PyPI - hammock-plot - Versions diffs - 0.2__tar.gz → 0.3__tar.gz - Mend

hammock-plot 0.2tar.gz → 0.3tar.gz

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hammock_plot-0.3/PKG-INFO ADDED Viewed

@@ -0,0 +1,179 @@
+Metadata-Version: 2.1
+Name: hammock_plot
+Version: 0.3
+Summary: Hammock - visualization of categorical or mixed categorical/continuous data
+Home-page: https://github.com/TianchengY/hammock_plot
+Author: Tiancheng Yang
+Author-email: t77yang@uwaterloo.ca
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Intended Audience :: Science/Research
+Requires-Python: >=3.6
+Description-Content-Type: text/markdown
+Requires-Dist: matplotlib
+Requires-Dist: numpy
+Requires-Dist: pandas
+# Hammock plot
+## Description
+    hammock draws a graph to visualize categorical data - though it also does fine with continuous data.
+    Variables are lined up parallel to the vertical axis. Categories within a variable are spread out along a
+    vertical line. Categories of adjacent variables are connected by boxes. (The boxes are parallelograms; we
+    use boxes for brevity). The "width" of a box is proportional to the number of observations that correspond
+    to that box (i.e. have the same values/categories for the two variables). The "width" of a box refers to the
+    distance between the longer set of parallel lines rather than the vertical distance.
+    If the boxes degenerate to a single line, and no labels or missing values are used the hammock plot
+    corresponds to a parallel coordinate plot. Boxes degenerate into a single line if barwidth is so small that
+    the boxes for categorical variables appear to be a single line. For continuous variables boxes will usually
+    appear to be a single line because each category typically only contains one observation.
+    The order of variables in varlist determines the order of variables in the graph.  All variables in varlist
+    must be numerical. String variables should be converted to numerical variables first, e.g. using encode or
+    destring.
+## Getting started
+You can install hammock from `pip`:
+```shell
+pip install hammock_plot
+```
+### Example: Asthma data
+We import the diabetes dataset:
+```python
+import hammock_plot
+import pandas as pd
+df = pd.read_csv('../examples/asthma/asth_all3_for_python.csv')
+```
+Minimal example of a hammock plot:
+```python
+var = ["hospitalizations","group","gender","comorbidities"]
+hammock = hammock_plot.Hammock(data_df = df)
+ax = hammock.plot(var=var)
+```
+The ordering of the child-adolescent-adult variable is not in the desired order; adult should not be in the middle. We now specify a specific order, child-adolescent-adult.
+```python
+var = ["hospitalizations","group","gender","comorbidities"]
+group_dict= {1: "child", 2: "adolescent",3: "adult"}
+value_order = {"group": group_dict}
+hammock = hammock_plot.Hammock(data_df = df)
+ax = hammock.plot(var=var, value_order=value_order )
+```
+We highlight observations with comorbidities=0  in red:
+```python
+ax = hammock.plot(var=var, value_order=value_order ,hi_var="comorbidities", hi_value=[0], color=["red"])
+```
+### Example Satisfaction scales for the diabetes data
+We import the diabetes dataset:
+```python
+import hammock_plot
+import pandas as pd
+df = pd.read_csv('../examples/diabetes_outlier/diabetes_for_python.csv')
+```
+The three variables represent different ordinal scales for satisfaction. We are checking for missing values:
+```python
+var = ["sataces","satcomm","satrate"]
+hammock = hammock_plot.Hammock(data_df = df)
+ax = hammock.plot(var=var,  default_color="blue", missing=True)
+```
+The missing value category is shown at the bottom for each variable. We find missing values for all 3 variables, but fewest for the last one. We also see a phenomenon called "top coding", where
+satisfied respondents simply choose the highest value.
+## API Reference
+```
+  hammock()
+```
+| Category | Parameter | Type     | Description                |
+| --- | :-------- | :------- | :-------------------------  |
+| General |     `var` | `List[str]` | List of variables to display. |
+| |             `value_order` | `Dict[str, Dict[int, str]]`  |  If specified, the order of the values in the plot follows the order of values in the list supplied in the dictionary. A specific value order is useful, for example, for ordered variables. The integer values affect spacing: for example the values 4,5,6 imply equal spacing between 4,5 and 5,6. The values 4,5,7 implies twice as much space between 5,7 as between 4,5.
