read_plate_layout: Read plate layout Reads a directory of plate layout CSVs...

In EricEdwardBryant/screenmill: Tools for working with ScreenMill data

Description

Read plate layout

Reads a directory of plate layout CSVs exported from Numbers (for mac) into a dataframe.

Usage

read_plate_layout(dir)

Arguments

dir	A directory.

Details

To generate a plate layout directory with Numbers, make a separate sheet for each plate and name each sheet "plate<number>" (Replace <number> with the plate number). Then create one table for each annotation with columns named "row", "1", "2", "3" etc. for the dimension of the plate. In the first "row" column, number each row "1", "2", "3" etc. for the dimension of the plate. Name each tabel with the intended annotation (e.g. "strain_id" for a table annotating strain IDs for each position in the plate). Once you have annotated your plates, you can export them to CSV (File>Export To>CSV...). Name the resulting directory with the desired strain collection ID (some combination of the date and a descriptive word is recommended). The files in this directory will be named <sheet>-<table>.csv (e.g. plate1-strain_id.csv).

These tables are required for every plate:

• strain_id - The strain identifier.

• strain_name - The human-readable name of the strain.

• plate_control - (T/F) is position intended to be used as a control for plate normalization?

• excluded - positions to exclude from analysis.

These tables are recommended (depending on the experiment):

• plasmid_id - A plasmid identifier

• OD600 - The culture density used for pinning.

• pinnings - The number of pinnings from source plate to target plate.

• start_temp - The starting temperature at the beginning of the experiment.

• end_temp - The ending temperature at the end of the experiment.

• start_humidity - The starting humidity at the beginning of the experiment.

• end_humidity - The ending humidity at the end of the experiment.

EricEdwardBryant/screenmill documentation built on March 13, 2020, 1:07 p.m.