Analysis Module

flyqma.analysis provides several tools for statistically comparing measured fluorescence levels between subpopulations of cells.

class flyqma.analysis.statistics.CelltypeComparison(measurements, basis, label='celltype', test='MW', **kwargs)

Summary of comparisons between all labeled celltypes.

Attributes:

measurements (pd.DataFrame) - measurement data

basis (str) - attribute on which populations are compared

label (str) - attribute used to define population labels

test (str) - statistical test used, one of (‘KS’, ‘t’, ‘MW’)

compare_celltype(type1, type2, **kwargs)

Args:

type1 (str) - first cell type

type2 (str) - second cell type

kwargs: keyword arguments for statistical test

Returns:

p (float) - p value for comparison statistic

is_greater_than (bool) - True if first population mean is greater

property pairs

Unique pairs of labels.

report(pvals)

Print summary of statistical comparisons for each condition.

Args:

pvals (dict) - {comparison: pvalue} pairs

run(**kwargs)

Compare all pairwise combinations of cell types.

kwargs: keyword arguments for statistical test

Returns:

pvals (dict) - {comparison: pvalue} pairs

class flyqma.analysis.statistics.PairwiseCelltypeComparison(measurements, type1, type2, basis, label='celltype', concurrent_only=True)

Pairwise statistical comparison between two concurrent cell types.

Attributes:

label (str) - attribute used to stratify populations

type1 (str) - first label

type2 (str) - second label

Inherited attributes:

x (pd.DataFrame) - measurements of first population

y (pd.DataFrame) - measurements of second population

basis (str) - attribute on which populations are compared

format_axis(ax, colors=None, axis_labels=None, mode='violin', ylabel=None)

Format axis.

Args:

ax (matplotlib.axes.AxesSubplot)

colors (dict) - color for each box/violin keyed by label

axis_labels (dict) - axis label for each box/violin keyed by label

mode (str) - type of comparison, either ‘box’, ‘violin’, or ‘strip’

ylabel (str) - label for y axis

plot(ax=None, colors=None, mode='violin', ylabel=None, **kwargs)

Visualize comparison using seaborn box or violinplot.

Args:

ax (matplotlib.axes.AxesSubplot)

colors (dict) - color for each box/violin keyed by label

mode (str) - type of comparison, either ‘box’, ‘violin’, or ‘strip’

ylabel (str) - label for yaxis

kwargs: keyword arguments for seaborn plotting function

class flyqma.analysis.statistics.PairwiseComparison(x, y, basis)

Pairwise statistical comparison between measurements of two populations.

Attributes:

x (pd.DataFrame) - measurements of first population

y (pd.DataFrame) - measurements of second population

basis (str) - attribute on which populations are compared

compare(test='MW', **kwargs)

Run statistical test.

Args:

test (str) - name of test used, one of (‘KS’, ‘t’, ‘MW’)

Returns:

p (float) - p-value

is_greater_than (bool) - True if first population mean is greater

kwargs: keyword arguments for statistical test

property is_greater_than

True if first population mean is greater than the second.