aind-dynamic-foraging-basic-analysis 0.3.27__tar.gz → 0.3.29__tar.gz

{aind_dynamic_foraging_basic_analysis-0.3.27 → aind_dynamic_foraging_basic_analysis-0.3.29}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: aind-dynamic-foraging-basic-analysis
-Version: 0.3.27
+Version: 0.3.29
 Summary: Generated from aind-library-template
 Author: Allen Institute for Neural Dynamics
 License: MIT
@@ -20,6 +20,7 @@ Requires-Dist: numpy
 Requires-Dist: pydantic
 Requires-Dist: hdmf_zarr
 Requires-Dist: aind-dynamic-foraging-data-utils>=0.1.25
+Requires-Dist: aind_hierarchical_bootstrap
 Provides-Extra: dev
 Requires-Dist: aind-dynamic-foraging-basic-analysis; extra == "dev"
 Requires-Dist: black; extra == "dev"
@@ -61,6 +62,14 @@ pip install -e .[dev]
 ```
 
 ## Usage
+
+Example notebooks to test and try different functions of this package (and the data-utils) package can be found here: 
+
+https://codeocean.allenneuraldynamics.org/capsule/6488619/tree
+
+Please duplicate the capsule to test the different functions. 
+
+
 ### Annotate licks
 To create a dataframe of licks that has been annotated with licking bout starts/stops, cue responsive licks, reward triggered licks, and intertrial choices.
 ```
@@ -138,6 +147,21 @@ To compare multiple channels to the same event type:
 pf.plot_fip_psth(nwb, 'goCue_start_time')
 ```
 
+### Hierarchical Bootstrapping and significance testing
+If you want to perform hierarchical bootstrapping, then you can select `hb_sem` as the error type
+```
+fig, ax, etrs = plot_fip_psth_compare_alignments(
+    nwbs, 
+    alignments, 
+    channel_name, 
+    error_type='hb_sem',
+    hierarchical_params={'nboots':10000}
+)
+```
+Then add significance with:
+```
+fip_psth_stats_plot(ax, etrs['stats'])`, color='k', threshold=0.05)
+```
 
 ## Contributing
 

{aind_dynamic_foraging_basic_analysis-0.3.27 → aind_dynamic_foraging_basic_analysis-0.3.29}/README.md

@@ -28,6 +28,14 @@ pip install -e .[dev]
 ```
 
 ## Usage
+
+Example notebooks to test and try different functions of this package (and the data-utils) package can be found here: 
+
+https://codeocean.allenneuraldynamics.org/capsule/6488619/tree
+
+Please duplicate the capsule to test the different functions. 
+
+
 ### Annotate licks
 To create a dataframe of licks that has been annotated with licking bout starts/stops, cue responsive licks, reward triggered licks, and intertrial choices.
 ```
@@ -105,6 +113,21 @@ To compare multiple channels to the same event type:
 pf.plot_fip_psth(nwb, 'goCue_start_time')
 ```
 
+### Hierarchical Bootstrapping and significance testing
+If you want to perform hierarchical bootstrapping, then you can select `hb_sem` as the error type
+```
+fig, ax, etrs = plot_fip_psth_compare_alignments(
+    nwbs, 
+    alignments, 
+    channel_name, 
+    error_type='hb_sem',
+    hierarchical_params={'nboots':10000}
+)
+```
+Then add significance with:
+```
+fip_psth_stats_plot(ax, etrs['stats'])`, color='k', threshold=0.05)
+```
 
 ## Contributing
 

{aind_dynamic_foraging_basic_analysis-0.3.27 → aind_dynamic_foraging_basic_analysis-0.3.29}/pyproject.toml

@@ -28,7 +28,8 @@ dependencies = [
     'numpy',
     'pydantic',
     'hdmf_zarr',
-    'aind-dynamic-foraging-data-utils >= 0.1.25'
+    'aind-dynamic-foraging-data-utils >= 0.1.25',
+    'aind_hierarchical_bootstrap'
 ]
 
 [project.optional-dependencies]

{aind_dynamic_foraging_basic_analysis-0.3.27 → aind_dynamic_foraging_basic_analysis-0.3.29}/src/aind_dynamic_foraging_basic_analysis/__init__.py

@@ -1,6 +1,6 @@
 """Init package"""
 
-__version__ = "0.3.27"
+__version__ = "0.3.29"
 
 from .metrics.foraging_efficiency import compute_foraging_efficiency  # noqa: F401
 from .plot.plot_foraging_session import plot_foraging_session  # noqa: F401

