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diskImageR

A Pipeline to Analyze Resistance and Tolerance from Drug Disk Diffusion Assays

A pipeline to analyze photographs of disk diffusion plates. This removes the need to analyze the plates themselves, and thus analysis can be done separate from the assay. Furthermore, diskImageR removes potential researcher bias, by quantitative assessment of drug resistance as the zone diameter at multiple cutoff values of growth inhibition. This method also extends the disk diffusion assay by measuring drug tolerance (in addition to drug resistance) as the fraction of the subpopulation that is able to grow above the resistance point ("FoG"), and drug sensitivity as the rate of change from no growth to full growth ("slope").

Functions (13)

Run an imageJ analysis macro on the folder that contains the photograph to be analyzed

Add factor column

aggregateData

Averages photographs of the same type

Convert RAD to MIC based on built-in or provided parameters or datasets

createDataframe

Dataframe creation

Maximum Likelihood Inference

oneParamPlot

Used to plot a single parameter

Used to plot the results of the imageJ analysis

readExistingDF

Read in an existing dataframe using the tcltk interface

readInExistingIJ

Used to read in existing imageJ analyses

saveMLParam

Save maximum likelihood output

threeParamPlot

Used to plot the RAD, slope and FoG parameter results

twoParamPlot

Used to plot the RAD and FoG results

diskImageR

A Pipeline to Analyze Resistance and Tolerance from Drug Disk Diffusion Assays

v1.0.0

GPL-3

Authors

Aleeza Gerstein [aut, cre], Inbal Hecht [ctb]

Initial release

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