py2ls 0.2.5.9__tar.gz → 0.2.5.10__tar.gz

{py2ls-0.2.5.9 → py2ls-0.2.5.10}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: py2ls
-Version: 0.2.5.9
+Version: 0.2.5.10
 Summary: py(thon)2(too)ls
 Author: Jianfeng
 Author-email: Jianfeng.Liu0413@gmail.com

{py2ls-0.2.5.9 → py2ls-0.2.5.10}/py2ls/ips.py

@@ -3589,6 +3589,7 @@ def fload(fpath, kind=None, **kwargs):
 
         # https://github.com/eyurtsev/fcsparser
         meta, data = fcsparser.parse(fpath, reformat_meta=True)
+        print("meta, data = fload(*.fcs)")
         return meta, data
 
     elif kind == "mplstyle":
@@ -10378,11 +10379,19 @@ def get_df_format(data, threshold_unique=0.5, verbose=False):
     from sklearn.cluster import AgglomerativeClustering
     from sklearn.preprocessing import StandardScaler
 
-    long_score = 0
-    wide_score = 0
-
+    long_score,wide_score,fs = 0,0,500
     n_rows, n_cols = data.shape
-
+    # -----to reduce memory, only check 500 rows/columns----
+    if n_rows > fs:
+        if verbose:
+            print(f"Sampling {fs} rows from {n_rows} rows.")
+        data = data.sample(n=fs, random_state=1)
+    if n_cols > fs:
+        if verbose:
+            print(f"Using first {fs} columns out of {n_cols} columns.")
+        data = data.iloc[:, :fs]
+    n_rows, n_cols = data.shape
+    
     # Step 1: Row-Column Ratio Heuristic
     if n_rows > 3 * n_cols:
         long_score += 2

{py2ls-0.2.5.9 → py2ls-0.2.5.10}/py2ls/plot.py

@@ -407,7 +407,7 @@ def heatmap(
             for k_, v_ in kwargs.items():
                 if "agg" in k_.lower():
                     aggfunc = v_
-            kwargs.pop(k_, None)
+                kwargs.pop(k_, None)
             data4heatmap = data.pivot_table(
                 index=index, columns=columns, values=values, aggfunc=aggfunc
             )
@@ -3307,11 +3307,15 @@ def plotxy(
         sns_info = pd.DataFrame(fload(current_directory / "data" / "sns_info.json"))
 
     valid_kinds = list(default_settings.keys())
-    # print(valid_kinds)
-    if kind_ is not None:
-        if isinstance(kind_, str):
-            kind_ = [kind_]
-        kind_ = [strcmp(i, valid_kinds)[0] for i in kind_]
+
+    # if kind_ is not None:
+    #     if isinstance(kind_, str):
+    #         kind_ = [kind_]
+    #     kind_ = [strcmp(i, valid_kinds)[0] for i in kind_]
+    # else:
+    #     verbose = True
+    if kind_:
+        kind_ = [strcmp(i, valid_kinds)[0] for i in ([kind_] if isinstance(kind_, str) else kind_)]
     else:
         verbose = True
 
@@ -3332,31 +3336,30 @@ def plotxy(
         print(f"currently support to plot:\n{valid_kinds}\n\nusage:\n{usage_str}")
         return  # Do not plot, just print the usage
 
-    kws_figsets = {}
-    for k_arg, v_arg in kwargs.items():
-        if "figset" in k_arg:
-            kws_figsets = v_arg
-            kwargs.pop(k_arg, None)
-            break
-    kws_add_text = {}
-    for k_arg, v_arg in kwargs.items():
-        if "add" in k_arg and "text" in k_arg:  # add_text
-            kws_add_text = v_arg
-            kwargs.pop(k_arg, None)
-            break
-    zorder = 0
-    for k in kind_:
-        # preprocess data
-        try:
-            data = df_preprocessing_(data, kind=k)
-            if "variable" in data.columns and "value" in data.columns:
-                x, y = "variable", "value"
-        except Exception as e:
-            print(e)
-        zorder += 1
-        # indicate 'col' features
-        col = kwargs.get("col", None)
-        sns_with_col = [
+    # kws_figsets = {}
+    # for k_arg, v_arg in kwargs.items():
+    #     if "figset" in k_arg:
+    #         kws_figsets = v_arg
+    #         kwargs.pop(k_arg, None)
+    #         break
+    # kws_add_text = {}
+    # for k_arg, v_arg in kwargs.items():
+    #     if "add" in k_arg and "text" in k_arg:  # add_text
+    #         kws_add_text = v_arg
+    #         kwargs.pop(k_arg, None)
+    #         break
+    kws_figsets = kwargs.pop("figset", {})
+    kws_add_text = kwargs.pop("add_text", {})
+    
+    # ============ preprocess data ============
+    try:
+        data = df_preprocessing_(data, kind=kind_[0])
+        if "variable" in data.columns and "value" in data.columns:
+            x, y = "variable", "value"
+    except Exception as e:
+        print(e)
+        
+    sns_with_col = [
             "catplot",
             "histplot",
             "relplot",
@@ -3365,11 +3368,17 @@ def plotxy(
             "displot",
             "kdeplot",
         ]
-        if col is not None:
-            if not k in sns_with_col:
-                print(
-                    f"tips:\n'{k}' has no 'col' param, you could try with {sns_with_col}"
-                )
+
+    # indicate 'col' features
+    col = kwargs.get("col", None)
+    if col and not any(k in sns_with_col for k in kind_):
+        print(f"Warning: '{kind_}' has no 'col' param, try using {sns_with_col}")
+
+    if ax is None:
+        ax = plt.gca()
+    zorder = 0
+    for k in kind_:
+        zorder += 1
         # (1) return FcetGrid
         if k == "jointplot":
             kws_joint = kwargs.pop("kws_joint", kwargs)
@@ -3610,9 +3619,6 @@ def plotxy(
             # displot creates a new figure and returns a FacetGrid
             g = sns.displot(data=data, x=x, y=y, **kws_dis)
 
