5 - Plate Layouts • miso

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. miso 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(miso)

## Also loading:

##   - dada2=1.28.0
##   - data.table=1.15.2
##   - ggplot2=3.5.0
##   - magrittr=2.0.3
##   - phyloseq=1.44.0
##   - ShortRead=1.58.0
##   - yaml=2.3.8

## Found tools:

##   - minimap2=2.27-r1193
##   - samtools=1.19.2

## 
## Attaching package: 'miso'

## 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
##    <char> <num>    <char> <char>
## 1:     S1    25    inulin      M
## 2:     S2    84    inulin      F
## 3:     S3    66    inulin      F
## 4:     S4    31   control      M
## 5:     S5    19    inulin      M
## 6:     S6    55    inulin      M

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 row. You can also specifically mark all empty wells as blanks. Helpful if you have pre-specified wells in the manifest.

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

Finally you can also just plot existing layouts. For this just specify the well and plate in the manifest.