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
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properties
¶ DataFrame of aliquot properties for each well, useful for groupby operations during plots
- Type
DataFrame
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readings
¶ DataFrame of readings for each well at different time points
- Type
DataFrame
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operation
¶ Operation used for generating these growth curves (e.g. Absorbance)
- Type
str
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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
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Imaging¶
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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
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raw
¶ Raw buffer of image bytes
- Type
BytesIO
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image
¶ Image object as rendered by PIL
- Type
PIL.Image