

bigrender

can set to TRUE for big plots (~50000 rows) that produce huge input lookup error

file

filename

wi

width of plot

hgt

height of plot

res

resolution of plot

Value

html file

Examples

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data(gwas)
qqdat <- data.frame(pvalue=gwas$pvalue, Color=gwas$Frame, Name=gwas$Frame)
iqqunif(d=qqdat, splitby="Color", db="https://www.google.com/search?q=")

anastasia-lucas/plotman documentation built on July 13, 2020, 11:47 p.m.