# -----------------------------------------------------------------------------
# Copyright (C) 2013-2022 Michael I. Love, Constantin Ahlmann-Eltze
# Copyright (C) 2023-2025 Maximilien Colange

# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.

# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.

# You should have received a copy of the GNU General Public License
# along with this program.  If not, see <https://www.gnu.org/licenses/>.
# -----------------------------------------------------------------------------

# This file is based on the file 'R/results.R' of the Bioconductor DESeq2
# package (version 3.16).


import numpy as np
import pandas as pd
import patsy
import scipy.stats
from statsmodels.nonparametric.smoothers_lowess import lowess
from statsmodels.stats.multitest import multipletests

from .. import __version__
from ..diffexp import DEResults
from ..utils import pnorm, pt
from .deseq2_cpp import fitBeta
from .misc import buildDataFrameWithNACols, getFactorName


def p_adjust(pvals, **kwargs):
    """
    Test results and p-value correction for multiple tests

    This is a wrapper around :func:`statsmodels.stats.multitest.multipletests`
    """
    res = np.zeros(pvals.shape)
    pvals_na = pvals.isna()
    res[pvals_na] = np.nan
    res[~pvals_na] = multipletests(pvals[~pvals_na], **kwargs)[1]
    return res


class DESeqResults(DEResults):
    """
    a class to store a results table

    This class would not typically constructed directly by "end users". This
    simple class extends :class:`pandas.DataFrame`. It is used by
    :meth:`.DESeqDataSet.results` to wrap up the results table.

    Attributes
    ----------
    priorInfo : array-like
        a list giving information on the log fold change prior
    """

    _metadata = [
        "priorInfo",
        "filterThreshold",
        "filterTheta",
        "filterNumRej",
        "lo_fit",
        "alpha",
    ]

    @property
    def _constructor(self):
        return DESeqResults

    @property
    def _constructor_sliced(self):
        return pd.Series

    def __init__(self, df, priorInfo=None, *args, **kwargs):
        super().__init__(df, *args, **kwargs)
        if priorInfo is not None:
            self.priorInfo = priorInfo

    def summary(self, alpha=None):
        """
        Print a summary of the results from a DESeq analysis.

        Arguments
        ---------
        alpha : float, optional
            the adjusted p-value cutoff. If not set, this defaults to the
            :code:`alpha` argument which was used in :meth:`results` to set the
            target FDR for independent filtering, or if independent filtering
            was not performed, to 0.1.

        Returns
        -------
        str
            a summary (multi-line) string
        """
        sval = "svalue" in self.columns
        if sval:
            test_col = "svalue"
            test_col_name = "s-value"
        else:
            test_col = "adj_pvalue"
            test_col_name = "adjusted p-value"

        if alpha is None:
            if sval:
                alpha = 0.005
            elif self.alpha is None:
                alpha = 0.1
            else:
                alpha = self.alpha

        if self.lfcThreshold is not None:
            T = self.lfcThreshold
            pT = f"{T:.2f} (up)    "
            mT = f"{-T:.2f} (down) "
        else:
            T = 0
        if T == 0:
            pT = "0 (up)       "
            mT = "0 (down)     "

        res = "\n"
        notallzero = (self.baseMean > 0).sum()
        up = np.nansum((self[test_col] < alpha) & (self["log2FoldChange"] > T))
        down = np.nansum((self[test_col] < alpha) & (self["log2FoldChange"] < -T))
        if not sval:
            filt = (~(self["pvalue"].isna()) & self["adj_pvalue"].isna()).sum()
            outlier = ((self["baseMean"] > 0) & self["pvalue"].isna()).sum()
            if self.filterThreshold is None:
                ft = 0
            else:
                ft = round(self.filterThreshold)

        ihw = (not sval) and "ihwResult" in self.columns

        res += f"out of {notallzero} with nonzero total read count\n"
        res += f"{test_col_name} < {alpha}\n"
        res += f"LFC > {pT}: {up}, {up / notallzero * 100:.2f}%\n"
        res += f"LFC < {mT}: {down}, {down / notallzero * 100:.2f}%\n"
        if not sval:
            res += (
                f"outliers [1]       : {outlier}, {outlier / notallzero * 100:.2f}%\n"
            )
        if not sval and not ihw:
            res += f"low counts [2]     : {filt}, {filt / notallzero * 100:.2f}%\n"
        if not sval and not ihw:
            res += f"(mean count < {ft})\n"
        if not sval:
            res += "[1] see 'cooksCutoff' argument of results()\n"
        if not sval and not ihw:
            res += "[2] see 'independentFiltering' argument of results()\n"
        if ihw:
            res += "see res['ihwResult'] on hypothesis weighting\n"

        return res


def results_dds(
    obj,
    contrast=None,
    name=None,
    lfcThreshold=0,
    altHypothesis="greaterAbs",
    listValues=(1, -1),
    cooksCutoff=None,
    independentFiltering=True,
    alpha=0.1,
    filter=None,
    theta=None,
    pAdjustMethod="fdr_bh",
    filterRun=None,
    saveCols=None,
    test=None,
    addMLE=False,
    tidy=False,
    parallel=False,
    minmu=0.5,
):
    r"""
    Extract results from a :func:`.DESeq` analysis

    This function extracts a result table from a DESeq analysis giving base
    means across samples, log2 fold changes, standard errors, test statistics,
    p-values and adjusted p-values.

    The results table when printed will provide the information about the
    comparison, *e.g.* "log2 fold change (MAP): condition treated vs.
    untreated", meaning that the estimates are of lof2(treated / untreated), as
    would be returned using :code:`contrast=c("condition", "treated",
    "untreated")`. Multiple results can be returned for analyses beyond a
    simple two group comparison, so this function takes arguments
    :code:`contrast` and :code:`name` to help the user pick out the comparisons
    of interest for printing a results table. The use of the :code:`contrast`
    argument is recommended for exact specification of the levels which should
    be compared and their order.

    If :code:`results` is run without specifying :code:`contrast` or
    :code:`name`, it will return the comparison of the last level of the last
    variable in the design formula over the first level of this variable. For
    example, for a simple two-group comparison, this would return the log2 fold
    changes of the second group over the first group (the reference level).

