skbio.stats.composition.ancom#

skbio.stats.composition.ancom(table, grouping, alpha=0.05, tau=0.02, theta=0.1, p_adjust='holm', sig_test='f_oneway', percentiles=None)[source]#

Perform differential abundance test using ANCOM.

Analysis of composition of microbiomes (ANCOM) is done by calculating pairwise log ratios between all features and performing a significance test to determine if there is a significant difference in feature ratios with respect to the variable of interest.

In an experiment with only two treatments, this tests the following hypothesis for feature \(i\):

\[H_{0i}: \mathbb{E}[\ln(u_i^{(1)})] = \mathbb{E}[\ln(u_i^{(2)})]\]

where \(u_i^{(1)}\) is the mean abundance for feature \(i\) in the first group and \(u_i^{(2)}\) is the mean abundance for feature \(i\) in the second group.

Changed in version 0.7.0: Computational efficiency significantly improved.

Parameters:
tabletable_like of shape (n_samples, n_features)

Matrix of strictly positive values (i.e. counts or proportions). See supported formats.

Note

If the table contains zero values, one should add a pseudocount or apply multi_replace to convert all values into positive numbers.

groupingpd.Series or 1-D array_like

Vector indicating the assignment of samples to groups. These could be strings or integers denoting which group a sample belongs to. If it is a pandas Series and the table contains sample IDs, its index will be filtered and reordered to match the sample IDs. Otherwise, it must be the same length as the samples in the table.

alphafloat, optional

Significance level for each of the statistical tests. This can can be anywhere between 0 and 1 exclusive.

taufloat, optional

A constant used to determine an appropriate cutoff. A value close to zero indicates a conservative cutoff. This can can be anywhere between 0 and 1 exclusive.

thetafloat, optional

Lower bound for the proportion for the W-statistic. If all W- statistics are lower than theta, then no features will be detected to be significantly different. This can can be anywhere between 0 and 1 exclusive.

p_adjuststr, optional

Method to correct p-values for multiple comparisons. Options are Holm- Boniferroni (“holm” or “holm-bonferroni”) (default), Benjamini- Hochberg (“bh”, “fdr_bh” or “benjamini-hochberg”), or any method supported by statsmodels’ multipletests function. Case-insensitive. If None, no correction will be performed.

Changed in version 0.6.0: Renamed from multiple_comparisons_correction. The old name is kept as an alias but is deprecated.

sig_teststr or callable, optional

A function to test for significance between classes. It must be able to accept at least two vectors of floats and returns a test statistic and a p-value. Functions under scipy.stats can be directly specified by name. The default is one-way ANOVA (“f_oneway”).

Changed in version 0.7.0: Test funcion must accept 2-D arrays as input, perform batch testing, and return 1-D arrays. SciPy functions have this capability. Custom functions may need modification.

Changed in version 0.6.0: Accepts test names in addition to functions.

Changed in version 0.7.0: Renamed from significance_test. The old name is kept as an alias but is deprecated.

percentilesiterable of floats, optional

Percentile abundances to return for each feature in each group. By default, will return the minimum, 25th percentile, median, 75th percentile, and maximum abundances for each feature in each group.

Returns:
pd.DataFrame

A table of features, their W-statistics and whether the null hypothesis is rejected.

  • W: W-statistic, or the number of features that the current feature is tested to be significantly different against.

  • Signif: Whether the feature is significantly differentially abundant across groups (True) or not (False).

Changed in version 0.7.0: Renamed Reject null hypothesis as Signif.

pd.DataFrame

A table of features and their percentile abundances in each group. If percentiles is empty, this will be an empty pd.DataFrame. The rows in this object will be features, and the columns will be a multi-index where the first index is the percentile, and the second index is the group.

See also

multi_replace
scipy.stats.ttest_ind
scipy.stats.f_oneway
scipy.stats.wilcoxon
scipy.stats.kruskal

Notes

The developers of ANCOM recommend the following significance tests ([1], Supplementary File 1, top of page 11):

  • If there are two groups, use the standard parametric t-test (ttest_ind) or the non-parametric Mann-Whitney rank test (mannwhitneyu).