+| |             `missing` | `bool` | Whether or not to add a category for missing values at the bottom of the plot.  If False, observations that have a missing value for any variable in the data frame (even those not used in the hammock plot) are removed.  Default is False. |
+| |             `label` | `bool` | Whether or not to display labels between the plotting segments |
+| Highlighting | `hi_var` | `str` |  Variable to be highlighted. Default is none. |
+| | `hi_value` | `List[str or int]` | List of values of `hi_var` to be highlighted. You can highlighted one or multiple values. |
+| | `hi_missing` | `bool` | Whether or not missing values for `hi_var` should be highlighted. |
+| | `color` | `List[str]` | List of colors corresponding to the list of values to be highlighted. Default highlight color list is ["red", "green", "yellow", "lightblue", "orange", "gray", "brown", "olive", "pink", "cyan", "magenta"] |
+| | `default_color` | `str` |  Default color of plotting elements for boxes that are not highlighted. Default is "blue" |
+| Manipulating Spacing and Layout |   `bar_width` | `float`  | Factor by which the default width is  increased or reduced. This allows reducing visual clutter. Default is 1.0. |
+| |              `space` |  `float`  | Space left for the labels between the plotting elements. Default is 0.5 |
+| |              `label_options` |  `Dict[str, Dict[str, Any]]`  | Manipulates the size and look of the labels. Args following the options in the website: https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.text.html Example:{"ExampleVarname":{"fontsize":12,"fontstyle":"italic","fontweight":"black","color":"b"}}  Default is None. |
+| |              `height` |  `float`  | Height of the plot in inches. Default is 10. |
+| |              `width` |  `float`  |  Width of the plot in inches. Default is 15. Caution: Width too narrow may distort the plot. |
+| Other options |              `shape` |  `str`  | Shape of the boxes. "rectangle" (default) or "parallelogram". |
+| |              `same_scale` |  `List[str]`  | List of variables that have the same scale. Default is None. |
+| |              `display_figure` |  `bool`  | Whether or not to display the figure. This can be useful if you just want to save the plots. Default is 'True'. |
+| |              `save_path` |  `str`  |   If it is not None, the figure will be saved to the given path with given name and format. Default is None. |
+## Historical context
+In 1898, Sankey diagrams were developed to visualize flows of energy and materials.
+In 1985, Inselberg popularized parallel coordinates to visualize continuous variables only. The central contribution is the use of parallel axes.
+In 2003, Schonlau proposed the hammock plot. This was the first plot to visualize categorical data (or mixed categorical continuous data) on parallel axes.
+In 2010, Rosvall proposed alluvial plots to visualize network variables over time. Rather than using bars to connect axes, alluvial plots use rounded curves. Alluvial plots are now also used to visualize categorical data.
+There are several additional variations that also visualize categorical data including Parallel Set plots (Bendix et al, 2005) and Right Angle plots (Hofmann and Vendettuoli, 2013).
+### References
+Bendix, F., Kosara, R., & Hauser, H. (2005). Parallel sets: visual analysis of categorical data. In IEEE Symposium on Information Visualization, 2005. INFOVIS 2005. 133-140.
+Hofmann, H., & Vendettuoli, M. (2013). Common angle plots as perception-true visualizations of categorical associations. IEEE transactions on visualization and computer graphics, 19(12), 2297-2305.
+Inselberg, A., & Dimsdale, B. (2009). Parallel coordinates. Human-Machine Interactive Systems, 199-233.
+Rosvall, Martin, & Bergstrom, C.T. (2010) "Mapping change in large networks." PloS one 5.1: e8694.
+Sankey, H. (1898). Introductory note on the thermal efficiency of steam-engines. report of
+the committee appointed on the 31st march, 1896, to consider and report to the council
+upon the subject of the definition of a standard or standards of thermal efficiency for
+steam-engines: With an introductory note. In Minutes of proceedings of the institution
+of civil engineers, Volume 134, pp. 278–283.
+Schonlau M.
+*[Visualizing Categorical Data Arising in the Health Sciences Using Hammock Plots.](http://www.schonlau.net/publication/03jsm_hammockplot.pdf)*
+In Proceedings of the Section on Statistical Graphics, American Statistical Association; 2003
+### Other implementations of the hammock plot
+There is also a Stata implementation `hammock` (available from the Stata archive SSC) and an R implementation as part of the package `ggparallel`.
+[![MIT License](https://img.shields.io/badge/License-MIT-green.svg)](https://choosealicense.com/licenses/mit/)
+## Authors
+- Tiancheng Yang t77yang@uwaterloo.ca

{hammock_plot-0.2 → hammock_plot-0.3}/hammock_plot/hammock_plot.py RENAMED Viewed

@@ -2,7 +2,7 @@ import pandas as pd
 import numpy as np
 import matplotlib.pyplot as plt
 from abc import ABC, abstractmethod
-from typing import List,Dict
+from typing import List, Dict
 import warnings
@@ -121,7 +121,7 @@ class Hammock:
     def plot(self,
              var: List[str] = None,
-             value_order: Dict[str, Dict[int,str]] = None,
+             value_order: Dict[str, Dict[int, str]] = None,
              missing: bool = False,
              hi_missing: bool = False,
              missing_label_space: float = 1.,
@@ -133,6 +133,7 @@ class Hammock:
              default_color="blue",
              # Manipulating Spacing and Layout
              bar_width: float = 1.,
+             min_bar_width: float = .05,
              space: float = .5,
              label_options: Dict = None,
              height: float = 10.,
@@ -151,7 +152,7 @@ class Hammock:
             if self.data_df[col].dtype.name == "category":
                 self.data_df[col] = self.data_df[col].cat.add_categories(self.missing_data_placeholder)
             elif "float" in self.data_df[col].dtype.name:
-                self.data_df[col] = self.data_df[col].apply(lambda x: np.round(x,2))
+                self.data_df[col] = self.data_df[col].apply(lambda x: np.round(x, 2))
         self.data_df_columns = self.data_df.columns.tolist()
         if not var_lst:
@@ -160,7 +161,6 @@ class Hammock:
             )
         if color and type(color) != type([]):
             raise ValueError(
                 f'Argument "color" must be a list os str.'