    The argument :code:`contrast` can be used to generate results tables for
    any comparison of interest, for example, the log2 fold change between two
    levels of a factor, and its usage is described below. It can also
    accomodate more complicated numeric comparisons. Note that :code:`contrast`
    will set to 0 the estimated LFC in a comparison of two groups, where all
    the counts in the two groups are equal to 0 (while other groups have
    positive counts), while :code:`name` will not automatically set these LFC
    to 0.  The test statistic used for a contrast is: :math:`c^t \\beta /
    \sqrt{c^t \Sigma c}`.

    The argument :code:`name` can be used to generate results tables for
    individual effects, which must be individual elements of
    :code:`obj.resultsNames()`.  These individual effects could represent
    continuous covariates, effects for individual levels, or individual
    interaction effects.

    Information on the comparison which was used to build the results table,
    and the statistical test which was used for p-values (Wald test or
    likelihood ratio test) is stored within the object returned by
    :meth:`results()`. This information is stored in the columns of the results
    table (see :class:`.DESeqResults`).

    .. rubric:: On p-values

    By default, independent filtering is performed to select a set of genes for
    multiples test correction which maximizes the number of adjusted p-values
    less than a given critical value :code:`alpha` (by default 0.1). See the
    reference in this page for details on independent filtering. The filter
    used for maximizing the number of rejections is the mean of normalized
    counts for all samples in the dataset. Several arguments from
    :func:`.filtered_p` of the genefilter package (used within :meth:`results`)
    are provided here to control the independent filtering behavior. Note that
    the code of :func:`.filtered_p` is copied into this package to avoid extra
    dependencies).

    The threshold that is chosen is the lowest quantile of the filter for which
    the number of rejections is close to the peack of a curve fit to the number
    of rejections over the filter quantiles. "Close to" is defined as within 1
    residuel standard deviation. The adjusted p-values for the genes which do
    not pass the filter threshold are set to :code:`nan`.

    By default, :meth:`results` assigns a p-value of :code:`nan` to genes
    containing count outliers, as identified using Cook's distance. See the
    :code:`cooksCutoff` argument for control of this behavior. Cook's distances
    for each sample are accessible as :code:`obj.layers["cooks"]`. This measure
    is useful for identifying rows where the observed counts might not fit to a
    Negative Binomial distribution.

    For analyses using the likelihood ratio test (using :func:`.nbinomLRT`),
    the p-values are determined solely by the difference in deviance between
    the full and reduced model formula. A single log2 fold change is printed in
    the results table for consistenct with other results table outputs, however
    the test statistic and p-values may nevertheless involve the testing of one
    or more log2 fold changes. Which log2 fold change is printed in the results
    table can be controlled using the :code:`name` argument, or by default this
    will be the estimated coefficient for the last element of
    :code:`obj.resultsNames()`.

    If :code:`useT = True` was specified when running :func:`.DESeq` or
    :func:`.nbinomWaldTest`, the the p-value generated by :meth:`results` will
    also make use of the t-distribution for the Wald statistic, using the
    degrees of freedom in :code:`obj.var["tDegreesFreedom"]`.

    Arguments
    ---------
    obj : DESeqDataSet
        a :class:`DESeqDataSet` one which one of the following function has
        already been called: :func:`.DESeq`, :func:`.nbinomWaldTest` or
        :func:`.nbinomLRT`.
    contrast
        this argument specifies what comparison to extract from :code:`obj` to
        build a results table. One of either:

        + a list of exactly three strings (simplest case):
            - the name of a factor in the design formula
            - the name of the numerator level for the fold change
            - the name of the denominator level for the fold change
        + a list of two string lists (more general case):
            - the names of the numerators for LFC
            - the names of the denominators for LFC
          These names should be elements of :code:`obj.resultsNames()`.
          If the list has a single element (the numerators) then the
          denominator list is considered empty.
        + a numeric list with one element for each element in
          :code:`obj.resultsNames()` (most general case)

        If specified, the :code:`name` argument is ignored.
    name : str
        the name of the individual effect (coefficient) for building a results
        table. Use this argument rahter than :code:`contrast` for continuous
        variables, individual effects or for individual interaction terms. The
        value provided to :code:`name` must be an element of
        :code:`obj.resultsNames()`.
    lfcThreshold : float
        a non-negative value which specifies a log2 fold change threshold. The
        default value is 0, corresponding to a test that the log2 fold changes
        are equal to zero. The user can specify the alternative hypothesis
        using the :code:`altHypothesis` argument, which defaults to testing for
        log2 fold changes greater in absolute value than a given threshold. If
        :code:`lfcThreshold` is specified, the results are for Wald tests, and
        LRT p-values will be overwritten.
    altHypothesis : str
        specifies the alternative hypothesis, *i.e.* those values of log2 fold
        change which the user is interested in finding. the complement of this
        set of values is the null hypothesis which will be tested. If the log2
        fold change specified by :code:`name` or by :code:`contrast` is written
        as :math:`\\beta`, then the possible values for :code:`altHypothesis`
        represent the following alternative hypotheses:

        * :code:`"greaterAbs"`: :math:`|\\beta| > \\text{lfcThreshold}`, and
          p-values are two-tailed
        * :code:`"lessAbs"`: :math:`|\\beta| < \\text{lfcThreshold}`, and
          p-values are the maximum of the upper and lower tests. The Wald
          statistic given is positive, an SE-scaled distance from the closest
          boundary
        * :code:`"greater"`: :math:`\\beta > \\text{lfcThreshold}`
        * :code:`"less"`: :math:`\\beta < \\text{lfcThreshold}`

