kbroman

kbroman

# modify prompt color for teaching

# color prompt to include branch information
function color_my_prompt {
    local __user_and_host="\[\033[01;30m\]\u@\h"
    local __cur_location="\[\033[01;30m\]\W" # use \w for full path; \W for last bit
    local __git_branch='`git branch 2> /dev/null | grep -e ^* | sed -E  s/^\\\\\*\ \(.+\)$/\(\\\\\1\)\ /`'
    local __prompt_tail="\[\033[01;30m\]$"
    local __last_color="\[\033[00;33m"

kbroman

## Stuff from Karl's ~/.Rprofile file

## hate those stars and scientific notation
options(show.signif.stars=FALSE, scipen=10)

## rstudio as my cran mirror
options(repos="http://cran.rstudio.com",
        CRAN = "http://cran.rstudio.com",
        browserNLdisabled = TRUE,
        deparse.max.lines = 2)

kbroman

if(!require(qtlcharts)) {
    library(devtools)
    install_github("kbroman/qtlcharts")
    library(qtlcharts)
}
library(qtl)
library(htmlwidgets)

data(grav)
grav$pheno <- grav$pheno

kbroman

message("Beware of recycling\n    \\\   \n     \\\

      \\`*-.
        )  _`-.
       .  : `. .
       : _   '  \
       ; *` _.   `*-._
       `-.-'          `-.
         ;       `       `.
         :.       .       \\

kbroman

---
title: "test qtlcharts"
author: "Karl Broman"
date: "February 23, 2015"
output: html_document
---

```{r load_lib}
library(devtools)
install_github("kbroman/qtlcharts", ref="htmlwidgets")

kbroman

## trying to understand sizingPolicy in htmlwidgets
#
#  It seems like viewer.defaultHeight/Width are ignored
#  within RStudio

# testjs package
if(!require(testjs)) {
  library(devtools)
  install_github("kbroman/testjs")
  library(testjs)

kbroman

An example that links two plots

This is an example to link two plots with D3, in response to a question posed by @keeghin.

See also this jsfiddle.

The typical thing I do is to assign a class to points that includes a

kbroman

library(qtl)
library(parallel)

# fake intercross data
data(fake.f2)

# single-QTL genome scan
fake.f2 <- calc.genoprob(fake.f2, step=1)
out <- scanone(fake.f2, method="hk")

kbroman

set.seed(91820205)

n <- 50
nlev <- 5
ncol <- 4
x <- rnorm(n)
y <- factor(sample(1:nlev, n, replace=TRUE), levels=1:nlev)
z <- factor(sample(1:ncol, n, replace=TRUE), levels=1:ncol)

library(broman)