update CI backend (closes #29, #28)

update CI backend to mpl ax.errorbar API (closes #29, ref #28)
LSYS · Oct 22, 2022 · 1bf2c10 · 1bf2c10
1 parent e12978a
commit 1bf2c10
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Showing 3 changed files with 26 additions and 20 deletions.
diff --git a/forestplot/graph_utils.py b/forestplot/graph_utils.py
@@ -11,12 +11,13 @@ def draw_ci(
     dataframe: pd.core.frame.DataFrame,
     estimate: str,
     yticklabel: str,
-    moerror: str,
+    ll: str,
+    hl: str,
     ax: Axes,
     **kwargs: Any
 ) -> Axes:
     """
-    Draw the confidence intervals using the horizontal bar plot (barh) from the pandas API.
+    Draw the confidence intervals using the Matplotlib errorbar API.
 
     Parameters
     ----------
@@ -28,9 +29,10 @@ def draw_ci(
             OR, regression estimates, etc.).
     yticklabel (str)
             Name of column in intermediate dataframe containing the formatted yticklabels.
-    moerror (str)
-            Name of column containing the margin of error in the confidence intervals.
-            Should be available if 'll' and 'hl' are left empty.
+    ll (str)
+            Name of column containing the lower limit of the confidence intervals.
+    hl (str)
+            Name of column containing the upper limit of the confidence intervals.
     ax (Matplotlib Axes)
             Axes to operate on.
 
@@ -40,15 +42,13 @@ def draw_ci(
     """
     lw = kwargs.get("lw", 1.4)
     linecolor = kwargs.get("linecolor", ".6")
-    ax = dataframe.plot(
-        y=estimate,
-        x=yticklabel,
-        kind="barh",
-        xerr=moerror,
-        color="none",
-        error_kw={"lw": lw, "ecolor": linecolor},
-        legend=False,
-        ax=ax,
+    ax.errorbar(
+        x=dataframe[estimate],
+        y=dataframe[yticklabel],
+        xerr=[dataframe[estimate] - dataframe[ll], dataframe[hl] - dataframe[estimate]],
+        ecolor=linecolor,
+        elinewidth=lw,
+        ls="none",
         zorder=0,
     )
     return ax

diff --git a/forestplot/plot.py b/forestplot/plot.py
@@ -93,10 +93,8 @@ def forestplot(
             Should be available if 'll' and 'hl' are left empty.
     ll (str)
             Name of column containing the lower limit of the confidence intervals.
-            Optional
     hl (str)
             Name of column containing the upper limit of the confidence intervals.
-            Optional
     form_ci_report (bool)
             If True, form the formatted confidence interval as a string.
     ci_report (bool)
@@ -364,7 +362,8 @@ def _make_forestplot(
         dataframe=dataframe,
         estimate=estimate,
         yticklabel=yticklabel,
-        moerror=moerror,
+        ll=ll,
+        hl=hl,
         ax=ax,
         **kwargs,
     )

diff --git a/tests/test_graph_utils.py b/tests/test_graph_utils.py
@@ -27,6 +27,8 @@
         "yticklabel": str_vector,
         "estimate": x,
         "moerror": y,
+        "ll": x,
+        "hl": y,
         "pval": y,
         "formatted_pval": y,
         "yticklabel1": str_vector,
@@ -38,12 +40,17 @@
 def test_draw_ci():
     _, ax = plt.subplots()
     ax = draw_ci(
-        input_df, estimate="estimate", yticklabel="yticklabel", moerror="moerror", ax=ax
+        dataframe=input_df,
+        estimate="estimate",
+        yticklabel="yticklabel",
+        ll="ll",
+        hl="hl",
+        ax=ax,
     )
     assert isinstance(ax, Axes)
 
-    xticklabels = [lab.get_text() for lab in ax.get_yticklabels()]
-    assert all(txt in xticklabels for txt in input_df["yticklabel"])
+    # Assert yticklabels are of correct length
+    assert len(ax.get_yticklabels()) == len(input_df["yticklabel"])
 
     # Assert yticks are integers
     assert (all(isinstance(tick, int)) for tick in ax.get_yticks())