    listValues : (float, float)
        only used if a numerators-denominators list is provided to
        :code:`contrast`.  The log2 fold changes in the list are multiplied by
        these values. The first number should be positive and the second one
        negative. Defaults to :code:`(1,-1)`.
    cooksCutoff : float
        threshold on Cook's distance, such that if one or more samples for a
        gene have a distance higher, the corresponding p-value is set to
        :code:`nan`. The default cutoff is the .99 quantile of the :math:`F(p,
        m-p)` distribution, where :math:`p` is the number of coefficients being
        fitted, and :math:`m` is the number of samples. Set to :code:`inf` or
        :code:`False` to disable the resetting of p-values to :code:`nan`.
        Note: this test excludes the Cook's distance of samples belonging to
        experimental groups with only 2 samples.
    independentFiltering : bool
        whether independent filtering should be applied automatically
    alpha : float
        the significance cutoff used for optimizing the independent filtering
        (defaults to 0.1). If the adjusted p-value cutoff (FDR) will be a value
        other than 0.1, :code:`alpha` should be set to that value.
    filter
        the vector of filter statistics over which the independent filtering
        will be optimized. By default, the mane of normalized counts is used.
    theta : array-like
        the quantiles at which to assess the number of rejections from
        independent filtering
    pAdjustMethod : str
        the method to use to adjust p-values, see :func:`.p_adjust`
    filterRun
        an optional custom function for performing independent filtering and
        p-value adjustment, with arguments :code:`res` (a
        :class:`.DESeqResults` object), :code:`filter` (the quantity for
        filtering tests), :code:`alpha` (the target FDR),
        :code:`pAdjustMethod`. This function should resturn a
        :class:`.DESeqResults` object with a :code:`adj_pvalue` column.
    saveCols : array-like
        the columns of :code:`obj.var` to pass into the output results table
    test : { "Wald", "LRT" }
        automatically detected if not provided. The one exception is after
        :func:`.nbinomLRT` has been run, :code:`test="Wald"` will generate Wald
        statistics and Wald test p-values.
    addMLE : bool
        if :code:`betaPrio=True` was used (non-default). This argument
        specifies if the "unshrunken" maximum likelihood estimates (MLE) of
        log2 fold change should be added as a column to the results table
        (defaults to :code:`False`).  This argument is preserved for backward
        compatibility, as now :code:`betaPrior=True` by default and the
        recommended pipeline is to generate shrunken MAP estimates using
        :func:`lfcShrink`. This argument functionality is only implemented for
        :code:`contrast` specified as a 3-element string list.
    tidy : bool
        whether to output the results table with a header
    parallel : bool
        unimplemented
    minmu : float
        lower bound on the estimated count (used when calculating contrasts)

    Returns
    -------
    DESeqResults
        a results table (subclass of :class:`~.DEResults`), containing the
        following results columns: :code:`"baseMean"`,
        :code:`"log2FoldChange"`, :code:`"lfcSE"`, :code:`"stat"`,
        :code:`"pvalue"` and :code:`"pad"`.  The :code:`"lfcSE"` gives the
        standard error of the :code:`"log2FoldChange"`.  For the Wald test,
        :code:`"stat"` is the Wald statistic: the :code:`"log2FoldChange"`
        divided by :code:`"lfcSE"`, which is compared to a standard Normal
        distribution to generate a two-tailed :code:`"pvalue"`.  For the
        likelihood ratio test (LRT), :code:`"stat"` is the difference in
        deviance between the reduced model and the full model, which is
        compared to a chi-squared distribution to generate a :code:`"pvalue"`.
    """
    if altHypothesis not in ["greaterAbs", "lessAbs", "greater", "less"]:
        raise ValueError(f"invalid value for altHypothesis: {altHypothesis}")
    if test not in [None, "Wald", "LRT"]:
        raise ValueError(f"invalid value for test: {test}")

    # initial argument testing
    if lfcThreshold < 0:
        raise ValueError("lfcThreshold should be positive")
    if alpha <= 0 or alpha >= 1:
        raise ValueError("alpha should be between 0 and 1")
    if not isinstance(listValues, (tuple, list)) or len(listValues) != 2:
        raise ValueError("listValues should be of length 2")
    if listValues[0] <= 0 or listValues[1] >= 0:
        raise ValueError("listValues should contain a positive and a negative number")
    if obj.var.type.filter(["results"]).empty:
        raise ValueError("could not find results in obj. first run DESeq()")
    if test is None:
        test = obj.test
    elif test == "Wald" and obj.test == "LRT":
        # initially test was LRT, now need to add Wald statistics and p-values
        raise NotImplementedError(
            "adding Wald statistics to LRT object is not implemented"
        )
        # obj = makeWaldTest(obj)
    elif test == "LRT" and obj.test == "Wald":
        raise ValueError(
            "the LRT requires the user to run nbinomLRT or DESeq(obj, test='LRT')"
        )
    if lfcThreshold == 0 and altHypothesis == "lessAbs":
        raise ValueError(
            "when testing altHypothesis='lessAbs', set the argument lfcThreshold to a positive value"
        )

    if addMLE:
        if obj.betaPrior is None:
            raise ValueError(
                "addMLE=True is only for when a beta prior was used. Otherwise, the log2 fold changes are already MLE"
            )
        if name is not None and contrast is None:
            raise ValueError(
                "addMLE=True should be used by providing string vector of length 3 to 'contrast' instead of using 'name'"
            )

    if saveCols is not None:
        try:
            obj.var[saveCols]
        except KeyError:
            raise ValueError(f"invalid value for saveCols: {saveCols}")

    hasIntercept = patsy.INTERCEPT in obj.design.design_info.terms
    isExpanded = obj.modelMatrixType == "expanded"
    noInteraction = all(len(t.factors) < 2 for t in obj.design.design_info.terms)
    # if no intercept was used or an expanded model matrix was used,
    # and neither 'contrast' nor 'name' were specified,
    # and no interactions...
    # then we create the result table: last / first level for last variable
    if (
        test == "Wald"
        and (isExpanded or not hasIntercept)
        and contrast is None
        and name is None
        and noInteraction
    ):
        designVars = [v for v in obj.design.design_info.factor_infos.values()]
        lastVarName = designVars[-1].factor.name()
        if designVars[-1].type == "categorical":
            if lastVarName.startswith("C("):
                lastVar = obj.obs[lastVarName]
            else:
                lastVar = obj.obs[f"C({lastVarName})"]
            contrast = [
                lastVarName,
                f"{lastVar.dtype.categories[-1]}",
                f"{lastVar.dtype.categories[0]}",
            ]

    if name is None:
        name = lastCoefName(obj)
    else:
        if not isinstance(name, str):
            raise ValueError("'name' should be a string")

    # done with input argument testing

    # this will be used in cleanContrast, and in the lfcThreshold chunks below
    useT = "tDegreesFreedom" in obj.var

    # if performing a contrast call the function cleanContrast()
    if contrast is not None:
        resNames = obj.resultsNames()
        # do some arg checking/cleaning
        contrast = checkContrast(contrast, resNames)

