bryanmayer

print_xtable = function(table_in, 
                        caption = "FILL IN CAPTION",
                        digits = NULL,
                        align = NULL,
                        include.rownames = F,
                        comment = F,
                        sanitize.text.function = function(x) x,
                        xtable.options = NULL, 
                        return_xtable = F,
                        ...){

bryanmayer

extract_legend = function(plot_in, theme_in = theme(legend.position = "top"))
  gtable::gtable_filter(ggplot_gtable(ggplot_build(plot_in + theme_in)), "guide-box")

bryanmayer

library(ggplot2)
library(RColorBrewer)

gg_color_hue <- function(n) {
  hues = seq(15, 375, length = n + 1)
  hcl(h = hues, l = 65, c = 100)[1:n]
}

n = 4
cols = gg_color_hue(n)

bryanmayer

# Setting PATH for Python 3.5
# The orginal version is saved in .bash_profile.pysave
PATH="/Library/Frameworks/Python.framework/Versions/3.5/bin:${PATH}"
export PATH

# added by Anaconda3 2.5.0 installer
#export PATH="/Users/bryanmayer/anaconda/bin:$PATH"

#export PYTHONPATH=/Users/bryanmayer/anaconda/bin/python:$PYTHONPATH

bryanmayer

library(xtable)
library(plyr)
 
fakedata = data.frame(
 Bacteria = c("G. vaginalis", "L. crispatus"),
 Count = log10(rlnorm(2*100, 13.5))
)

table1 = ddply(fakedata, .(Bacteria), summarize,
  Bacteria = paste("\\textit{",unique(Bacteria),"}", sep=""),

bryanmayer

library(ggplot2)

fakedata = data.frame(
    Bacteria = c("G. vaginalis", "BVAB", "L. crispatus"),
    Count = log10(rlnorm(3*100, 13.5))
)

#create functions to map fontface and colour to bacteria category
#just using sapply
fontFaceFunction = function(bacteriaList)

bryanmayer

library(plyr)

testdata = data.frame(
  ID = rep(c("A", "B", "C"), each = 6),
  time = rep(seq(0, 5, 1), 3),
  output = rnorm(3 * 6)
  )

testdata = merge(testdata,
  ddply(