In Gibbons-Lab/mbtools: Provides helper functions for microbiome preprocessing and analysis

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)

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)

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

Gibbons-Lab/mbtools documentation built on Jan. 28, 2024, 11:08 a.m.