Merge pull request #21 from UTAustin-SwarmLab/lineplot_and_p_value_fixes

Fixed P value plots and line plots naming

pyproject.toml

@@ -20,7 +20,7 @@ dependencies = [
     "numpy",
     "pandas",
     "seaborn",
-    "statannot",
+    "statannotations",
     "scipy"
 ]
 

swarm_visualizer/lineplot.py

@@ -5,18 +5,18 @@
 from swarm_visualizer.utility.general_utils import set_axis_infos
 
 
-def plot_basic_plot_ts(
-    ts_vector=None,
+def plot_basic_lineplot(
+    vector=None,
     title_str: str = None,
     ylabel: str = None,
     lw: float = 3.0,
     ylim=None,
-    xlabel: str = "time",
+    xlabel: str = "x",
     ax=None,
 ) -> None:
-    """Basic plot of a time series.
+    """Basic lineplot.
 
-    :param ts_vector: time series
+    :param vector: vector to plot
     :param title_str: title of the plot
     :param ylabel: y-axis label
     :param lw: line width
@@ -26,18 +26,18 @@ def plot_basic_plot_ts(
     :return: None.
     """
     # Plot time series
-    ax.plot(ts_vector, lw=lw)
+    ax.plot(vector, lw=lw)
 
     set_axis_infos(
         ax, xlabel=xlabel, ylabel=ylabel, ylim=ylim, title_str=title_str
     )
 
 
-def plot_overlaid_ts(
+def plot_overlaid_lineplot(
     normalized_ts_dict: Dict = None,
     title_str: str = None,
     ylabel: str = None,
-    xlabel: str = "time",
+    xlabel: str = "x",
     xticks=None,
     ylim=None,
     DEFAULT_ALPHA: float = 1.0,
@@ -46,9 +46,9 @@ def plot_overlaid_ts(
     delete_yticks: bool = False,
     ax=None,
 ) -> None:
-    """Overlaid time series plot.
+    """Overlaid line plot.
     
-    :param normalized_ts_dict: dictionary with time series to plot
+    :param normalized_ts_dict: dictionary with values to plot
     :param title_str: title of the plot
     :param ylabel: y-axis label
     :param xlabel: x-axis label

swarm_visualizer/utility/statistics_utils.py

@@ -1,4 +1,5 @@
-from statannot import add_stat_annotation
+from statannotations.Annotator import Annotator
+
 
 
 def add_wilcoxon_value(
@@ -15,17 +16,7 @@ def add_wilcoxon_value(
     fontsize=20,
     verbose=0,
 ) -> None:
-    add_stat_annotation(
-        ax,
-        data=df,
-        x=x_var,
-        y=y_var,
-        hue=hue,
-        order=order_list,
-        box_pairs=box_pairs,
-        test=test_type,
-        text_format=text_format,
-        loc=loc,
-        verbose=verbose,
-        fontsize=fontsize,
-    )
+
+    annotator = Annotator(ax,box_pairs,data=df, x=x_var, y=y_var, hue = hue, order=order_list)
+    annotator.configure(test=test_type, text_format=text_format, loc=loc, verbose=verbose, fontsize=fontsize)
+    annotator.apply_and_annotate()

tests/test_lineplot.py

@@ -6,7 +6,7 @@
 import numpy as np
 import pytest
 
-from swarm_visualizer.lineplot import plot_basic_plot_ts, plot_overlaid_ts
+from swarm_visualizer.lineplot import plot_basic_lineplot, plot_overlaid_lineplot
 from swarm_visualizer.utility.general_utils import save_fig, set_plot_properties
 
 _X_DATA = np.arange(0, 10, 0.1) + np.random.normal(0, 0.1, 100)
@@ -56,7 +56,7 @@
 
 
 @pytest.mark.parametrize(("ts_vector"), ([_X_DATA]))
-def test_basic_ts_plot(ts_vector) -> None:
+def test_basic_lineplot(ts_vector) -> None:
     """Tests basic time series plot.
 
     :param ts_vector: time series
@@ -68,9 +68,9 @@ def test_basic_ts_plot(ts_vector) -> None:
     fig, ax = plt.subplots(figsize=(10, 10))
 
     # Plot time series
-    plot_basic_plot_ts(
-        ts_vector=ts_vector,
-        title_str="Basic Time Series Plot",
+    plot_basic_lineplot(
+        vector=ts_vector,
+        title_str="Basic Line Plot",
         ylabel="$y$",
         lw=3.0,
         ylim=None,
@@ -84,7 +84,7 @@ def test_basic_ts_plot(ts_vector) -> None:
 
 
 @pytest.mark.parametrize(("normalized_ts_dict"), ([_NORMALIZED_TS_DICT]))
-def test_overlaid_ts_plot(normalized_ts_dict) -> None:
+def test_overlaid_lineplot(normalized_ts_dict) -> None:
     """Tests overlaid time series plot.
 
     :param normalized_ts_dict: dictionary with time series to plot
@@ -96,9 +96,9 @@ def test_overlaid_ts_plot(normalized_ts_dict) -> None:
     fig, ax = plt.subplots(figsize=(10, 10))
 
     # Plot overlaid time series
-    plot_overlaid_ts(
+    plot_overlaid_lineplot(
         normalized_ts_dict=normalized_ts_dict,
-        title_str="Overlaid Time Series Plot",
+        title_str="Overlaid Line Plot",
         ylabel="$y$",
         xlabel="$x$",
         xticks=None,

tests/test_p_value.py

@@ -30,15 +30,15 @@
 )
 
 _DATA_FRAME = pd.DataFrame(
-    {"$y$": _X_DATA, "$x$": _X_LABEL, "_GROUPS": _GROUPS}
+    {"$y$": _X_DATA, "$x$": _X_LABEL, "hue": _GROUPS}
 )
 _SAVE_LOC = os.path.abspath(
     os.path.join(os.path.dirname(__file__), "example_plots")
 )
 
 
 @pytest.mark.parametrize(
-    ("df", "x_var", "y_var", "hue"), [(_DATA_FRAME, "$x$", "$y$", _GROUPS)]
+    ("df", "x_var", "y_var", "hue"), [(_DATA_FRAME, "$x$", "$y$", "hue")]
 )
 def test_star_pvalue(df, x_var, y_var, hue) -> None:
     """Tests paired boxplot.