  • For paired samples, use the parametric paired t-test (ttest_rel) or the non-parametric Wilcoxon signed-rank test (wilcoxon).

  • If there are more than two groups, use the parametric one-way ANOVA (f_oneway) or the non-parametric Kruskal-Wallis test (kruskal).

  • If there are multiple measurements obtained from the individuals, use a Friedman test (friedmanchisquare).

Because one-way ANOVA is equivalent to the standard t-test when the number of groups is two, we default to f_oneway here, which can be used when there are two or more groups.

Users should refer to the documentation of these tests in SciPy to understand the assumptions made by each test.

This method cannot handle any zero counts as input, since the logarithm of zero cannot be computed. While this is an unsolved problem, many studies, including [1], have shown promising results by adding pseudocounts to all values in the matrix. In [1], a pseudocount of 0.001 was used, though the authors note that a pseudocount of 1.0 may also be useful. Zero counts can also be addressed using the multi_replace method.

References

[1] (1,2,3)

Mandal et al. “Analysis of composition of microbiomes: a novel method for studying microbial composition”, Microbial Ecology in Health & Disease, (2015), 26.

Examples

>>> from skbio.stats.composition import ancom
>>> import pandas as pd

Let’s load in a DataFrame with six samples and seven features (e.g., these may be bacterial taxa):

>>> table = pd.DataFrame([[12, 11, 10, 10, 10, 10, 10],
...                       [9,  11, 12, 10, 10, 10, 10],
...                       [1,  11, 10, 11, 10, 5,  9],
...                       [22, 21, 9,  10, 10, 10, 10],
...                       [20, 22, 10, 10, 13, 10, 10],
...                       [23, 21, 14, 10, 10, 10, 10]],
...                      index=['s1', 's2', 's3', 's4', 's5', 's6'],
...                      columns=['b1', 'b2', 'b3', 'b4', 'b5', 'b6',
...                               'b7'])

Then create a grouping vector. In this example, there is a treatment group and a placebo group.

>>> grouping = pd.Series(['treatment', 'treatment', 'treatment',
...                       'placebo', 'placebo', 'placebo'],
...                      index=['s1', 's2', 's3', 's4', 's5', 's6'])

Now run ancom to determine if there are any features that are significantly different in abundance between the treatment and the placebo groups. The first DataFrame that is returned contains the ANCOM test results, and the second contains the percentile abundance data for each feature in each group.

>>> ancom_df, percentile_df = ancom(table, grouping)
>>> ancom_df['W']
b1    0
b2    4
b3    0
b4    1
b5    1
b6    0
b7    1
Name: W, dtype: ...

The W-statistic is the number of features that a single feature is tested to be significantly different against. In this scenario, b2 was detected to have significantly different abundances compared to four of the other features. To summarize the results from the W-statistic, let’s take a look at the results from the hypothesis test. The Signif column in the table indicates whether the null hypothesis was rejected, and that a feature was therefore observed to be differentially abundant across the groups.

>>> ancom_df['Signif']
b1    False
b2     True
b3    False
b4    False
b5    False
b6    False
b7    False
Name: Signif, dtype: bool

From this we can conclude that only b2 was significantly different in abundance between the treatment and the placebo. We still don’t know, for example, in which group b2 was more abundant. We therefore may next be interested in comparing the abundance of b2 across the two groups. We can do that using the second DataFrame that was returned. Here we compare the median (50th percentile) abundance of b2 in the treatment and placebo groups:

>>> percentile_df[50.0].loc['b2']
Group
placebo      21.0
treatment    11.0
Name: b2, dtype: float64

We can also look at a full five-number summary for b2 in the treatment and placebo groups:

>>> percentile_df.loc['b2']
Percentile  Group
0.0         placebo      21.0
25.0        placebo      21.0
50.0        placebo      21.0
75.0        placebo      21.5
100.0       placebo      22.0
0.0         treatment    11.0
25.0        treatment    11.0
50.0        treatment    11.0
75.0        treatment    11.0
100.0       treatment    11.0
Name: b2, dtype: float64

Taken together, these data tell us that b2 is present in significantly higher abundance in the placebo group samples than in the treatment group samples.

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