        ### cleanContrast call ###
        # need to go back to C++ code in order to build the beta covariance matrix
        # then this is multiplied by the numeric contrast to get the Wald statistic.
        # with 100s of samples, this can get slow, so offer parallelization
        if not parallel:
            res = cleanContrast(
                obj,
                contrast,
                expanded=isExpanded,
                listValues=listValues,
                test=test,
                useT=useT,
                minmu=minmu,
            )
        else:
            raise NotImplementedError("parallelization not implemented yet")

    else:
        # if not performing a contrast
        # pull relevant columns from obj.var
        log2FoldChange = getCoef(obj, name)
        lfcSE = getCoefSE(obj, name)
        stat = getStat(obj, name, test)
        pvalue = getPvalue(obj, name, test)
        res = pd.DataFrame(
            {
                "baseMean": obj.var["baseMean"],
                "log2FoldChange": log2FoldChange,
                "lfcSE": lfcSE,
                "stat": stat,
                "pvalue": pvalue,
            }
        )

    res.index = obj.var_names

    # add unshrunken MLE coefficients to the results table
    if addMLE:
        if not isinstance(contrast, (tuple, list)) or len(contrast) != 3:
            raise ValueError(
                "addMLE only implemented for contrast=['condition', 'B', 'A']"
            )
        res = pd.concat([res, mleContrast(obj, contrast)], axis=1)
        res = res[["baseMean", "log2FoldChange", "lfcMLE", "lfcSE", "stat", "pvalue"]]
        # if an all zero contrast, also zero out the lfcMLE
        res.loc[(res["log2FoldChange"] == 0) & (res["stat"] == 0), "lfcMLE"] = 0

    # only if we need to generate new p-values
    if not (lfcThreshold == 0 and altHypothesis == "greaterAbs"):
        if test == "LRT":
            raise ValueError(
                "tests of log fold change above or below a threshold must be Wald test."
            )
        # check requirement if betaPrior was set to False
        if altHypothesis == "lessAbs" and obj.betaPrior:
            raise ValueError(
                "testing altHypothesis='lessAbs' requires setting the DESeq() argument betaPrior=False"
            )

        # easier to read
        LFC = res.log2FoldChange
        SE = res.lfcSE
        T = lfcThreshold

        if useT:
            df = obj.var["tDegreesFreedom"]

            def pfunc(q):
                return pt(q, df=df, lower_tail=False)
        else:

            def pfunc(q):
                return pnorm(q, lower_tail=False)

        if altHypothesis == "greaterAbs":
            newStat = np.sign(LFC) * np.maximum((np.abs(LFC) - T) / SE, 0)
            newPvalue = np.minimum(1, 2 * pfunc((np.abs(LFC) - T) / SE))
        elif altHypothesis == "lessAbs":
            newStatAbove = np.maximum((T - LFC) / SE, 0)
            pvalueAbove = pfunc((T - LFC) / SE)
            newStatBelow = np.maximum((LFC + T) / SE, 0)
            pvalueBelow = pfunc((LFC + T) / SE)
            newStat = np.minimum(newStatAbove, newStatBelow)
            newPvalue = np.maximum(pvalueAbove, pvalueBelow)
        elif altHypothesis == "greater":
            newStat = np.maximum((LFC - T) / SE, 0)
            newPvalue = pfunc((LFC - T) / SE)
        elif altHypothesis == "less":
            newStat = np.minimum((LFC + T) / SE, 0)
            newPvalue = pfunc((-T - LFC) / SE)

        res.stat = newStat
        res.pvalue = newPvalue

    # calculate Cook's cutoff
    m, p = obj.dispModelMatrix.shape

    if cooksCutoff is None or (isinstance(cooksCutoff, bool) and cooksCutoff):
        cooksCutoff = scipy.stats.f.ppf(0.99, p, m - p)

    # apply cutoff based on maximum Cook's distance
    # NB: cooksCutoff is not necessarily a Boolean
    performCooksCutoff = not (cooksCutoff == False)  # noqa: E712
    if performCooksCutoff:
        cooksOutlier = obj.var["maxCooks"] > cooksCutoff

        # BEGIN heuristic to avoid filtering genes with low count outliers
        # as according to Cook's cutoff. only for two group designs.
        # do not filter if three or more counts are larger
        if np.any(cooksOutlier[~np.isnan(cooksOutlier)]):
            designVars = obj.design.design_info.factor_infos
            if len(designVars) == 1:
                var = [v for v in designVars.values()][0]
                if var.type == "categorical" and len(var.categories) == 2:
                    maxIndices = np.argmax(obj.layers["cooks"][:, cooksOutlier], axis=0)
                    outliers = obj.counts()[:, cooksOutlier]
                    # counts for the outliers with max cooks
                    outCount = np.take_along_axis(
                        outliers, maxIndices[None], 0
                    ).squeeze()
                    # if three or more counts larger than the outlier
                    # do not filter out the p-value for those genes
                    dontFilter = np.sum(outliers > outCount, axis=0) >= 3
                    # reset the outlier status for these genes
                    # NB: pandas 2.2 raises a warning here, but it should not. See
                    #     https://github.com/pandas-dev/pandas/issues/57338
                    cooksOutlier[cooksOutlier] &= ~dontFilter
        # END heuristic

        res.loc[cooksOutlier, "pvalue"] = np.nan

    # if original baseMean was positive, but now zero due to replaced counts,
    # fill in results
    if "replace" in obj.var and np.nansum(obj.var["replace"]) > 0:
        nowZero = obj.var["replace"] & (obj.var["baseMean"] == 0)
        res.loc[nowZero, "log2FoldChange"] = 0
        if addMLE:
            res.loc[nowZero, "lfcMLE"] = 0
        res.loc[nowZero, "lfcSE"] = 0
        res.loc[nowZero, "stat"] = 0
        res.loc[nowZero, "pvalue"] = 1

    # add prior information
    if not obj.betaPrior:
        priorInfo = {
            "type": "none",
            "package": "inmoose.deseq2",
            "version": __version__,
        }
    else:
        priorInfo = {
            "type": "normal",
            "package": "inmoose.deseq2",
            "version": __version__,
            "betaPriorVar": obj.betaPriorVar,
        }

    # make results object
    deseqRes = DESeqResults(res, priorInfo=priorInfo)

    # p-value adjustment
    if filterRun is None:
        deseqRes = pvalueAdjustment(
            deseqRes, independentFiltering, filter, theta, alpha, pAdjustMethod
        )
    else:
        deseqRes = filterRun(deseqRes, filter, alpha, pAdjustMethod)