{aind_dynamic_foraging_basic_analysis-0.3.27 → aind_dynamic_foraging_basic_analysis-0.3.29}/src/aind_dynamic_foraging_basic_analysis/plot/plot_fip.py

@@ -2,12 +2,18 @@
 Tools for plotting FIP data
 """
 
+from functools import partial
+from multiprocessing import Pool
+
+import aind_hierarchical_bootstrap.bootstrap as hb
+import aind_hierarchical_bootstrap.stats as hb_stats
 import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pd
 from aind_dynamic_foraging_data_utils import alignment as an
 from aind_dynamic_foraging_data_utils import nwb_utils as nu
 
+import aind_dynamic_foraging_basic_analysis.plot.style as style
 from aind_dynamic_foraging_basic_analysis.plot.style import FIP_COLORS, STYLE
 
 
@@ -22,9 +28,12 @@ def plot_fip_psth_compare_alignments(  # NOQA C901
     extra_colors={},
     data_column="data",
     error_type="sem",
+    hierarchical_params={},
 ):
     """
     Compare the same FIP channel aligned to multiple event types
+
+    ARGS
     nwb, nwb object for the session, or a list of nwbs
     alignments, with one session alignments can be either a list of
         event types in df_events, or a dictionary whose keys are
@@ -38,15 +47,39 @@ def plot_fip_psth_compare_alignments(  # NOQA C901
     extra_colors (dict), a dictionary of extra colors.
         keys should be alignments, or colors are random
     data_column (string), name of data column in nwb.df_fip
-    error_type, (string), either "sem" or "sem_over_sessions" to define
+    error_type, (string), either "sem", "hb_sem", or "sem_over_sessions" to define
         the error bar for the PSTH
+    hierarchical_params, (dict), parameters to be passed to compute_hierarchical_error()
+
+    RETURNS
+    fig - matplotlib figure
+    ax - matplotlib axis
+    etrs - dictionary containing PSTH traces for each alignment. If hierarchical
+        bootstrapping is performed, then also contains the bootstraps and statistics dataframe
+
+        The stats_df will have timepoints in the PSTH as rows. If more than 2 groups
+        are present, then there will be a row for each timepoint X each combination of groups.
+        For each timepoint the columns are
+        name - "<group 1>_<group 2>", the two groups being compared
+        group1 - The name of the first group (channel or alignment)
+        group2 - The name of the second group
+        p - the p-value of the comparison
+        nboots - the number of bootstraps used in the comparison
+
+        The bootstraps will be a list with the same length as the number of timepoints
+        in the PSTH. For each timepoint, it has a dictionary:
+            <group i> - for each group (channel or alignemtn) the list of bootstrapped means
+                with length = nboots
+            <group i>_sem - the hierarchically computed SEM for that group
+            groups - a list of all the groups present at this timepoint
+            time - the timepoint value
 
     EXAMPLE
     *******************
     plot_fip_psth_compare_alignments(nwb,['left_reward_delivery_time',
         'right_reward_delivery_time'],'G_1_preprocessed')
     """
-    if error_type not in ["sem", "sem_over_sessions"]:
+    if error_type not in ["sem", "sem_over_sessions", "hb_sem"]:
         raise Exception("unknown error type")
 
     nwb_list = nwb if isinstance(nwb, list) else [nwb]
@@ -132,12 +165,37 @@ def plot_fip_psth_compare_alignments(  # NOQA C901
     colors = {**FIP_COLORS, **extra_colors}
 
     align_label = "Time (s)"
+    etrs = {}
+    bootstraps = {}
     for alignment in align_list[0]:
         this_align = [x[alignment] for x in align_list]
-        etr = fip_psth_multiple_inner_compute(
-            nwb_list, this_align, channel, True, tw, censor, censor_times_list, data_column
+        etr, bootstrap = fip_psth_multiple_inner_compute(
+            nwb_list,
+            this_align,
+            channel,
+            True,
+            tw,
+            censor,
+            censor_times_list,
+            data_column,
+            compute_hierarchical=error_type == "hb_sem",
+            hierarchical_params=hierarchical_params,
         )
         fip_psth_inner_plot(ax, etr, colors.get(alignment, ""), alignment, data_column, error_type)
+        etrs[alignment] = etr
+        if error_type == "hb_sem":
+            for b in bootstrap:
+                b[alignment] = b[data_column]
+                b["{}_sem".format(alignment)] = b["{}_sem".format(data_column)]
+                b["groups"] = [alignment]
+                del b[data_column]
+                del b["{}_sem".format(data_column)]
+        bootstraps[alignment] = bootstrap
+
+    if error_type == "hb_sem":
+        bootstraps, stats_df = aggregate_bootstrap_statistics(bootstraps)
+        etrs["stats"] = stats_df
+        etrs["bootstraps"] = bootstraps
 
