9 - Plate Layouts

Before even having sequencing data you will have to extract DNA or RNA from possibly many samples. This is often done on 96-well plates which requires designing layouts for many plates. mbtools provides a few helpers for that.

The only thing you will need is yet again a sample manifest. This will need to have an id column again. Let’s make one for a somewhat larger experiment.

library(mbtools)

## Also loading:

##   - dada2=1.12.1
##   - data.table=1.12.6
##   - ggplot2=3.2.1
##   - magrittr=1.5
##   - phyloseq=1.28.0
##   - ShortRead=1.42.0
##   - yaml=2.2.0

## Found tools:

##   - minimap2=2.17-r941
##   - slimm=0.3.4
##   - samtools=1.9

## 
## Attaching package: 'mbtools'

## The following object is masked _by_ 'package:BiocGenerics':
## 
##     normalize

## The following object is masked from 'package:graphics':
## 
##     layout

manifest <- data.table(
    id = paste0("S", 1:640),
    age = runif(640, 18, 97) %>% ceiling(),
    treatment = c("control", "inulin")[(runif(640) > 0.5) + 1],
    sex = c("F", "M")[(runif(640) > 0.5) + 1]
)

head(manifest)

##    id age treatment sex
## 1: S1  46    inulin   F
## 2: S2  36    inulin   M
## 3: S3  21   control   F
## 4: S4  40    inulin   M
## 5: S5  48    inulin   F
## 6: S6  65   control   F

You can now get plate layouts by using layout.

lo <- layout(manifest)

This will annotate your manifest with wells and also add in blanks (those have empty IDs):

lo$manifest

This will create a plate map as well. You can control the number of columns with the ncol argument.

layout(manifest, ncol = 2)$layout

You can control the frequency of blanks with the blank_step argument. Set it to Inf or NA to get no blanks.

layout(manifest, blank_step = 9, ncol = 3)$layout

Depending on how you like to arrange your samples you could also do so by column:

layout(manifest, blank_step = 10, by = "col", ncol = 3)$layout