    # stash lfcThreshold
    deseqRes.lfcThreshold = lfcThreshold

    # remove rownames and attach a new column 'row'
    if tidy:
        raise NotImplementedError()

    if saveCols is not None:
        deseqRes.mrows2Save = obj.var[saveCols]

    return deseqRes


def lastCoefName(obj):
    """convenience function to guess the name of the last coefficient
    in the model matrix, unless specified this will be used for plots and
    accessor functions.
    """
    return obj.resultsNames()[-1]


def getCoef(obj, name):
    if name is None:
        name = lastCoefName(obj)
    return obj.var[name]


def getCoefSE(obj, name):
    if name is None:
        name = lastCoefName(obj)
    return obj.var[f"SE_{name}"]


def getStat(obj, name, test="Wald"):
    if name is None:
        name = lastCoefName(obj)

    if test == "Wald":
        return obj.var[f"WaldStatistic_{name}"]
    elif test == "LRT":
        return obj.var["LRTStatistic"]
    else:
        raise ValueError(f"unknown test: {test}")


def getPvalue(obj, name, test="Wald"):
    if name is None:
        name = lastCoefName(obj)

    if test == "Wald":
        return obj.var[f"WaldPvalue_{name}"]
    elif test == "LRT":
        return obj.var["LRTPvalue"]
    else:
        raise ValueError(f"unknown test: {test}")


def pvalueAdjustment(res, independentFiltering, filter, theta, alpha, pAdjustMethod):
    # perform independent filtering
    if independentFiltering:
        if filter is None:
            filter = res.baseMean
        if theta is None:
            lowerQuantile = np.mean(filter == 0)
            if lowerQuantile < 0.95:
                upperQuantile = 0.95
            else:
                upperQuantile = 1.0
            theta = np.linspace(lowerQuantile, upperQuantile, 50)

        # do filtering using genefilter
        if len(theta) <= 1:
            raise ValueError("theta should be a list")
        if len(filter) != res.shape[0]:
            raise ValueError("filter should have as many elements as res has rows")
        filtPadj = filtered_p(
            filter_=filter, test=res.pvalue, theta=theta, method=pAdjustMethod
        )
        numRej = np.nansum(filtPadj < alpha, axis=0)
        # prevent over-aggressive filtering when all genes are null,
        # by requiring the max number of rejections is above a fitted curve.
        # If the max number of rejection is not greater than 10, then don't
        # perform independent filtering at all.
        lo_fit = lowess(numRej, theta, frac=1 / 5)
        if np.max(numRej) <= 10:
            j = 0
        else:
            if np.all(numRej == 0):
                residual = 0
            else:
                residual = numRej[numRej > 0] - lo_fit[numRej > 0, 1]
            thresh = np.max(lo_fit[:, 1]) - np.sqrt(np.mean(residual**2))
            if np.any(numRej > thresh):
                j = np.nonzero(numRej > thresh)[0][0]
            else:
                j = 0

        adj_pvalue = filtPadj[:, j]
        cutoffs = np.quantile(filter, theta)
        filterThreshold = cutoffs[j]
        filterNumRej = pd.DataFrame({"theta": theta, "numRej": numRej})
        filterTheta = theta[j]

        res.filterThreshold = filterThreshold
        res.filterTheta = filterTheta
        res.filterNumRej = filterNumRej
        res.lo_fit = lo_fit
        res.alpha = alpha

    else:
        # regular p-value adjustment
        # does not include those rows which were removed
        # by maximum Cook's distance
        adj_pvalue = p_adjust(res.pvalue, method=pAdjustMethod)

    res["adj_pvalue"] = adj_pvalue
    res.type["adj_pvalue"] = "results"
    res.description["adj_pvalue"] = f"{pAdjustMethod} adjusted p-values"

    return res


def filtered_p(filter_, test, theta, method, data=None):
    """
    compute and adjust p-values, with filtering

    Given filter and test statistics in the form of unadjusted p-values, or
    functions able to compute these statistics from the data, filter and then
    correct the p-values across a range of filtering stringencies.

    NB: this function is copied and ported from the R package `genefilter
    <https://bioconductor.org/packages/release/bioc/html/genefilter.html>`_.
    This copy was already done in the original DESeq2 R code.

    Arguments
    ---------
    filter_
        a list of stage-one filter statistics, or a function which is able to
        compute such a list from :code:`data`, if :code:`data` is supplied
    test
        a list of unadjusted p-values, or a function which is able to compute
        such a list from the filtered portions of :code:`data`, if :code:`data`
        is supplied. The option to supply a function is useful when the value
        of the test statistic depends on which hypotheses are filtered out at
        stage one.
    theta
        a list with one or more filtering fractions to consider. Actual cutoffs
        are then computed internally by applying :code:`quantile` to the filter
        statistics contained in (or produced by) the :code:`filter_` argument.
    method
        the unadjusted p-values contained in (or produced by) :code:`test` will
        be adjusted for multiple testing after filtering, using
        :func:`p_adjust`. See the :code:`method` argument of this function for
        more options.
    data
        if :code:`filter_` and/or :code:`test` are functions rather than lists
        of statistics, they will be applied to :code:`data`. The functions will
        be passed the whole :code:`data` object, and must work over rows etc.
        themselves as appropriate.

    Returns
    -------
    ndarray
        a matrix of p-values, possibly adjusted for multiple testing, with one
        row per  null hypothesis and one column per filtering fraction given in
        :code:`theta`. For a given column, entries which have been filtered out
        are :code:`nan`.
    """
    if callable(filter_):
        U1 = filter_(data)
    else:
        U1 = filter_

    cutoffs = np.quantile(U1, theta)
    result = np.full((len(U1), len(cutoffs)), np.nan)
    for i in range(len(cutoffs)):
        use = U1 >= cutoffs[i]
        if np.any(use):
            if callable(test):
                U2 = test(data[use, :])
            else:
                U2 = test[use]
            result[use, i] = p_adjust(U2, method=method)
    return result


def getContrast(obj, contrast, useT, minmu):
    """takes a DESeqDataSet obj and a numeric vector specifying a contrast
    and returns a vector of Wald statistics corresponding to the contrast.
    """
    if contrast is None:
        raise ValueError("must provide a contrast")
    modelMatrix = obj.modelMatrix

