transcriptic.analysis

Kinetics

class transcriptic.analysis.kinetics.Spectrophotometry(datasets)[source]

Bases: transcriptic.analysis.kinetics._Kinetics

A Spectrophotomery object is used to analyze a kinetic series of PlateRead datasets

properties

DataFrame of aliquot properties for each well, useful for groupby operations during plots

Type

DataFrame

readings

DataFrame of readings for each well at different time points

Type

DataFrame

operation

Operation used for generating these growth curves (e.g. Absorbance)

Type

str

plot(wells='*', groupby=None, title=None, xlabel=None, ylabel=None, max_legend_len=20)[source]

This generates a plot of the kinetics curve. Note that this function is meant for use under a Jupyter notebook environment

Example Usage:

from transcriptic.analysis.kinetics import Spectrophotometry
growth_curve = Spectrophotometry(myRun.data.Datasets)
growth_curve.plot(wells=["A1", "A2", "B1", "B2"])
growth_curve.plot(wells=["A1", "A2", "B1", "B2"], groupby="row", title="Row Groups")
growth_curve.plot(wells=["A1", "A2", "B1", "B2"], groupby="name", ylabel="Absorbance Units")
growth_curve.plot(groupby="name", max_legend_len=40)
Parameters

  • wells (Optional[list or str]) – If not specified, this plots all the wells associated with the Datasets given. Otherwise, specifiy a list of well indices ([“A1”, “B1”]) or a specific well (“A1”)

  • groupby (Optional[str]) – When specified, this groups the wells with the same property value together. On the plot, each group will be represented by a single curve with the mean values and error bars of 1 std. dev. away from the mean

  • title (Optional[str]) – Plot title. Default: “Kinectics Curve (run-id)”

  • xlabel (Optional[str]) – Plot x-axis label. Default: “Time”

  • ylabel (Optional[str]) – Plot y-axis label. Default: “Operation (Wavelength)”

  • max_legend_len – Maximum number of characters for the legend labels before truncating. Default: 20

Returns

Plotly iplot object. Will be rendered nicely in Jupyter notebook instance

Return type

IPlot

Imaging

class transcriptic.analysis.imaging.ImagePlate(dataset)[source]

Bases: object

An ImagePlate object generalizes the parsing of datasets derived from the plate camera for easy visualization.

Parameters

dataset (dataset) – Single dataset selected from datasets object

raw

Raw buffer of image bytes

Type

BytesIO

image

Image object as rendered by PIL

Type

PIL.Image

display()[source]

Displays the original full-sized image. Helpful when used in an IPython kernel

Returns

Returns a HTML iframe of the full-size image which is rendered nicely in IPython (if IPython is present)

Return type

HTML

Spectrophotometry