cytoflow.views.base_views¶
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class
cytoflow.views.base_views.
BaseView
[source]¶ Bases:
traits.has_traits.HasStrictTraits
The base class for facetted plotting.
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xfacet, yfacet
Set to one of the
conditions
in theExperiment
, and a new row or column of subplots will be added for every unique value of that condition.Type: String
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huefacet
¶ Set to one of the
conditions
in the in theExperiment
, and a new color will be added to the plot for every unique value of that condition.Type: String
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plot
(experiment, data, **kwargs)[source]¶ Base function for facetted plotting
Parameters: - experiment (Experiment) – The
Experiment
to plot using this view. - title (str) – Set the plot title
- xlabel, ylabel (str) – Set the X and Y axis labels
- huelabel (str) – Set the label for the hue facet (in the legend)
- legend (bool) – Plot a legend for the color or hue facet? Defaults to True.
- sharex, sharey (bool) – If there are multiple subplots, should they share axes? Defaults to True.
- height (float) – The height of each row in inches. Default = 3.0
- aspect (float) – The aspect ratio of each subplot. Default = 1.5
- col_wrap (int) – If xfacet is set and yfacet is not set, you can “wrap” the subplots around so that they form a multi-row grid by setting col_wrap to the number of columns you want.
- sns_style ({“darkgrid”, “whitegrid”, “dark”, “white”, “ticks”}) – Which seaborn style to apply to the plot? Default is whitegrid.
- sns_context ({“paper”, “notebook”, “talk”, “poster”}) – Which seaborn context to use? Controls the scaling of plot elements such as tick labels and the legend. Default is talk.
- despine (Bool) – Remove the top and right axes from the plot? Default is True.
Other Parameters: - cmap (matplotlib colormap) – If plotting a huefacet with many values, use this color map instead of the default.
- norm (matplotlib.colors.Normalize) – If plotting a huefacet with many values, use this object for color scale normalization.
- experiment (Experiment) – The
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class
cytoflow.views.base_views.
BaseDataView
[source]¶ Bases:
cytoflow.views.base_views.BaseView
The base class for data views (as opposed to statistics views).
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plot
(experiment, **kwargs)[source]¶ Plot some data from an experiment. This function takes care of checking for facet name validity and subsetting, then passes the underlying dataframe to BaseView.plot
Parameters: - min_quantile (float (>0.0 and <1.0, default = 0.001)) – Clip data that is less than this quantile.
- max_quantile (float (>0.0 and <1.0, default = 1.00)) – Clip data that is greater than this quantile.
Other Parameters: - lim (Dict(Str : (float, float))) – Set the range of each channel’s axis. If unspecified, assume that the limits are the minimum and maximum of the clipped data. Required.
- scale (Dict(Str : IScale)) – Scale the data on each axis. Required.
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class
cytoflow.views.base_views.
Base1DView
[source]¶ Bases:
cytoflow.views.base_views.BaseDataView
A data view that plots data from a single channel.
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channel
¶ The channel to view
Type: Str
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scale
¶ The scale applied to the data before plotting it.
Type: {‘linear’, ‘log’, ‘logicle’}
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class
cytoflow.views.base_views.
Base2DView
[source]¶ Bases:
cytoflow.views.base_views.BaseDataView
A data view that plots data from two channels.
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xchannel, ychannel
The channels to view
Type: Str
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xscale, yscale
The scales applied to the data before plotting it.
Type: {‘linear’, ‘log’, ‘logicle’} (default = ‘linear’)
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xlim, ylim
Set the min and max limits of the plots’ x and y axes.
Type: (float, float)
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class
cytoflow.views.base_views.
BaseNDView
[source]¶ Bases:
cytoflow.views.base_views.BaseDataView
A data view that plots data from one or more channels.
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channels
¶ The channels to view
Type: List(Str)
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scale
¶ Re-scale the data in the specified channels before plotting. If a channel isn’t specified, assume that the scale is linear.
Type: Dict(Str : {“linear”, “logicle”, “log”})
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class
cytoflow.views.base_views.
BaseStatisticsView
[source]¶ Bases:
cytoflow.views.base_views.BaseView
The base class for statisticxs views (as opposed to data views).
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variable
¶ The condition that varies when plotting this statistic: used for the x axis of line plots, the bar groups in bar plots, etc.
Type: str
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subset
¶ An expression that specifies the subset of the statistic to plot.
Type: str
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class
cytoflow.views.base_views.
Base1DStatisticsView
[source]¶ Bases:
cytoflow.views.base_views.BaseStatisticsView
The base class for 1-dimensional statistic views – ie, the
variable
attribute is on the x axis, and the statistic value is on the y axis.-
statistic
¶ The name of the statistic to plot. Must be a key in the
statistics
attribute of theExperiment
being plotted.Type: (str, str)
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error_statistic
¶ The name of the statistic used to plot error bars. Must be a key in the
statistics
attribute of theExperiment
being plotted.Type: (str, str)
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scale
¶ The scale applied to the data before plotting it.
Type: {‘linear’, ‘log’, ‘logicle’}
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REMOVED_ERROR
= 'Statistics changed dramatically in 0.5; please see the documentation'¶
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class
cytoflow.views.base_views.
Base2DStatisticsView
[source]¶ Bases:
cytoflow.views.base_views.BaseStatisticsView
The base class for 2-dimensional statistic views – ie, the
variable
attribute varies independently, and the corresponding values from the x and y statistics are plotted on the x and y axes.-
xstatistic, ystatistic
The name of the statistics to plot. Must be a keys in the
statistics
attribute of theExperiment
being plotted.Type: (str, str)
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x_error_statistic, y_error_statistic
The name of the statistics used to plot error bars. Must be keys in the
statistics
attribute of theExperiment
being plotted.Type: (str, str)
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xscale, yscale
The scales applied to the data before plotting it.
Type: {‘linear’, ‘log’, ‘logicle’}
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STATS_REMOVED
= '{} has been removed. Statistics changed dramatically in 0.5; please see the documentation.'¶
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