lgatto

##' @title Compute the MZ deltas
##'
##' @description
##'
##' The M/Z delta plot illustrates the suitability of MS2 spectra for
##' identification by plotting the M/Z differences of the most intense
##' peaks. The resulting histogram should optimally shown outstanding
##' bars at amino acid residu masses. The plots have been described in
##' Foster et al. 2011.
##'

lgatto

library(magrittr)
library(ggplot2)
library(rpx)

rpx:::apply_fix_issue_5(FALSE)

## https://www.ebi.ac.uk/pride/archive/projects/PXD022816
## RawBeans: A Simple, Vendor-Independent, Raw-Data Quality-Control
## Tool (10.1021/acs.jproteome.0c00956)

lgatto

(defun insert-md-code-chunk ()
  "Insert Rmd code chunk"
  (interactive)
  (insert "```\n\n```")
  (backward-char 4))

(defun insert-rmd-code-chunk ()
  "Insert Rmd code chunk"
  (interactive)
  (insert "```{r}\n\n```")

lgatto

set.seed(123)
max_corrs <- function(d, n = 60, n_iter = 1000)
    replicate(n_iter, {
        m <- matrix(rnorm(n * d), ncol = d)
        max(cor(m)[-1, 1])
    })

r1 <- data.frame(d = 800, r = max_corrs(800))
r2 <- data.frame(d = 6400, r = max_corrs(6400))
r <- rbind(r1, r2)

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

##' 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".