     plt.legend()
     ax.set_xlabel(align_label, fontsize=STYLE["axis_fontsize"])
@@ -159,7 +217,7 @@ def plot_fip_psth_compare_alignments(  # NOQA C901
     else:
         ax.set_title("{} sessions".format(len(nwb_list)), fontsize=STYLE["axis_fontsize"])
     plt.tight_layout()
-    return fig, ax
+    return fig, ax, etrs
 
 
 def plot_fip_psth_compare_channels(  # NOQA C901
@@ -179,17 +237,43 @@ def plot_fip_psth_compare_channels(  # NOQA C901
     censor=True,
     data_column="data",
     error_type="sem",
+    hierarchical_params={},
 ):
     """
-    nwb, the nwb object for the session of interest, or a list of nwb objects
+    ARGS
+    nwb, the nwb object, etrs for the session of interest, or a list of nwb objects
     align should either be a string of the name of an event type in nwb.df_events,
         or a list of timepoints. if nwb is a list, then align should be a list containing
         lists of timepoints for each session.
     channels should be a list of channel names (strings)
     censor, censor important timepoints before and after aligned timepoints
     data_column (string), name of data column in nwb.df_fip
-    error_type, (string), either "sem" or "sem_over_sessions" to define
+    error_type, (string), either "sem", "hb_sem", or "sem_over_sessions" to define
         the error bar for the PSTH
+    hierarchical_params, (dict), parameters to be passed to compute_hierarchical_error()
+
+    RETURNS
+    fig - matplotlib figure
+    ax - matplotlib axis
+    etrs - dictionary containing PSTH traces for each alignment. If hierarchical
+        bootstrapping is performed, then also contains the bootstraps and statistics dataframe
+
+        The stats_df will have timepoints in the PSTH as rows. If more than 2 groups
+        are present, then there will be a row for each timepoint X each combination of groups.
+        For each timepoint the columns are
+        name - "<group 1>_<group 2>", the two groups being compared
+        group1 - The name of the first group (channel or alignment)
+        group2 - The name of the second group
+        p - the p-value of the comparison
+        nboots - the number of bootstraps used in the comparison
+
+        The bootstraps will be a list with the same length as the number of timepoints
+        in the PSTH. For each timepoint, it has a dictionary:
+            <group i> - for each group (channel or alignemtn) the list of bootstrapped means
+                with length = nboots
+            <group i>_sem - the hierarchically computed SEM for that group
+            groups - a list of all the groups present at this timepoint
+            time - the timepoint value
 
     EXAMPLE
     ********************
@@ -198,7 +282,7 @@ def plot_fip_psth_compare_channels(  # NOQA C901
     plot_fip_psth(nwb_list, [session_1_timepoints, session_2_timepoints, ... ])
     """
 
-    if error_type not in ["sem", "sem_over_sessions"]:
+    if error_type not in ["sem", "sem_over_sessions", "hb_sem"]:
         raise Exception("Unknown error type")
 
     # Check if nwb is a list, otherwise put it in a list to check
@@ -258,9 +342,11 @@ def plot_fip_psth_compare_channels(  # NOQA C901
 
     # Iterate through channels and plot
     colors = [FIP_COLORS.get(c, "") for c in channels]
+    etrs = {}
+    bootstraps = {}
     for dex, c in enumerate(channels):
         include = [c in nwb.df_fip["event"].values for nwb in nwb_list]
-        etr = fip_psth_multiple_inner_compute(
+        etr, bootstrap = fip_psth_multiple_inner_compute(
             [x for dex, x in enumerate(nwb_list) if include[dex]],
             [x for dex, x in enumerate(align_timepoints_list) if include[dex]],
             c,
@@ -268,8 +354,24 @@ def plot_fip_psth_compare_channels(  # NOQA C901
             tw,
             censor,
             data_column=data_column,
+            compute_hierarchical=error_type == "hb_sem",
+            hierarchical_params=hierarchical_params,
         )
         fip_psth_inner_plot(ax, etr, colors[dex], c, data_column, error_type)
+        etrs[c] = etr
+        if error_type == "hb_sem":
+            for b in bootstrap:
+                b[c] = b[data_column]
+                b["{}_sem".format(c)] = b["{}_sem".format(data_column)]
+                b["groups"] = [c]
+                del b[data_column]
+                del b["{}_sem".format(data_column)]
+        bootstraps[c] = bootstrap
+
+    if error_type == "hb_sem":
+        bootstraps, stats_df = aggregate_bootstrap_statistics(bootstraps)
+        etrs["stats"] = stats_df
+        etrs["bootstraps"] = bootstraps
 
