plot_mic_plate: Make a MIC Plate Diagram

In KerrLab/introbiocure: Tools for Managing BIO 180 and BIO 200

Description

plot_mic_plate makes a MIC Plate Diagram using the data supplied. This data frame must contain the columns described below.

Usage

plot_mic_plate(d, title = NULL, subtitle = NULL, threshold = 0,
  absorbance_max = 3, show.values = FALSE, show.unused = FALSE,
  well_size = 13, ...)

Arguments

d	A data frame containing absorbance and antibiotic data
title	A title for the plot. If not provided, one will be created using the Section and Group.
subtitle	A subtitle for the plot. If not provided, one will be created using the Drug.
threshold	Value above which values can be trusted. If a value is below the threshold, that well will be highlighted in red (default: 0).
absorbance_max	Value to be set as the maximum possible absorbance. Useful for having consistent greyscale across many plots (default: 3, which is approx. where the spex maxes out).
show.values	Whether or not to display the absorbance values for each well (default: FALSE)
show.unused	Whether or not to display unused wells. (default: FALSE)
well_size	Size of points used to represent each well. You may need to tweak this. (default: 13)
...	Additional arguments (not currently used)

Details

The following columns must be present in the data:

Drug

3-letter code indicating the drug used for the MIC assay (e.g., 'RIF' or 'STR'). Must have one unique value.

Well

Well in the microtiter plate (e.g., 'D6')

Pro.or.Des

Strain information. Either 'Progenitor' or 'Descendant'

Drug.at.Isolation

Drug used when strain was isolated, either 'None' or 3-letter code (e.g., 'RIF')

Absorbance

Absorbance value for the well

Concentration

Concentration of antibiotic present in the well

Additional columns that can be used:

Section

BIO 180 Section name (e.g., 'A'). Must have one unique value.

Group

BIO 180 Group number. Must have one unique value.

Strain

Strain name (e.g., 'RIF.R.D'). If not present, this will be created using Pro.or.Des and Drug.at.Isolation

Value

A ggplot2 plot object

Examples

## Not run: 
plot_mic_plate(my_mic_data)

## End(Not run)

KerrLab/introbiocure documentation built on May 17, 2019, 11:36 a.m.