Plotting Tutorial

The Hail plot module allows for easy plotting of data. This notebook contains examples of how to use the plotting functions in this module, many of which can also be found in the first tutorial.

[1]:
import hail as hl
hl.init()

from bokeh.io import show
from bokeh.layouts import gridplot
Loading BokehJS ...
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
Running on Apache Spark version 3.5.0
SparkUI available at http://hostname-2e8ed49dc0:4040
Welcome to
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  /_/ /_/\_,_/_/_/   version 0.2.131-11d9b2ff89da
LOGGING: writing to /io/hail/python/hail/docs/tutorials/hail-20240605-1703-0.2.131-11d9b2ff89da.log
[2]:
hl.utils.get_1kg('data/')
mt = hl.read_matrix_table('data/1kg.mt')
table = (hl.import_table('data/1kg_annotations.txt', impute=True)
         .key_by('Sample'))
mt = mt.annotate_cols(**table[mt.s])
mt = hl.sample_qc(mt)

mt.describe()
SLF4J: Failed to load class "org.slf4j.impl.StaticMDCBinder".
SLF4J: Defaulting to no-operation MDCAdapter implementation.
SLF4J: See http://www.slf4j.org/codes.html#no_static_mdc_binder for further details.
----------------------------------------
Global fields:
    None
----------------------------------------
Column fields:
    's': str
    'Population': str
    'SuperPopulation': str
    'isFemale': bool
    'PurpleHair': bool
    'CaffeineConsumption': int32
    'sample_qc': struct {
        dp_stats: struct {
            mean: float64,
            stdev: float64,
            min: float64,
            max: float64
        },
        gq_stats: struct {
            mean: float64,
            stdev: float64,
            min: float64,
            max: float64
        },
        call_rate: float64,
        n_called: int64,
        n_not_called: int64,
        n_filtered: int64,
        n_hom_ref: int64,
        n_het: int64,
        n_hom_var: int64,
        n_non_ref: int64,
        n_singleton: int64,
        n_snp: int64,
        n_insertion: int64,
        n_deletion: int64,
        n_transition: int64,
        n_transversion: int64,
        n_star: int64,
        r_ti_tv: float64,
        r_het_hom_var: float64,
        r_insertion_deletion: float64
    }
----------------------------------------
Row fields:
    'locus': locus<GRCh37>
    'alleles': array<str>
    'rsid': str
    'qual': float64
    'filters': set<str>
    'info': struct {
        AC: array<int32>,
        AF: array<float64>,
        AN: int32,
        BaseQRankSum: float64,
        ClippingRankSum: float64,
        DP: int32,
        DS: bool,
        FS: float64,
        HaplotypeScore: float64,
        InbreedingCoeff: float64,
        MLEAC: array<int32>,
        MLEAF: array<float64>,
        MQ: float64,
        MQ0: int32,
        MQRankSum: float64,
        QD: float64,
        ReadPosRankSum: float64,
        set: str
    }
----------------------------------------
Entry fields:
    'GT': call
    'AD': array<int32>
    'DP': int32
    'GQ': int32
    'PL': array<int32>
----------------------------------------
Column key: ['s']
Row key: ['locus', 'alleles']
----------------------------------------

Histogram

The histogram() method takes as an argument an aggregated hist expression, as well as optional arguments for the legend and title of the plot.

[3]:
dp_hist = mt.aggregate_entries(hl.expr.aggregators.hist(mt.DP, 0, 30, 30))
p = hl.plot.histogram(dp_hist, legend='DP', title='DP Histogram')
show(p)
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This method, like all Hail plotting methods, also allows us to pass in fields of our data set directly. Choosing not to specify the range and bins arguments would result in a range being computed based on the largest and smallest values in the dataset and a default bins value of 50.

[4]:
p = hl.plot.histogram(mt.DP, range=(0, 30), bins=30)
show(p)
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Cumulative Histogram

The cumulative_histogram() method works in a similar way to histogram().

[5]:
p = hl.plot.cumulative_histogram(mt.DP, range=(0,30), bins=30)
show(p)
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Scatter

The scatter() method can also take in either Python types or Hail fields as arguments for x and y.

[6]:
p = hl.plot.scatter(mt.sample_qc.dp_stats.mean, mt.sample_qc.call_rate, xlabel='Mean DP', ylabel='Call Rate')
show(p)
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We can also pass in a Hail field as a label argument, which determines how to color the data points.

[7]:
mt = mt.filter_cols((mt.sample_qc.dp_stats.mean >= 4) & (mt.sample_qc.call_rate >= 0.97))
ab = mt.AD[1] / hl.sum(mt.AD)
filter_condition_ab = ((mt.GT.is_hom_ref() & (ab <= 0.1)) |
                        (mt.GT.is_het() & (ab >= 0.25) & (ab <= 0.75)) |
                        (mt.GT.is_hom_var() & (ab >= 0.9)))
mt = mt.filter_entries(filter_condition_ab)
mt = hl.variant_qc(mt).cache()
common_mt = mt.filter_rows(mt.variant_qc.AF[1] > 0.01)
gwas = hl.linear_regression_rows(y=common_mt.CaffeineConsumption, x=common_mt.GT.n_alt_alleles(), covariates=[1.0])
pca_eigenvalues, pca_scores, _ = hl.hwe_normalized_pca(common_mt.GT)
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[8]:
p = hl.plot.scatter(pca_scores.scores[0], pca_scores.scores[1],
                    label=common_mt.cols()[pca_scores.s].SuperPopulation,
                    title='PCA', xlabel='PC1', ylabel='PC2',
                    n_divisions=None)
show(p)

Hail’s downsample aggregator is incorporated into the scatter(), qq(), join_plot and manhattan() functions. The n_divisions parameter controls the factor by which values are downsampled. Using n_divisions=None tells the plot function to collect all values.

[9]:
p2 = hl.plot.scatter(pca_scores.scores[0], pca_scores.scores[1],
                    label=common_mt.cols()[pca_scores.s].SuperPopulation,
                    title='PCA (downsampled)', xlabel='PC1', ylabel='PC2',
                    n_divisions=50)
show(gridplot([p, p2], ncols=2, width=400, height=400))

2-D histogram

For visualizing relationships between variables in large datasets (where scatter plots may be less informative since they highlight outliers), the histogram_2d() function will create a heatmap with the number of observations in each section of a 2-d grid based on two variables.

[10]:
p = hl.plot.histogram2d(pca_scores.scores[0], pca_scores.scores[1])
show(p)

Q-Q (Quantile-Quantile)

The qq() function requires either a Python type or a Hail field containing p-values to be plotted. This function also allows for downsampling.

[11]:
p = hl.plot.qq(gwas.p_value, n_divisions=None)
p2 = hl.plot.qq(gwas.p_value, n_divisions=75)

show(gridplot([p, p2], ncols=2, width=400, height=400))

Manhattan

The manhattan() function requires a Hail field containing p-values.

[12]:
p = hl.plot.manhattan(gwas.p_value)
show(p)

We can also pass in a dictionary of fields that we would like to show up as we hover over a data point, and choose not to downsample if the dataset is relatively small.

[13]:
hover_fields = dict([('alleles', gwas.alleles)])
p = hl.plot.manhattan(gwas.p_value, hover_fields=hover_fields, n_divisions=None)
show(p)