     plt.legend()
     ax.set_xlabel(align_label, fontsize=STYLE["axis_fontsize"])
@@ -290,7 +392,52 @@ def plot_fip_psth_compare_channels(  # NOQA C901
     else:
         ax.set_title("{} sessions".format(len(nwb_list)))
     plt.tight_layout()
-    return fig, ax
+    return fig, ax, etrs
+
+
+def fip_psth_stats_plot(ax, stats_df, threshold=0.05):
+    """
+    Plots markers where a significant threshold is reached
+
+    Does not perform multiple comparisons testing.
+
+    If multiple unique tests are in the stats_df, each test
+    is plotted separately.
+
+    ARGS
+    ax - axis to plot on
+    stats_df - dataframe of stats results. See aind_hierarchical_bootstrap
+        for more details on the format. This dataframe is returned in the
+        etr dictionary with calls to either plot_fip_psth_compare_alignments
+        or plot_fip_psth_compare_channels. The stats_df will have timepoints
+        in the PSTH as rows. If more than 2 groups are present, then there will
+        be a row for each timepoint X each combination of groups.
+        For each timepoint the columns are
+        name - "<group 1>_<group 2>", the two groups being compared
+        group1 - The name of the first group (channel or alignment)
+        group2 - The name of the second group
+        p - the p-value of the comparison
+        nboots - the number of bootstraps used in the comparison
+    threshold - significance level
+
+    EXAMPLE
+    fig, ax, etrs = plot_fip_psth_compare_alignments(...)
+    fip_psth_stats_plot(ax, etrs['stats'], threshold=0.05)
+
+    """
+    unique_tests = stats_df["name"].unique()
+    colors = style.get_colors(list(unique_tests), offset=0.25, cmap_name="plasma")
+    for test in unique_tests:
+        significant = stats_df.query("name == @test").query("p < @threshold")
+        if len(significant) > 0:
+            ax.plot(
+                significant.index,
+                [ax.get_ylim()[0]] * len(significant),
+                "o",
+                color=colors[test],
+                label="{}: p < {}".format(test, threshold),
+            )
+    plt.legend()
 
 
 def fip_psth_inner_plot(ax, etr, color, label, data_column, error_type="sem"):
@@ -325,6 +472,8 @@ def fip_psth_multiple_inner_compute(
     censor=True,
     censor_times=None,
     data_column="data",
+    compute_hierarchical=False,
+    hierarchical_params={},
 ):
     """
     Wrapper function for fip_psth_inner_compute that takes a list of NWB files
@@ -373,7 +522,14 @@ def fip_psth_multiple_inner_compute(
         # Compute SEM collapsing over sessions
         result["sem"] = etr_all.groupby("time")[data_column].sem()
 
-        return result
+        if compute_hierarchical:
+            result, bootstraps = compute_hierarchical_error(
+                result, etr_all, data_column=data_column, **hierarchical_params
+            )
+        else:
+            bootstraps = None
+
+        return result, bootstraps
     else:
         return etr_all
 
