Stefano Mangiola stemangiola

stemangiola / .gitignore

Last active June 6, 2019 01:36

List of functions for transcriptional data that are useful to use with tidy data


	counts.csv

stemangiola / traceback_plus.R

Created November 14, 2018 04:19

better traceback

rlang::last_error()

stemangiola / tidy_extensions.R

Last active September 9, 2019 00:31

This is a collection of custom tidy functions

	future::plan(future:::multiprocess)

	do_and_return = function(tbl, code){

	# Execute future
	dummy = future::future(code())

	# Return
	tbl
	}

stemangiola / approximated_modified_bessel_second_kind_log.R

Created March 11, 2019 05:10

approximated modified bessel second kind log

	approximated_modified_bessel_second_kind_log = function(z, v, s = max(0,v-10)){

	# s = 0 not approximated

	0.5 * ( log(pi) - log(2) ) + (-z - 0.5 * log(z)) +


	foreach(j = s:floor(v-0.5), .combine = c) %do% {

	lgamma(j + abs(v) - 0.5 + 1) -

stemangiola / gamma_sum.R

Created March 19, 2019 10:04

	generate_gamma_sum <- function(N, k, theta) {
	n_means = length(k)
	sums = numeric(N)
	for(n in 1:N) sums[n] = sum(rgamma(n_means, shape = k, scale = theta))
	list(sums = sums, shape = k, scale = theta)
	}

	k=c(3,4,5)
	theta=c(1, 2, 1)
	generate_gamma_sum(10000, c(3,4,5), c(1, 2, 1)) %$%

stemangiola / rstan_installation.txt

Last active March 21, 2019 04:47

Installation of rstan for big machines

	####################################################################
	# From within R
	####################################################################

	####################################################################
	# Initialisation of makefiles
	####################################################################

	dotR <- file.path(Sys.getenv("HOME"), ".R")
	if (!file.exists(dotR)) dir.create(dotR)

stemangiola / stan_tidy_tools.R

Created April 16, 2019 23:41

Some useful functions about bayes object parsing

	get_bimodality = function(fit) {
	fit %>%
	tidybayes::gather_draws(exposure_rate[S]) %>% summarise(
	bimodal = diptest::dip.test(`.value`) %$% `p.value`
	)
	}

stemangiola / tidy_data_tree.R

Last active June 7, 2019 05:54

tidy_data_tree

	ToDataFrameTypeColFull = function(tree, ...){
	tree %>%
	Clone() %>%
	{
	t = (.)
	foreach(l=1:(t %$% Get("level") %>% max), .combine = bind_rows) %do% {
	data.tree::Clone(t) %>%
	{ data.tree::Prune(., function(x) x$level <= l + 1); . } %>%
	data.tree::ToDataFrameTypeCol(...) %>%
	as_tibble

stemangiola / aggregate_cells.R

Last active November 25, 2020 01:27

code for ABACBS 2020

	#' Convert array of quosure (e.g. c(col_a, col_b)) into character vector
	#'
	#' @keywords internal
	#'
	#' @importFrom rlang quo_name
	#' @importFrom rlang quo_squash
	#' @importFrom purrr when
	#' @importFrom magrittr equals
	#'
	#' @param v A array of quosures (e.g. c(col_a, col_b))

stemangiola / ggplot_theme_multipanel

Last active July 5, 2022 04:46

	# Theme
	friendly_cols <- dittoSeq::dittoColors()

	# scale_fill_manual(values = friendly_cols)
	# scale_color_manual(values = friendly_cols)

	theme_multipanel =
	theme_bw() +
	theme(
	panel.border = element_blank(),