             )
@@ -178,9 +178,9 @@ class Hammock:
             )
         if value_order:
-            for k,v_ori in value_order.items():
+            for k, v_ori in value_order.items():
                 uni_val_set = set(self.data_df[k].dropna().unique())
-                v = [value_name for order,value_name in v_ori.items()]
+                v = [value_name for order, value_name in v_ori.items()]
                 if not set(v) >= uni_val_set:
                     error_values = (set(v) ^ uni_val_set) & set(v)
                     raise ValueError(
@@ -218,23 +218,25 @@ class Hammock:
                 self.hi_value.append(self.missing_data_placeholder)
             else:
                 self.hi_value = [self.missing_data_placeholder]
-        colors = ["red", "green", "yellow", "lightblue","orange", "gray", "brown", "olive", "pink", "cyan", "magenta"]
+        colors = ["red", "green", "yellow", "lightblue", "orange", "gray", "brown", "olive", "pink", "cyan", "magenta"]
         self.color_lst = [color for color in color_lst] if color_lst else (
             colors[:len(self.hi_value)] if hi_var else None)
         if hi_var:
             if hi_value and len(self.color_lst) < len(hi_value):
-                for i in range(len(hi_value)-len(self.color_lst)):
+                for i in range(len(hi_value) - len(self.color_lst)):
                     for c in colors:
                         if c not in self.color_lst:
                             self.color_lst.append(c)
                             break
-                warnings.warn(f"Warning: The length of color is less than the total number of (high values and missing), color was automatically extended to {self.color_lst}")
+                warnings.warn(
+                    f"Warning: The length of color is less than the total number of (high values and missing), color was automatically extended to {self.color_lst}")
         if hi_var and default_color in self.color_lst:
             raise ValueError(
                 f'The current highlight colors {self.color_lst} conflict with the default color {default_color}. Please choose another default color or other highlight colors'
             )
         # Manipulating Spacing and Layout
         self.bar_width = bar_width
+        self.min_bar_width = min_bar_width
         self.space = space
         self.label_options = label_options
         self.height = height
@@ -257,7 +259,7 @@ class Hammock:
                 raise ValueError(
                     f'the values: {error_values} in highlight value is not in data.'
                 )
             value_color_dict = dict(zip(self.hi_value, self.color_lst))
             self.data_df[self.color_coloumn_placeholder] = self.data_df[hi_var].apply(
@@ -301,7 +303,7 @@ class Hammock:
         ax, coordinates_dict = self._list_labels(ax, self.height, self.width, self.label)
         space = self.space * 10 if label else 0
-        bar = self.bar_width*3.5/max(data_point_numbers)
+        bar = self.bar_width * 3.5 / max(data_point_numbers)
         if self.shape == "parallelogram":
             figure_type = Parallelogram()
@@ -314,6 +316,8 @@ class Hammock:
                 left_label = k[0]
                 right_label = k[1]
                 width = bar * v
+                if self.min_bar_width and width <= self.min_bar_width:
+                    width = self.min_bar_width
                 left_coordinate = (coordinates_dict[left_label][0] + space, coordinates_dict[left_label][1])
                 right_coordinate = (coordinates_dict[right_label][0] - space, coordinates_dict[right_label][1])
                 widths.append(width)
@@ -335,6 +339,8 @@ class Hammock:
                         right_label = k[1]
                         if v.get(color):
                             width_temp = bar * v.get(color)
+                            if self.min_bar_width and width_temp <= self.min_bar_width:
+                                width_temp = self.min_bar_width
                         else:
                             width_temp = 0
@@ -359,7 +365,7 @@ class Hammock:
     def _get_varname(self, x):
         return x.split(self.same_var_placeholder)[:-1][0]
     def is_float(self, element: any) -> bool:
         if element is None:
             return False
@@ -390,10 +396,10 @@ class Hammock:
         return var_pair_lst
-    def _gen_coordinate(self, start, n, edge, spacing, total_range,val_type="str"):
+    def _gen_coordinate(self, start, n, edge, spacing, total_range, val_type="str"):
         coor_lst = []
-        if val_type=="str":
+        if val_type == "str":
             for i in range(n):
                 coor_lst.append(start + i * spacing)
@@ -405,17 +411,17 @@ class Hammock:
             coor_lst.append(total_range + (start - edge) - edge)
         return coor_lst
-    def _get_same_scale_minmax(self,original_unique_value):
-        min,max = 0,0
-        for i,varname in enumerate(self.same_scale):
+    def _get_same_scale_minmax(self, original_unique_value):
+        min, max = 0, 0
+        for i, varname in enumerate(self.same_scale):
             var_type = str(self.data_df_origin[varname].dtype.name)
             if "int" in var_type or "float" in var_type:
                 min_val, max_val = original_unique_value[varname][0], original_unique_value[varname][-1]
                 if i == 0:
-                    min,max = min_val, max_val
+                    min, max = min_val, max_val
                 else:
-                    min = min_val if min_val<min else min
-                    max = max_val if max_val>max else max
+                    min = min_val if min_val < min else min
+                    max = max_val if max_val > max else max
             else:
                 min_val, max_val = 1, len(original_unique_value[varname])
@@ -424,7 +430,7 @@ class Hammock:
                 else:
                     min = min_val if min_val < min else min
                     max = max_val if max_val > max else max
-        return (min,max)
+        return (min, max)