    # only continue on the cols with non-zero col mean
    objNZ = obj[:, ~obj.var["allZero"]]
    normalizationFactors = objNZ.getSizeOrNormFactors()
    alpha_hat = objNZ.var["dispersion"]
    # convert beta to log scale
    beta_mat = np.log(2) * objNZ.var.description.filter(regex="log2 fold change")
    # convert beta prior variance to log scale
    lambda_ = 1 / (np.log(2) ** 2 * obj.betaPriorVar)

    # check if DESeq() replaced outliers
    if "replaceCounts" in obj.layers:
        countsMatrix = objNZ.layers["replaceCounts"]
    else:
        countsMatrix = objNZ.counts()

    # use weights if they are present
    if "weights" in obj.layers:
        useWeights = True
        weights = objNZ.layers["weights"]
        if not np.all(weights >= 0):
            raise ValueError("all weights must be positive")
        weights = weights / np.max(weights, axis=0)
    else:
        useWeights = False
        weights = np.ones(objNZ.shape)

    betaRes = fitBeta(
        y=countsMatrix,
        x=modelMatrix,
        nf=normalizationFactors,
        alpha_hat=alpha_hat.values,
        contrast=contrast,
        beta_mat=beta_mat.values,
        lambda_=lambda_,
        weights=weights,
        useWeights=useWeights,
        tol=1e-8,
        maxit=0,
        useQR=False,  # QR not relevant, fitting loop is not entered
        minmu=minmu,
    )
    # convert back to log2 scale
    contrastEstimate = np.log2(np.exp(1)) * betaRes["contrast_num"]
    contrastSE = np.log2(np.exp(1)) * betaRes["contrast_denom"]
    contrastStatistic = contrastEstimate / contrastSE

    if useT:
        if "tDegreesFreedom" not in obj.var:
            raise ValueError("tDegreesFreedom should be in obj.var")
        df = objNZ.var["tDegreesFreedom"]
        contrastPvalue = 2 * pt(np.abs(contrastStatistic), df=df, lower_tail=False)
    else:
        contrastPvalue = 2 * pnorm(np.abs(contrastStatistic), lower_tail=False)

    contrastResults = pd.DataFrame(
        {
            "log2FoldChange": contrastEstimate,
            "lfcSE": contrastSE,
            "stat": contrastStatistic,
            "pvalue": contrastPvalue,
        }
    )
    contrastResults = buildDataFrameWithNACols(contrastResults, obj.var["allZero"])
    contrastResults.index = obj.var_names
    return contrastResults


def cleanContrast(obj, contrast, expanded, listValues, test, useT, minmu):
    """this function takes a desired contrast as specified by results(),
    performs checks, and then either returns the already existing contrast
    or generates the contrast by calling getContrast() using a numeric vector
    """
    # get the names of columns in the beta matrix
    resNames = obj.resultsNames()
    # if possible, return pre-computed columns, which are
    # already stored in obj.var. This will be the case using
    # results() with 'name', or if expanded model matrices were not
    # run and the contrast contains the reference level as numerator and denominator

    resReady = False

    if all(isinstance(c, str) for c in contrast):
        contrastFactor = contrast[0]
        if not contrastFactor.startswith("C("):
            contrastFactor = f"C({contrastFactor})"
        contrastFactorName = getFactorName(contrastFactor)
        if contrastFactorName not in obj.obs:
            raise ValueError(
                f"{contrastFactorName} should be the name of a factor in the obs data of the DESeqDataSet"
            )
        if contrastFactor not in obj.obs or not isinstance(
            obj.obs[contrastFactor].dtype, pd.api.types.CategoricalDtype
        ):
            raise ValueError(f"{contrastFactorName} is not a factor")

        contrastNumLevel = contrast[1]
        contrastDenomLevel = contrast[2]
        # make sure contrastBaseLevel is a string
        contrastBaseLevel = f"{obj.obs[contrastFactor].dtype.categories[0]}"

        # check for intercept
        hasIntercept = 0 in [len(t.factors) for t in obj.design.design_info.terms]
        firstVar = (
            contrast[0]
            == [t.name() for t in obj.design.design_info.terms if len(t.factors) > 0][0]
        )

        # tricky case: if the design has no intercept, the factor is not the
        # first variable in the design, and one of the numerator or
        # denominator is the reference level, then the desired contrast is
        # simply a coefficient (or -1 times)
        noInterceptPullCoef = (
            not hasIntercept
            and not firstVar
            and (contrastBaseLevel in [contrastNumLevel, contrastDenomLevel])
        )

        # case 1: standard model matrices: pull coef or build the appropriate contrast
        # coefficients names are of the form "factor_level_vs_baselevel"
        # output: contrastNumColumn and contrastDenomColumn
        if not expanded and (hasIntercept or noInterceptPullCoef):
            contrastNumColumn = (
                f"{contrastFactorName}_{contrastNumLevel}_vs_{contrastBaseLevel}"
            )
            contrastDenomColumn = (
                f"{contrastFactorName}_{contrastDenomLevel}_vs_{contrastBaseLevel}"
            )
            # check that the desired contrast is already available in obj.var,
            # and then we can either take it directly or multiply the log fold
            # change and Wald stat by -1
            if contrastDenomLevel == contrastBaseLevel:
                cleanName = (
                    f"{contrastFactorName} {contrastNumLevel} vs {contrastDenomLevel}"
                )
                # the results can be pulled directly from obj.var
                if hasIntercept or not firstVar:
                    name = f"{contrastFactorName}_{contrastNumLevel}_vs_{contrastDenomLevel}"
                else:
                    name = f"{contrastFactorName}[{contrastNumLevel}]"

                if name not in resNames:
                    raise ValueError(
                        f"as {contrastDenomLevel} is the reference level, was expecting {name} to be present in 'resultsNames(obj)'"
                    )

                log2FoldChange = getCoef(obj, name)
                lfcSE = getCoefSE(obj, name)
                stat = getStat(obj, name, test)
                pvalue = getPvalue(obj, name, test)
                res = pd.DataFrame(
                    {
                        "baseMean": obj.var["baseMean"],
                        "log2FoldChange": log2FoldChange,
                        "lfcSE": lfcSE,
                        "stat": stat,
                        "pvalue": pvalue,
                    }
                )
                lfcType = "MAP" if obj.betaPrior else "MLE"
                res.description["log2FoldChange"] = (
                    f"log2 fold change ({lfcType}): {cleanName}"
                )
                resReady = True

