yannabraham

---
title: "AI for Health Winter School Poster"
author: "Yann Abraham"
date: "2022-01-10"
params:
  fold.lim:
    label: the limit applied to absolute fold change
    value: 1
    input: numeric
  sig.lim:

yannabraham

This is an example loading data from an ACS experiment downloaed from the community Cytobank

https://community.cytobank.org/cytobank/experiments/60068

Corresponding to the following publication

https://www.sciencedirect.com/science/article/pii/S009286741631738X

yannabraham

---
title: "NextGen OMICS 2021 - The Polyfunctionality Challenge"
author: "Yann Abraham"
date: "2021-11-05"
params:
  fold.lim:
    label: the limit applied to absolute fold change
    value: 1
    input: numeric
  sig.lim:

yannabraham

# 
# Author: ABRAHYA1
###############################################################################

rm(list=ls())
graphics.off()

## libraries
library(ggplot2)
library(Radviz)

yannabraham

library(ggplot2)
library(dplyr)
library(tidyr)
library(cytofan)
library(bodenmiller)

## let's prepare some data:
cur.mat <- cbind(rbind(refPhenoMat,untreatedPhenoMat),
                 rbind(refFuncMat,untreatedFuncMat))
cur.annot <- bind_rows(refAnnots %>% 

yannabraham

## https://en.wikipedia.org/wiki/Andrews_plot
library(dplyr)
library(ggplot2)

do.andrews <- function(x,breaks=30) {
  require(reshape2)
  
  t <- seq(-pi, pi, pi/breaks)
  m<-nrow(x)
  n<-ncol(x)

yannabraham

library(stringr)

screwed <- readLines(con='http://www.uniprot.org/docs/cdlist.txt')
screwed <- screwed[76:521]

parser <- c(0,8,21,29,37,55,1000000L) # use fixed length parsing

screwed <- lapply(screwed,function(scr) {
        sapply(seq(length(parser)-1),function(i) str_trim(substr(scr,parser[i]+1,parser[i+1])))
    }

yannabraham

data(warpbreaks)

my.summary <- function(vals) {
	return(c(avg=mean(vals),sd=sd(vals)))
}

sum.warpbreaks <- with(warpbreaks,tapply(breaks,list(tension,wool),my.summary))

sum.warpbreaks <- array(unlist(sum.warpbreaks),
	dim=c(length(sum.warpbreaks[1,1][[1]]),dim(sum.warpbreaks)),

yannabraham

## build a fan plot from scratch using dplyr & ggplot2 for visualization of Flow data
## after an original idea by Guy J. Abel
## http://gjabel.wordpress.com/category/r/fanplot/

## libraries
library(flowCore)
library(reshape2)
library(dplyr)
library(ggplot2)
library(RColorBrewer)

yannabraham

library(Biobase)
library(flowCore)
library(flowViz)

# simply replace the dummy dta below with your CSV data
dta <- matrix(rnorm(10000),ncol=10)
dimnames(dta)[[2]] <- LETTERS[1:10]

head(dta)