     def _list_labels(self, ax, figsize_y, figsize_x, label):
@@ -440,24 +446,26 @@ class Hammock:
         unique_value = []
         original_unique_value = {}
         varname_lst = [self._get_varname(var) for var in self.var_lst]
         for var, varname in zip(self.var_lst, varname_lst):
             unique_valnames = self.data_df[varname].dropna().unique().tolist()
             sorted_unique_valnames = []
             if self.value_order and varname in self.value_order:
                 varname_value_order_dict = self.value_order[varname]
                 sorted_unique_valnames_temp = [v for k, v in
-                                          sorted(varname_value_order_dict.items(), key=lambda item: item[0])]
+                                               sorted(varname_value_order_dict.items(), key=lambda item: item[0])]
                 for v in sorted_unique_valnames_temp:
                     if v in unique_valnames:
                         sorted_unique_valnames.append(v)
             if self.missing_data_placeholder in unique_valnames:
                 unique_valnames.remove(self.missing_data_placeholder)
-                sorted_unique_valnames = sorted(unique_valnames) if not sorted_unique_valnames else sorted_unique_valnames
+                sorted_unique_valnames = sorted(
+                    unique_valnames) if not sorted_unique_valnames else sorted_unique_valnames
                 original_unique_value[varname] = sorted_unique_valnames.copy()
                 sorted_unique_valnames.append(self.missing_data_placeholder)
             else:
-                sorted_unique_valnames = sorted(unique_valnames) if not sorted_unique_valnames else sorted_unique_valnames
+                sorted_unique_valnames = sorted(
+                    unique_valnames) if not sorted_unique_valnames else sorted_unique_valnames
                 original_unique_value[varname] = sorted_unique_valnames.copy()
             unique_value.append([(var, x) for x in sorted_unique_valnames])
@@ -472,11 +480,11 @@ class Hammock:
         # prepare for same_scale variabels
         if self.same_scale:
-            same_scale_min,same_scale_max = self._get_same_scale_minmax(original_unique_value)
-            same_scale_range = same_scale_max-same_scale_min
+            same_scale_min, same_scale_max = self._get_same_scale_minmax(original_unique_value)
+            same_scale_range = same_scale_max - same_scale_min
         # plot labels for each variables
-        for var_i,(x, uni_val) in enumerate(zip(label_coordinates, unique_value)):
+        for var_i, (x, uni_val) in enumerate(zip(label_coordinates, unique_value)):
             label_num = len(uni_val) - 2 if (uni_val[0][0], self.missing_data_placeholder) in uni_val else len(
                 uni_val) - 1
             varname = varname_lst[var_i]
@@ -487,21 +495,22 @@ class Hammock:
                 temp_value_range = (y_range - 2 * edge_y_range)
                 # handle the variables in same_scale
                 if self.same_scale and varname in self.same_scale:
-                    min_val, max_val = same_scale_min,same_scale_max
+                    min_val, max_val = same_scale_min, same_scale_max
                 else:
-                    min_val,max_val = original_unique_value[varname][0],original_unique_value[varname][-1]
-                value_interval = [temp_value_range*(x_val-min_val)/(max_val-min_val) for x_val in original_unique_value[varname]]
+                    min_val, max_val = original_unique_value[varname][0], original_unique_value[varname][-1]
+                value_interval = [temp_value_range * (x_val - min_val) / (max_val - min_val) for x_val in
+                                  original_unique_value[varname]]
                 uni_val_coordinates = self._gen_coordinate(y_start, label_num, edge_y_range,
-                                                       value_interval, y_range,val_type = "number")
+                                                           value_interval, y_range, val_type="number")
             else:
                 # handle the variables in same_scale
                 if self.same_scale and varname in self.same_scale:
                     temp_value_range = (y_range - 2 * edge_y_range)
-                    quant_val = list(range(1,len(original_unique_value[varname])+1))
+                    quant_val = list(range(1, len(original_unique_value[varname]) + 1))
                     min_val, max_val = same_scale_min, same_scale_max
                     value_interval = [temp_value_range * (x_val - min_val) / (max_val - min_val) for x_val in quant_val]
                     uni_val_coordinates = self._gen_coordinate(y_start, label_num, edge_y_range,
-                                                        value_interval, y_range, val_type = "number")
+                                                               value_interval, y_range, val_type="number")
                 else:
                     value_interval = (y_range - 2 * edge_y_range) / (label_num)
                     uni_val_coordinates = self._gen_coordinate(y_start, label_num, edge_y_range,
@@ -525,8 +534,6 @@ class Hammock:
                         ax.text(x, y, val[1], ha='center', va='center')
                 coordinates_dict[val] = (x, y)
         return ax, coordinates_dict

hammock_plot-0.3/hammock_plot.egg-info/PKG-INFO ADDED Viewed

@@ -0,0 +1,179 @@
+Metadata-Version: 2.1
+Name: hammock-plot
+Version: 0.3
+Summary: Hammock - visualization of categorical or mixed categorical/continuous data
+Home-page: https://github.com/TianchengY/hammock_plot
+Author: Tiancheng Yang
+Author-email: t77yang@uwaterloo.ca
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Intended Audience :: Science/Research
+Requires-Python: >=3.6
+Description-Content-Type: text/markdown
+Requires-Dist: matplotlib
+Requires-Dist: numpy
+Requires-Dist: pandas
+# Hammock plot
+## Description
+    hammock draws a graph to visualize categorical data - though it also does fine with continuous data.