            elif contrastNumLevel == contrastBaseLevel:
                # fetch the results for denom vs num
                # and multiply the log fold change and stat by -1
                cleanName = (
                    f"{contrastFactorName} {contrastNumLevel} vs {contrastDenomLevel}"
                )
                if hasIntercept or not firstVar:
                    swapName = f"{contrastFactorName}_{contrastDenomLevel}_vs_{contrastNumLevel}"
                else:
                    swapName = f"{contrastFactorName}[{contrastDenomLevel}]"

                if swapName not in resNames:
                    raise ValueError(
                        f"as {contrastNumLevel} is the reference level, was expecting {swapName} to be present in resultsNames(obj)"
                    )

                log2FoldChange = getCoef(obj, swapName)
                lfcSE = getCoefSE(obj, swapName)
                stat = getStat(obj, swapName, test)
                pvalue = getPvalue(obj, swapName, test)
                res = pd.DataFrame(
                    {
                        "baseMean": obj.var["baseMean"],
                        "log2FoldChange": log2FoldChange,
                        "lfcSE": lfcSE,
                        "stat": stat,
                        "pvalue": pvalue,
                    }
                )
                res["log2FoldChange"] *= -1
                if test == "Wald":
                    res["stat"] *= -1
                lfcType = "MAP" if obj.betaPrior else "MLE"
                res.description["log2FoldChange"] = (
                    f"log2 fold change ({lfcType}): {cleanName}"
                )
                res.description["lfcSE"] = f"standard error: {cleanName}"
                # rename some of the columns using the flipped contrast
                if test == "Wald":
                    res.description["stat"] = f"Wald statistic: {cleanName}"
                    res.description["pvalue"] = f"Wald test p-value: {cleanName}"

                resReady = True

            else:
                # check for the case where neither are present
                # as comparisons against reference level
                if not (
                    contrastNumColumn in resNames and contrastDenomColumn in resNames
                ):
                    raise ValueError(
                        f"{contrastNumLevel} and {contrastDenomLevel} should be levels of {contrastFactorName} such that {contrastNumLevel} and {contrastDenomLevel} are contained in 'resultsNames(obj)'"
                    )

        # case 2: expanded model matrices or no intercept and first variable
        # need to then build the appropriate contrast.
        # these coefficient names have the form "factorLevel"
        # output: contrastNumColumn and contrastDenomColumn
        else:
            # we only need to check validity
            if hasIntercept:
                contrastNumColumn = f"{contrastFactorName}[T.{contrastNumLevel}]"
                contrastDenomColumn = f"{contrastFactorName}[T.{contrastDenomLevel}]"
            elif not firstVar:
                contrastNumColumn = (
                    f"{contrastFactorName}_{contrastNumLevel}_vs_{contrastBaseLevel}"
                )
                contrastDenomColumn = (
                    f"{contrastFactorName}_{contrastDenomLevel}_vs_{contrastBaseLevel}"
                )
            else:
                contrastNumColumn = f"{contrastFactorName}[{contrastNumLevel}]"
                contrastDenomColumn = f"{contrastFactorName}[{contrastDenomLevel}]"
            if not (contrastNumColumn in resNames and contrastDenomColumn in resNames):
                raise ValueError(
                    f"{contrastNumColumn} and {contrastDenomColumn} are expected to be in resultsNames(obj): {resNames}"
                )

        # check if both level have all zero counts
        # (this has to be done here to make use of error checking above)
        contrastAllZero = contrastAllZeroCharacter(
            obj, contrastFactor, contrastNumLevel, contrastDenomLevel
        )

    # if the result table not already built in the above code
    if not resReady:
        # here, a numeric / list / string contrast which will be converted
        # into a numeric contras and run through getContrast()
        if all(isinstance(c, (int, float, np.number)) for c in contrast):
            # make name for numeric contrast
            signMap = ["", "", "+"]
            contrastSigns = [signMap[x + 1] for x in np.sign(contrast)]
            contrastName = ",".join(
                [f"{s}{c}" for s, c in zip(contrastSigns, contrast)]
            )
            # make sure the contrast is an np array
            contrast = np.asarray(contrast)
        elif all(isinstance(c, str) for c in contrast):
            # interpret string contrast into numeric and make a name for the contrast
            contrastNumeric = np.zeros(len(resNames))
            contrastNumeric[resNames == contrastNumColumn] = 1
            contrastNumeric[resNames == contrastDenomColumn] = -1
            contrast = contrastNumeric
            contrastName = (
                f"{contrastFactorName} {contrastNumLevel} vs {contrastDenomLevel}"
            )
        else:
            # interpret 2-list contrast into numeric and make a name for the contrast
            lc1 = len(contrast[0])
            lc2 = len(contrast[1])
            # these just used for naming
            listvalname1 = round(listValues[0], 3)
            listvalname2 = round(listValues[1], 3)
            if lc1 > 0 and lc2 > 0:
                listvalname2 = np.abs(listvalname2)
                listvalname1 = "" if listvalname1 == 1 else f"{listvalname1} "
                listvalname2 = "" if listvalname2 == 1 else f"{listvalname2} "
                contrastName = f"{listvalname1}{'+'.join(contrast[0])} vs {listvalname2}{'+'.join(contrast[1])}"
            elif lc1 > 0 and lc2 == 0:
                listvalname1 = "" if listvalname1 == 1 else f"{listvalname1} "
                contrastName = f"{listvalname1}{'+'.join(contrast[0])} effect"
            elif lc1 == 0 and lc2 > 0:
                contrastName = f"{listvalname2}{'+'.join(contrast[1])} effect"

            contrastNumeric = np.zeros(len(resNames))
            contrastNumeric[resNames.isin(contrast[0])] = listValues[0]
            contrastNumeric[resNames.isin(contrast[1])] = listValues[1]
            contrast = contrastNumeric

        contrastAllZero = contrastAllZeroNumeric(obj, contrast)