@@ -422,6 +578,85 @@ def fip_psth_inner_compute(
     return etr
 
 
+def compute_hierarchical_error(
+    result, etr_all, levels=["ses_idx"], nboots=10000, data_column="data"
+):
+    """
+    Computes hierarchical bootstraps at each timepoint.
+    result, summary dataframe
+    etr_al, dataframe with all datapoints
+    levels, list of hierarchy to bootstrap. Slows considerably with each level
+    nboots, number of bootstraps
+    data_column, column to use in etr_all
+
+    Computing hierarchical bootstraps is slow. Consider using
+    error_type='sem_over_sessions' until analyses are finalized.
+    You may also speed up this computation by adding more CPUs,
+    as this function is optimized for multiprocessing. Additionally,
+    you can reduce 'nboots' for faster processing.
+
+    See aind_hierarchical_boostrap for more information
+    """
+
+    # Set up partial function that wraps other parameters
+    temp_func = partial(hb.bootstrap, metric=data_column, levels=levels, nboots=nboots)
+
+    # Split dataframe by timepoint
+    dfs = []
+    for num in result.index.values:
+        dfs.append(etr_all.query("time == @num"))
+
+    # Run multiprocess pool
+    with Pool() as pool:
+        bootstraps = pool.map(temp_func, dfs)
+
+    # Organize results
+    for index, val in enumerate(result.index.values):
+        bootstraps[index]["time"] = val
+    result["hb_sem"] = [x["data_sem"] for x in bootstraps]
+
+    return result, bootstraps
+
+
+def aggregate_bootstrap_statistics(bootstraps):
+    """
+    Computes statistics on bootstrap results across groups (alignments or channels)
+    bootstraps - a dictionary of lists. The keys are the groups to compare,
+        either alignments or channels. The lists are the timepoints of the PSTH
+        The lengths of the lists must be the same for all groups.
+    Returns
+        combined_dicts - a list of dictionaries, one for each timepoint of the PSTH.
+            The dictionary for each timepoint is the merged dictionaries from each group
+        stats_df - a dataframe with statistics results, from aind_hierarchical_bootstrap
+    """
+    # check that the lists are always the same length
+    lens = set()
+    for key in bootstraps:
+        lens.add(len(bootstraps[key]))
+    if len(lens) > 1:
+        raise Exception("Event triggered responses for each alignment are different lengths")
+
+    combined_dicts = []
+    for i in range(lens.pop()):
+        temp = {}
+        for key in bootstraps:
+            temp[key] = bootstraps[key][i][key]
+            temp["{}_sem".format(key)] = bootstraps[key][i]["{}_sem".format(key)]
+        temp["groups"] = list(bootstraps.keys())
+        temp["time"] = bootstraps[key][i]["time"]
+        combined_dicts.append(temp)
+
+    # now compute statistics for each timepoint
+    stats_dfs = []
+    for d in combined_dicts:
+        stats_df = hb_stats.compute_stats(d)
+        stats_df["time"] = d["time"]
+        stats_dfs.append(stats_df)
+    stats_df = pd.concat(stats_dfs).set_index("time", drop=True)
+
+    return combined_dicts, stats_df
+
+
 def plot_histogram(nwb, preprocessed=True, edge_percentile=2, data_column="data"):
     """
     Generates a histogram of values of each FIP channel

{aind_dynamic_foraging_basic_analysis-0.3.27 → aind_dynamic_foraging_basic_analysis-0.3.29}/src/aind_dynamic_foraging_basic_analysis.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: aind-dynamic-foraging-basic-analysis
-Version: 0.3.27
+Version: 0.3.29
 Summary: Generated from aind-library-template
 Author: Allen Institute for Neural Dynamics
 License: MIT
@@ -20,6 +20,7 @@ Requires-Dist: numpy
 Requires-Dist: pydantic
 Requires-Dist: hdmf_zarr
 Requires-Dist: aind-dynamic-foraging-data-utils>=0.1.25
+Requires-Dist: aind_hierarchical_bootstrap
 Provides-Extra: dev
 Requires-Dist: aind-dynamic-foraging-basic-analysis; extra == "dev"
 Requires-Dist: black; extra == "dev"
@@ -61,6 +62,14 @@ pip install -e .[dev]
 ```
 
 ## Usage
+
+Example notebooks to test and try different functions of this package (and the data-utils) package can be found here: 
+
+https://codeocean.allenneuraldynamics.org/capsule/6488619/tree
+
+Please duplicate the capsule to test the different functions. 
+
+
 ### Annotate licks
 To create a dataframe of licks that has been annotated with licking bout starts/stops, cue responsive licks, reward triggered licks, and intertrial choices.
 ```
@@ -138,6 +147,21 @@ To compare multiple channels to the same event type:
 pf.plot_fip_psth(nwb, 'goCue_start_time')
 ```
 
+### Hierarchical Bootstrapping and significance testing
+If you want to perform hierarchical bootstrapping, then you can select `hb_sem` as the error type
+```
+fig, ax, etrs = plot_fip_psth_compare_alignments(
+    nwbs, 
+    alignments, 
+    channel_name, 
+    error_type='hb_sem',
+    hierarchical_params={'nboots':10000}
+)
+```
+Then add significance with:
+```
+fip_psth_stats_plot(ax, etrs['stats'])`, color='k', threshold=0.05)
+```
 
 ## Contributing
 

{aind_dynamic_foraging_basic_analysis-0.3.27 → aind_dynamic_foraging_basic_analysis-0.3.29}/src/aind_dynamic_foraging_basic_analysis.egg-info/requires.txt

@@ -10,6 +10,7 @@ numpy
 pydantic
 hdmf_zarr
 aind-dynamic-foraging-data-utils>=0.1.25
+aind_hierarchical_bootstrap
 
 [dev]
 aind-dynamic-foraging-basic-analysis