+    Variables are lined up parallel to the vertical axis. Categories within a variable are spread out along a
+    vertical line. Categories of adjacent variables are connected by boxes. (The boxes are parallelograms; we
+    use boxes for brevity). The "width" of a box is proportional to the number of observations that correspond
+    to that box (i.e. have the same values/categories for the two variables). The "width" of a box refers to the
+    distance between the longer set of parallel lines rather than the vertical distance.
+    If the boxes degenerate to a single line, and no labels or missing values are used the hammock plot
+    corresponds to a parallel coordinate plot. Boxes degenerate into a single line if barwidth is so small that
+    the boxes for categorical variables appear to be a single line. For continuous variables boxes will usually
+    appear to be a single line because each category typically only contains one observation.
+    The order of variables in varlist determines the order of variables in the graph.  All variables in varlist
+    must be numerical. String variables should be converted to numerical variables first, e.g. using encode or
+    destring.
+## Getting started
+You can install hammock from `pip`:
+```shell
+pip install hammock_plot
+```
+### Example: Asthma data
+We import the diabetes dataset:
+```python
+import hammock_plot
+import pandas as pd
+df = pd.read_csv('../examples/asthma/asth_all3_for_python.csv')
+```
+Minimal example of a hammock plot:
+```python
+var = ["hospitalizations","group","gender","comorbidities"]
+hammock = hammock_plot.Hammock(data_df = df)
+ax = hammock.plot(var=var)
+```
+The ordering of the child-adolescent-adult variable is not in the desired order; adult should not be in the middle. We now specify a specific order, child-adolescent-adult.
+```python
+var = ["hospitalizations","group","gender","comorbidities"]
+group_dict= {1: "child", 2: "adolescent",3: "adult"}
+value_order = {"group": group_dict}
+hammock = hammock_plot.Hammock(data_df = df)
+ax = hammock.plot(var=var, value_order=value_order )
+```
+We highlight observations with comorbidities=0  in red:
+```python
+ax = hammock.plot(var=var, value_order=value_order ,hi_var="comorbidities", hi_value=[0], color=["red"])
+```
+### Example Satisfaction scales for the diabetes data
+We import the diabetes dataset:
+```python
+import hammock_plot
+import pandas as pd
+df = pd.read_csv('../examples/diabetes_outlier/diabetes_for_python.csv')
+```
+The three variables represent different ordinal scales for satisfaction. We are checking for missing values:
+```python
+var = ["sataces","satcomm","satrate"]
+hammock = hammock_plot.Hammock(data_df = df)
+ax = hammock.plot(var=var,  default_color="blue", missing=True)
+```
+The missing value category is shown at the bottom for each variable. We find missing values for all 3 variables, but fewest for the last one. We also see a phenomenon called "top coding", where
+satisfied respondents simply choose the highest value.
+## API Reference
+```
+  hammock()
+```
+| Category | Parameter | Type     | Description                |
+| --- | :-------- | :------- | :-------------------------  |
+| General |     `var` | `List[str]` | List of variables to display. |
+| |             `value_order` | `Dict[str, Dict[int, str]]`  |  If specified, the order of the values in the plot follows the order of values in the list supplied in the dictionary. A specific value order is useful, for example, for ordered variables. The integer values affect spacing: for example the values 4,5,6 imply equal spacing between 4,5 and 5,6. The values 4,5,7 implies twice as much space between 5,7 as between 4,5.
