## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set(collapse=TRUE, comment="#>") set.seed(123) ## ----loadPackages, warning=FALSE, message=FALSE------------------------------- library(Omixer) library(tibble) library(forcats) library(stringr) library(dplyr) library(ggplot2) library(magick) ## ----echo=FALSE, out.width='100%'--------------------------------------------- knitr::include_graphics('./omixer_48col.png') ## ----echo=FALSE, out.width='100%'--------------------------------------------- knitr::include_graphics('./omixer_48row.png') ## ----echo=FALSE, out.width='100%'--------------------------------------------- knitr::include_graphics('./omixer_48colblock.png') ## ----------------------------------------------------------------------------- layout <- tibble(plate=rep(1, 96), well=1:96, row=factor(rep(1:8, each=12), labels=toupper(letters[1:8])), column=rep(1:12, 8), chip=as.integer(ceiling(column/2)), chipPos=ifelse(column %% 2 == 0, as.numeric(row)+8, row)) techVars <- c("chip", "chipPos") layout ## ----rna_toy_data------------------------------------------------------------- sampleList <- tibble(sampleId=str_pad(1:48, 4, pad="0"), sex=as_factor(sample(c("m", "f"), 48, replace=TRUE)), age=round(rnorm(48, mean=30, sd=8), 0), smoke=as_factor(sample(c("yes", "ex", "never"), 48, replace=TRUE)), date=sample(seq(as.Date('2008/01/01'), as.Date('2016/01/01'), by="day"), 48)) sampleList ## ----rna_var_setup------------------------------------------------------------ randVars <- c("sex", "age", "smoke", "date") ## ----rna_omixer_rand---------------------------------------------------------- omixerLayout <- omixerRand(sampleList, sampleId="sampleId", block="block", iterNum=100, wells=48, div="row", plateNum=1, randVars=randVars) ## ----------------------------------------------------------------------------- head(omixerLayout[1:11]) ## ----omixer_specific_rna, eval=FALSE------------------------------------------ # load("randomSeed.Rdata") # .GlobalEnv$.Random.seed <- randomSeed # # omixerLayout <- omixerSpecific(sampleList, sampleId="sampleId", # block="block", wells=96, div="row", # plateNum=1, randVars=randVars) ## ----omixer_sheet_rna--------------------------------------------------------- omixerSheet(omixerLayout) ## ----echo=FALSE, out.width='100%'--------------------------------------------- knitr::include_graphics('./omixer_sample_sheets_rna.PNG') ## ----dna_toy_data------------------------------------------------------------- sampleList<- tibble(sampleId=str_pad(1:616, 4, pad="0"), block=rep(1:308, each=2), time=rep(0:1, 308), tissue=as_factor(rep(c("blood", "fat", "muscle", "saliva"), each=2, 77)), sex=as_factor(rep(sample(c("male", "female"), 77, replace=TRUE), each=8)), age=round(rep(rnorm(77, mean=60, sd=10), each=8), 0), bmi=round(rep(rnorm(77, mean=25, sd=2), each=8) , 1), date=rep(sample(seq(as.Date('2015/01/01'), as.Date('2020/01/01'), by="day"), 77), each=8)) sampleList save(sampleList, file="sampleList.Rdata") ## ----dna_var_setup------------------------------------------------------------ randVars <- c("tissue", "sex", "age", "bmi", "date") ## ----dna_mask----------------------------------------------------------------- mask <- rep(c(rep(0, 88), rep(1, 8)), 7) ## ----dna_omixer_rand, fig.wide = TRUE----------------------------------------- omixerLayout <- omixerRand(sampleList, sampleId="sampleId", block="block", iterNum=100, wells=96, div="col", plateNum=7, randVars=randVars, mask=mask) ## ----omixer_v_simple, fig.wide = TRUE----------------------------------------- simpleLayout <- omixerRand(sampleList, sampleId="sampleId", block="block",iterNum=1, wells=96, div="col", plateNum=7, randVars=randVars, mask=mask) ## ----omixer_specific_dna, eval=FALSE------------------------------------------ # load("randomSeed.Rdata") # .GlobalEnv$.Random.seed <- randomSeed # # omixerLayout <- omixerSpecific(sampleList, sampleId="sampleId", # block="block", wells=96, div="col", plateNum=7, # randVars=randVars, mask=mask) ## ----omixer_sheet------------------------------------------------------------- omixerSheet(omixerLayout, group="tissue") ## ----echo=FALSE, out.width='100%'--------------------------------------------- knitr::include_graphics('./omixer_sample_sheets_dna.PNG') ## ----sessioninfo-------------------------------------------------------------- sessionInfo()