-        # (2) return axis
-        if ax is None:
-            ax = plt.gca()
         if k == "catplot":
             kws_cat = kwargs.pop("kws_cat", kwargs)
             g = catplot(data=data, x=x, y=y, ax=ax, **kws_cat)
@@ -3799,7 +3805,7 @@ def plotxy(
             kws_line = {k: v for k, v in kws_line.items() if not k.startswith("kws_")}
             ax = sns.lineplot(ax=ax, data=data, x=x, y=y, zorder=zorder, **kws_line)
 
-        figsets(ax=ax, **kws_figsets)
+        figsets(ax=ax, **kws_figsets) if kws_figsets else None
         if kws_add_text:
             add_text(ax=ax, **kws_add_text) if kws_add_text else None
     if run_once_within(10):
@@ -4388,29 +4394,32 @@ def venn(
     if ax is None:
         ax = plt.gca()
     if isinstance(lists, dict):
-        labels = list(lists.keys())
-        lists = list(lists.values())
+        labels,lists = list(lists.keys()),list(lists.values())
     if isinstance(lists[0], set):
         lists = [list(i) for i in lists]
+
     lists = [set(flatten(i, verbose=False)) for i in lists]
     # Function to apply text styles to labels
     if colors is None:
         colors = ["r", "b"] if len(lists) == 2 else ["r", "g", "b"]
+    # if labels is None:
+    #     if len(lists) == 2:
+    #         labels = ["set1", "set2"]
+    #     elif len(lists) == 3:
+    #         labels = ["set1", "set2", "set3"]
+    #     elif len(lists) == 4:
+    #         labels = ["set1", "set2", "set3", "set4"]
+    #     elif len(lists) == 5:
+    #         labels = ["set1", "set2", "set3", "set4", "set55"]
+    #     elif len(lists) == 6:
+    #         labels = ["set1", "set2", "set3", "set4", "set5", "set6"]
+    #     elif len(lists) == 7:
+    #         labels = ["set1", "set2", "set3", "set4", "set5", "set6", "set7"]
     if labels is None:
-        if len(lists) == 2:
-            labels = ["set1", "set2"]
-        elif len(lists) == 3:
-            labels = ["set1", "set2", "set3"]
-        elif len(lists) == 4:
-            labels = ["set1", "set2", "set3", "set4"]
-        elif len(lists) == 5:
-            labels = ["set1", "set2", "set3", "set4", "set55"]
-        elif len(lists) == 6:
-            labels = ["set1", "set2", "set3", "set4", "set5", "set6"]
-        elif len(lists) == 7:
-            labels = ["set1", "set2", "set3", "set4", "set5", "set6", "set7"]
-    if edgecolor is None:
-        edgecolor = colors
+        labels = [f"set{i+1}" for i in range(len(lists))]
+    # if edgecolor is None:
+    #     edgecolor = colors
+    edgecolor = edgecolor or colors
     colors = [desaturate_color(color, saturation) for color in colors]
     universe = len(set.union(*lists))
 

{py2ls-0.2.5.9 → py2ls-0.2.5.10}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "py2ls"
-version = "0.2.5.9"
+version = "0.2.5.10"
 description = "py(thon)2(too)ls"
 authors = ["Jianfeng <Jianfeng.Liu0413@gmail.com>"]
 readme = "README.md"