+| |             `missing` | `bool` | Whether or not to add a category for missing values at the bottom of the plot.  If False, observations that have a missing value for any variable in the data frame (even those not used in the hammock plot) are removed.  Default is False. |
+| |             `label` | `bool` | Whether or not to display labels between the plotting segments |
+| Highlighting | `hi_var` | `str` |  Variable to be highlighted. Default is none. |
+| | `hi_value` | `List[str or int]` | List of values of `hi_var` to be highlighted. You can highlighted one or multiple values. |
+| | `hi_missing` | `bool` | Whether or not missing values for `hi_var` should be highlighted. |
+| | `color` | `List[str]` | List of colors corresponding to the list of values to be highlighted. Default highlight color list is ["red", "green", "yellow", "lightblue", "orange", "gray", "brown", "olive", "pink", "cyan", "magenta"] |
+| | `default_color` | `str` |  Default color of plotting elements for boxes that are not highlighted. Default is "blue" |
+| Manipulating Spacing and Layout |   `bar_width` | `float`  | Factor by which the default width is  increased or reduced. This allows reducing visual clutter. Default is 1.0. |
+| |              `space` |  `float`  | Space left for the labels between the plotting elements. Default is 0.5 |
+| |              `label_options` |  `Dict[str, Dict[str, Any]]`  | Manipulates the size and look of the labels. Args following the options in the website: https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.text.html Example:{"ExampleVarname":{"fontsize":12,"fontstyle":"italic","fontweight":"black","color":"b"}}  Default is None. |
+| |              `height` |  `float`  | Height of the plot in inches. Default is 10. |
+| |              `width` |  `float`  |  Width of the plot in inches. Default is 15. Caution: Width too narrow may distort the plot. |
+| Other options |              `shape` |  `str`  | Shape of the boxes. "rectangle" (default) or "parallelogram". |
+| |              `same_scale` |  `List[str]`  | List of variables that have the same scale. Default is None. |
+| |              `display_figure` |  `bool`  | Whether or not to display the figure. This can be useful if you just want to save the plots. Default is 'True'. |
+| |              `save_path` |  `str`  |   If it is not None, the figure will be saved to the given path with given name and format. Default is None. |
+## Historical context
+In 1898, Sankey diagrams were developed to visualize flows of energy and materials.
+In 1985, Inselberg popularized parallel coordinates to visualize continuous variables only. The central contribution is the use of parallel axes.
+In 2003, Schonlau proposed the hammock plot. This was the first plot to visualize categorical data (or mixed categorical continuous data) on parallel axes.
+In 2010, Rosvall proposed alluvial plots to visualize network variables over time. Rather than using bars to connect axes, alluvial plots use rounded curves. Alluvial plots are now also used to visualize categorical data.
+There are several additional variations that also visualize categorical data including Parallel Set plots (Bendix et al, 2005) and Right Angle plots (Hofmann and Vendettuoli, 2013).
+### References
+Bendix, F., Kosara, R., & Hauser, H. (2005). Parallel sets: visual analysis of categorical data. In IEEE Symposium on Information Visualization, 2005. INFOVIS 2005. 133-140.
+Hofmann, H., & Vendettuoli, M. (2013). Common angle plots as perception-true visualizations of categorical associations. IEEE transactions on visualization and computer graphics, 19(12), 2297-2305.
+Inselberg, A., & Dimsdale, B. (2009). Parallel coordinates. Human-Machine Interactive Systems, 199-233.
+Rosvall, Martin, & Bergstrom, C.T. (2010) "Mapping change in large networks." PloS one 5.1: e8694.
+Sankey, H. (1898). Introductory note on the thermal efficiency of steam-engines. report of
+the committee appointed on the 31st march, 1896, to consider and report to the council
+upon the subject of the definition of a standard or standards of thermal efficiency for
+steam-engines: With an introductory note. In Minutes of proceedings of the institution
+of civil engineers, Volume 134, pp. 278–283.
+Schonlau M.
+*[Visualizing Categorical Data Arising in the Health Sciences Using Hammock Plots.](http://www.schonlau.net/publication/03jsm_hammockplot.pdf)*
+In Proceedings of the Section on Statistical Graphics, American Statistical Association; 2003
+### Other implementations of the hammock plot
+There is also a Stata implementation `hammock` (available from the Stata archive SSC) and an R implementation as part of the package `ggparallel`.
+[![MIT License](https://img.shields.io/badge/License-MIT-green.svg)](https://choosealicense.com/licenses/mit/)
+## Authors
+- Tiancheng Yang t77yang@uwaterloo.ca

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@@ -1,4 +1,5 @@
 README.md
+setup.cfg
 setup.py
 hammock_plot/__init__.py
 hammock_plot/hammock_plot.py

{hammock_plot-0.2 → hammock_plot-0.3}/setup.py RENAMED Viewed

@@ -6,7 +6,7 @@ with open("README.md", "r", encoding="utf8") as fh:
 setuptools.setup(
     name="hammock_plot",
-    version='0.2',
+    version='0.3',
     author="Tiancheng Yang",
     author_email="t77yang@uwaterloo.ca",
     description="Hammock - visualization of categorical or mixed categorical/continuous data",

hammock_plot-0.2/PKG-INFO DELETED Viewed

@@ -1,178 +0,0 @@
-Metadata-Version: 2.1
-Name: hammock_plot
-Version: 0.2
-Summary: Hammock - visualization of categorical or mixed categorical/continuous data
-Home-page: https://github.com/TianchengY/hammock_plot
-Author: Tiancheng Yang
-Author-email: t77yang@uwaterloo.ca
-License: UNKNOWN
-Description: # Hammock plot
-        ## Description
-            hammock draws a graph to visualize categorical data - though it also does fine with continuous data.