        # now get the contrast
        res = getContrast(obj, contrast, useT=useT, minmu=minmu)
        lfcType = "MAP" if obj.betaPrior else "MLE"
        for c in res.columns:
            res.type[c] = "results"
        res.description["log2FoldChange"] = (
            f"log2 fold change ({lfcType}): {contrastName}"
        )
        res.description["lfcSE"] = f"standard error: {contrastName}"
        res.description["stat"] = f"Wald statistic: {contrastName}"
        res.description["pvalue"] = f"Wald test p-value: {contrastName}"
        res["baseMean"] = obj.var["baseMean"]
        res.type["baseMean"] = obj.var.type["baseMean"]
        res.description["baseMean"] = obj.var.description["baseMean"]

    # if the counts in all samples included in contrast are zero
    # then zero out the LFC, Wald stat and p-value set to 1
    contrastAllZero = contrastAllZero & ~obj.var["allZero"]
    contrastAllZero.index = res.index
    if np.sum(contrastAllZero) > 0:
        res.loc[contrastAllZero, "log2FoldChange"] = 0
        res.loc[contrastAllZero, "stat"] = 0
        res.loc[contrastAllZero, "pvalue"] = 1

    # if test is "LRT", overwrite the statistic and p-value
    # (we only ran contrast for the coefficient)
    if test == "LRT":
        stat = getStat(obj, name=None, test=test)
        pvalue = getPvalue(obj, name=None, test=test)
        res = res[["baseMean", "log2FoldChange", "lfcSE"]]
        res["stat"] = stat
        res["pvalue"] = pvalue

    return res


def mleContrast(obj, contrast):
    contrastFactor = contrast[0]
    contrastNumLevel = contrast[1]
    contrastDenomLevel = contrast[2]
    contrastRefLevel = obj.obs[contrastFactor].dtype.categories[0]
    contrastNumColumn = f"MLE_{contrastFactor}_{contrastNumLevel}_vs_{contrastRefLevel}"
    contrastDenomColumn = (
        f"MLE_{contrastFactor}_{contrastDenomLevel}_vs_{contrastRefLevel}"
    )
    cleanName = f"log2 fold change (MLE): {contrastFactor} {contrastNumLevel} vs {contrastDenomLevel}"

    if contrastDenomLevel == contrastRefLevel:
        name = f"MLE_{contrastFactor}_{contrastNumLevel}_vs_{contrastDenomLevel}"
        lfcMLEName = name
        lfcMLE = obj.var[name]
    elif contrastNumLevel == contrastRefLevel:
        swapName = f"MLE_{contrastFactor}_{contrastDenomLevel}_vs_{contrastNumLevel}"
        lfcMLEName = swapName
        lfcMLE = -1 * obj.var[swapName]
    else:
        numMLE = obj.var[contrastNumColumn]
        denomMLE = obj.var[contrastDenomColumn]
        lfcMLEName = contrastNumColumn
        lfcMLE = numMLE - denomMLE

    res = pd.DataFrame({"lfcMLE": lfcMLE})
    res.type["lfcMLE"] = obj.var.type[lfcMLEName]
    res.description["lfcMLE"] = cleanName
    return res


def is_iterable(x):
    try:
        return not isinstance(x, str) and all(True for y in x)
    except TypeError:
        return False


def checkContrast(contrast, resNames):
    if not is_iterable(contrast):
        contrast = [contrast]
    is_numeric = all(isinstance(c, (int, float, np.number)) for c in contrast)
    is_string = all(isinstance(c, str) for c in contrast)

    if is_string and len(contrast) == 3:
        if contrast[1] == contrast[2]:
            raise ValueError(
                f"{contrast[1]} and {contrast[2]} should be different level names"
            )

    elif is_numeric:
        if len(contrast) != len(resNames):
            raise ValueError(
                "numeric contrast vector should have one element for every element of 'resultsNames(obj)'"
            )
        if np.all(np.equal(contrast, 0)):
            raise ValueError(
                "numeric contrast vector cannot have all elements equal to 0"
            )
    else:
        if len(contrast) == 1:
            contrast = [contrast[0], []]
        if len(contrast) != 2:
            raise ValueError(
                "'contrast', as a pair of lists, should have length 2, or if length 1, an empty list will be added as the second element"
            )

        # make sure contrast is a pair of iterables
        contrast = [c if is_iterable(c) else [c] for c in contrast]

        if not all(isinstance(c, str) for cc in contrast for c in cc):
            raise ValueError(
                "'contrast', as a pair of lists, should have lists of strings as elements"
            )
        if not all(c in resNames for cc in contrast for c in cc):
            raise ValueError(
                "all elements of the 2-element contrast should be elements of 'resultsNames(obj)'"
            )
        if len(np.intersect1d(contrast[0], contrast[1])) > 0:
            raise ValueError(
                "elements in the 2-element contrast should only appear in the numerator (first element of contrast) or the denominator(second element), but not both"
            )
        if len(contrast[0]) + len(contrast[1]) == 0:
            raise ValueError(
                "one the 2 elements in the list should be contain at least one element"
            )

    return contrast


def contrastAllZeroCharacter(obj, contrastFactor, contrastNumLevel, contrastDenomLevel):
    cts = obj.counts()
    f = obj.obs[contrastFactor]
    if np.issubdtype(f.dtype.categories.dtype, np.number):
        contrastNumLevel = int(contrastNumLevel)
        contrastDenomLevel = int(contrastDenomLevel)
    cts_sub = cts[f.isin([contrastNumLevel, contrastDenomLevel])]
    return np.sum(cts_sub == 0, axis=0) == cts_sub.shape[0]


def contrastAllZeroNumeric(obj, contrast):
    modelMatrix = obj.modelMatrix
    # this extra leg-work to zero out FLC, lfcSE, and set p-value to 1
    # for contrasts comparing groups where both groups have all zeros.

    # it is only implemented for the case in which we can identify
    # the relevant samples by multiplying the model matrix
    # with a vector where the non-zero elements of the numeric contrast
    # are replaced with 1.

    # so, this code will not zero out in the case of standard model matrices
    # where the user supplies a numeric contrast that pulls out a single column
    # of the model matrix, for example.

    if np.all(np.greater_equal(contrast, 0)) or np.all(np.less_equal(contrast, 0)):
        return np.repeat(False, obj.n_vars)

    contrastBinary = np.where(contrast == 0, 0, 1)
    whichSamples = np.where(modelMatrix @ contrastBinary == 0, 0, 1)
    zeroTest = obj.counts().T @ whichSamples
    return zeroTest == 0
