annotate: Interactive plate annotation
In EricEdwardBryant/screenmill: Tools for working with ScreenMill data

Description Usage Arguments Details Queries Strain Collections Strain Collection Keys Media Treatments

View source: R/annotate.R

This function launches a Shiny gadget that allows a user to record information about plate images for arrayed colony growth experiments.

annotate(
  dir = ".",
  queries,
  strain_collections,
  strain_collection_keys,
  media,
  treatments,
  temperatures = c(23, 27, 30, 33, 37),
  overwrite = FALSE,
  update = TRUE,
  ...
)

`dir`	Directory of images to process. Defaults to the current working directory.
`queries`	A dataframe of available queries. Uses `getOption('screenmill.queries')` by default (see Details).
`strain_collections`	A dataframe of available strain collections. Uses `getOption('screenmill.strain_collections')` by default (see Details).
`strain_collection_keys`	A dataframe of strain collection keyfiles. Uses `getOption('screenmill.strain_collection_keys')` by default (see Details).
`media`	A dataframe of available media. Uses `getOption('screenmill.media')` by default (see Details).
`treatments`	A dataframe of available treatments. Uses `getOption('screenmill.treatments')` by default (see Details).
`temperatures`	A vector of recommended temperatures.
`overwrite`	Should existing annotations be overwritten? Defaults to `FALSE`.
`update`	Should annotation tables be updated? Defaults to `TRUE`. Ignored if overwrite is `TRUE`, or annotation is incomplete.
`...`	Currently unused.

This application is provided to make annotation of plates in colony growth experiments easier and safer. It will try to warn, or prevent the user from entering invalid data. If the user does not supply annotation tables (i.e. missing the arguments queries, strain_collections, strain_collection_keys, media, or treatments) then the user defined options will be used (via getOption('screenmill.<table>')) The rothfreezer package database will be used as a fallback if available.

The resulting annotation tables are saved as CSV files in the chosen directory.

To quit without saving, just press "Cancel".

Required fields for annotation tables are described in the following sections.

query_id (chr): Query IDs (e.g. plasmid/strain IDs). Must be unique.
query_name (chr): Shorthand name of the query. Does not need to be unique.
control_query_id (chr): The query ID of the control (e.g. empty vector). Should also be present as a query ID.

strain_collection_id (chr): Unique IDs for strain collections.
description (chr): A description of the strain collection.

strain_collection_id (chr): The strain's corresponding collection ID.
strain_id (chr): Unique identifiers for each strain.
strain_name (chr): Shorthand name of the strain. Does not need to be unique.
plate (int): The collection plate number.
row (int): The row number.
column (int): The column number.
plate_control (lgl): TRUE/FALSE is the strain a plate control? Strains marked TRUE will be used for plate level normalization.

media_id (chr): A unique ID for the base media used in the final plate of the experiment.
media_name (chr): Shorthand name of the media.

treatment_id (chr): A unique ID for the treatment condition.
treatment_name (chr): Shorthand name of the treatment condition.
control_treatment_id (chr): The treatment ID of the control condition (e.g. Untreated).