-            Variables are lined up parallel to the vertical axis. Categories within a variable are spread out along a
-            vertical line. Categories of adjacent variables are connected by boxes. (The boxes are parallelograms; we
-            use boxes for brevity). The "width" of a box is proportional to the number of observations that correspond
-            to that box (i.e. have the same values/categories for the two variables). The "width" of a box refers to the
-            distance between the longer set of parallel lines rather than the vertical distance.
-            If the boxes degenerate to a single line, and no labels or missing values are used the hammock plot
-            corresponds to a parallel coordinate plot. Boxes degenerate into a single line if barwidth is so small that
-            the boxes for categorical variables appear to be a single line. For continuous variables boxes will usually
-            appear to be a single line because each category typically only contains one observation.
-            The order of variables in varlist determines the order of variables in the graph.  All variables in varlist
-            must be numerical. String variables should be converted to numerical variables first, e.g. using encode or
-            destring.
-        ## Getting started
-        You can install hammock from `pip`:
-        ```shell
-        pip install hammock_plot
-        ```
-        ### Example: Asthma data
-        We import the diabetes dataset:
-        ```python
-        import hammock_plot
-        import pandas as pd
-        df = pd.read_csv('../examples/asthma/asth_all3_for_python.csv')
-        ```
-        Minimal example of a hammock plot:
-        ```python
-        var = ["hospitalizations","group","gender","comorbidities"]
-        hammock = hammock_plot.Hammock(data_df = df)
-        ax = hammock.plot(var=var)
-        ```
-        The ordering of the child-adolescent-adult variable is not in the desired order; adult should not be in the middle. We now specify a specific order, child-adolescent-adult.
-        ```python
-        var = ["hospitalizations","group","gender","comorbidities"]
-        group_dict= {1: "child", 2: "adolescent",3: "adult"}
-        value_order = {"group": group_dict}
-        hammock = hammock_plot.Hammock(data_df = df)
-        ax = hammock.plot(var=var, value_order=value_order )
-        ```
-        We highlight observations with comorbidities=0  in red:
-        ```python
-        ax = hammock.plot(var=var, value_order=value_order ,hi_var="comorbidities", hi_value=[0], color=["red"])
-        ```
-        ### Example Satisfaction scales for the diabetes data
-        We import the diabetes dataset:
-        ```python
-        import hammock_plot
-        import pandas as pd
-        df = pd.read_csv('../examples/diabetes_outlier/diabetes_for_python.csv')
-        ```
-        The three variables represent different ordinal scales for satisfaction. We are checking for missing values:
-        ```python
-        var = ["sataces","satcomm","satrate"]
-        hammock = hammock_plot.Hammock(data_df = df)
-        ax = hammock.plot(var=var,  default_color="blue", missing=True)
-        ```
-        The missing value category is shown at the bottom for each variable. We find missing values for all 3 variables, but fewest for the last one. We also see a phenomenon called "top coding", where
-        satisfied respondents simply choose the highest value.
-        ## API Reference
-        ```
-          hammock()
-        ```
-        | Category | Parameter | Type     | Description                |
-        | --- | :-------- | :------- | :-------------------------  |
-        | General |     `var` | `List[str]` | List of variables to display. |
-        | |             `value_order` | `Dict[str, Dict[int, str]]`  |  If specified, the order of the values in the plot follows the order of values in the list supplied in the dictionary. A specific value order is useful, for example, for ordered variables. The integer values affect spacing: for example the values 4,5,6 imply equal spacing between 4,5 and 5,6. The values 4,5,7 implies twice as much space between 5,7 as between 4,5.
-        | |             `missing` | `bool` | Whether or not to add a category for missing values at the bottom of the plot.  If False, observations that have a missing value for any variable in the data frame (even those not used in the hammock plot) are removed.  Default is False. |
-        | |             `label` | `bool` | Whether or not to display labels between the plotting segments |
-        | Highlighting | `hi_var` | `str` |  Variable to be highlighted. Default is none. |
-        | | `hi_value` | `List[str or int]` | List of values of `hi_var` to be highlighted. You can highlighted one or multiple values. |
-        | | `hi_missing` | `bool` | Whether or not missing values for `hi_var` should be highlighted. |
-        | | `color` | `List[str]` | List of colors corresponding to the list of values to be highlighted. Default highlight color list is ["red", "green", "yellow", "lightblue", "orange", "gray", "brown", "olive", "pink", "cyan", "magenta"] |
-        | | `default_color` | `str` |  Default color of plotting elements for boxes that are not highlighted. Default is "blue" |
-        | Manipulating Spacing and Layout |   `bar_width` | `float`  | Factor by which the default width is  increased or reduced. This allows reducing visual clutter. Default is 1.0. |
-        | |              `space` |  `float`  | Space left for the labels between the plotting elements. Default is 0.5 |
-        | |              `label_options` |  `Dict[str, Dict[str, Any]]`  | Manipulates the size and look of the labels. Args following the options in the website: https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.text.html Example:{"ExampleVarname":{"fontsize":12,"fontstyle":"italic","fontweight":"black","color":"b"}}  Default is None. |
-        | |              `height` |  `float`  | Height of the plot in inches. Default is 10. |
-        | |              `width` |  `float`  |  Width of the plot in inches. Default is 15. Caution: Width too narrow may distort the plot. |
-        | Other options |              `shape` |  `str`  | Shape of the boxes. "rectangle" (default) or "parallelogram". |
-        | |              `same_scale` |  `List[str]`  | List of variables that have the same scale. Default is None. |
-        | |              `display_figure` |  `bool`  | Whether or not to display the figure. This can be useful if you just want to save the plots. Default is 'True'. |
-        | |              `save_path` |  `str`  |   If it is not None, the figure will be saved to the given path with given name and format. Default is None. |
-        ## Historical context
-        In 1898, Sankey diagrams were developed to visualize flows of energy and materials.
