lgatto

• open != reproducible
• it's not about open vs closed - there is are multiple dimensions/gradients of openness
• it's not about reproducible vs non-reproducible
• The goal is trust, verification and guarantees
• Five selfish reasons to work reproducibly
• Technical solutions
• Inclusivity: Open research and open research

lgatto

setClass("CharacterVariableFilter",
         contains = "CharacterFilter")

setClass("NumericVariableFilter",
         contains = "DoubleFilter")

VariableFilter <- function(field,
                           value,
                           condition = "==") {
    if (is.numeric(value))

lgatto

#Usimg @micahgallen's nice raincloud plot code 
#and fork of benmarwick/geom_flat_violin.R code

devtools::install_github('thomasp85/gganimate')

library(tidyverse)
library(gganimate)
library(RColorBrewer)
library(plyr)
#the following is a fork of benmarwick/geom_flat_violin.R

lgatto

#!/bin/bash

if [ -z "$1" ]; then
    WHICH=patched
else
    WHICH=$1
fi

## (1) set up variables
case $WHICH in

lgatto

pca <- prcomp(exprs(object), scale = TRUE, center = TRUE)
pcadata <- pca$x
vars <- (pca$sdev)^2
vars <- vars / sum(vars) * 100

lgatto

#!/usr/bin/perl

## Based on convert.txt by Mike Love
## https://gist.github.com/mikelove/5618f935ace6e389d3fbac03224860cd

## The script ignores labels and references, un-numbered sections
## (section*), quotes and probably a couple of more. It won't deal
## with the pre-amble, bibliography and document tags either. Still
## useful, though.

lgatto

##' This function can be used to create a hexagonal sticker following
##' the guidelines described in the BioC-sticker sticker
##' repository. The function requires the following packages: ggplot2,
##' ggforce, ggtree, showtext and grid, if lattice objects are used.
##'
##' @title Create a BioC sticker.
##' @param x The package logo. Can either be a ggplot, lattice or grob
##'     object.
##' @param package Package name, to be used as label on the
##'     sticker. Default is "MyPackage".

lgatto

@Article{foo,
  author = 	 {Foo, Bar},
  title = 	 {Just a references},
  journal = 	 {Journal of references},
  year = 	 {2016}
}

lgatto

library("EBImage")

resize_to_smallest <- function(x, y) {
    dx <- dim(x)
    dy <- dim(y)
    w <- min(dx[1], dy[1])
    h <- min(dx[2], dy[2])
    list(x = EBImage::resize(x, w, h),
         y = EBImage::resize(y, w, h))
}

lgatto

## Run https://gist.github.com/lgatto/1875f858f4af543990ce3dc84825d9ee

fls <- dir(pattern = "rda")

fps <- lapply(fls, readRDS)
names(fps) <- fls
fps <- lapply(fps, "[[", 1)

.ref <- 3
ref <- fps[[.ref]]