-        In 1985, Inselberg popularized parallel coordinates to visualize continuous variables only. The central contribution is the use of parallel axes.
-        In 2003, Schonlau proposed the hammock plot. This was the first plot to visualize categorical data (or mixed categorical continuous data) on parallel axes.
-        In 2010, Rosvall proposed alluvial plots to visualize network variables over time. Rather than using bars to connect axes, alluvial plots use rounded curves. Alluvial plots are now also used to visualize categorical data.
-        There are several additional variations that also visualize categorical data including Parallel Set plots (Bendix et al, 2005) and Right Angle plots (Hofmann and Vendettuoli, 2013).
-        ### References
-        Bendix, F., Kosara, R., & Hauser, H. (2005). Parallel sets: visual analysis of categorical data. In IEEE Symposium on Information Visualization, 2005. INFOVIS 2005. 133-140.
-        Hofmann, H., & Vendettuoli, M. (2013). Common angle plots as perception-true visualizations of categorical associations. IEEE transactions on visualization and computer graphics, 19(12), 2297-2305.
-        Inselberg, A., & Dimsdale, B. (2009). Parallel coordinates. Human-Machine Interactive Systems, 199-233.
-        Rosvall, Martin, & Bergstrom, C.T. (2010) "Mapping change in large networks." PloS one 5.1: e8694.
-        Sankey, H. (1898). Introductory note on the thermal efficiency of steam-engines. report of
-        the committee appointed on the 31st march, 1896, to consider and report to the council
-        upon the subject of the definition of a standard or standards of thermal efficiency for
-        steam-engines: With an introductory note. In Minutes of proceedings of the institution
-        of civil engineers, Volume 134, pp. 278–283.
-        Schonlau M.
-        *[Visualizing Categorical Data Arising in the Health Sciences Using Hammock Plots.](http://www.schonlau.net/publication/03jsm_hammockplot.pdf)*
-        In Proceedings of the Section on Statistical Graphics, American Statistical Association; 2003
-        ### Other implementations of the hammock plot
-        There is also a Stata implementation `hammock` (available from the Stata archive SSC) and an R implementation as part of the package `ggparallel`.
-        [![MIT License](https://img.shields.io/badge/License-MIT-green.svg)](https://choosealicense.com/licenses/mit/)
-        ## Authors
-        - Tiancheng Yang t77yang@uwaterloo.ca
-Platform: UNKNOWN
-Classifier: Programming Language :: Python :: 3
-Classifier: License :: OSI Approved :: MIT License
-Classifier: Operating System :: OS Independent
-Classifier: Intended Audience :: Science/Research
-Requires-Python: >=3.6
-Description-Content-Type: text/markdown

hammock_plot-0.2/hammock_plot.egg-info/PKG-INFO DELETED Viewed

@@ -1,178 +0,0 @@
-Metadata-Version: 2.1
-Name: hammock-plot
-Version: 0.2
-Summary: Hammock - visualization of categorical or mixed categorical/continuous data
-Home-page: https://github.com/TianchengY/hammock_plot
-Author: Tiancheng Yang
-Author-email: t77yang@uwaterloo.ca
-License: UNKNOWN
-Description: # Hammock plot
-        ## Description
-            hammock draws a graph to visualize categorical data - though it also does fine with continuous data.
-            Variables are lined up parallel to the vertical axis. Categories within a variable are spread out along a
-            vertical line. Categories of adjacent variables are connected by boxes. (The boxes are parallelograms; we
-            use boxes for brevity). The "width" of a box is proportional to the number of observations that correspond
-            to that box (i.e. have the same values/categories for the two variables). The "width" of a box refers to the
-            distance between the longer set of parallel lines rather than the vertical distance.
-            If the boxes degenerate to a single line, and no labels or missing values are used the hammock plot
-            corresponds to a parallel coordinate plot. Boxes degenerate into a single line if barwidth is so small that
-            the boxes for categorical variables appear to be a single line. For continuous variables boxes will usually
-            appear to be a single line because each category typically only contains one observation.
-            The order of variables in varlist determines the order of variables in the graph.  All variables in varlist
-            must be numerical. String variables should be converted to numerical variables first, e.g. using encode or
-            destring.
-        ## Getting started
-        You can install hammock from `pip`:
-        ```shell
-        pip install hammock_plot
-        ```
-        ### Example: Asthma data
-        We import the diabetes dataset:
-        ```python
-        import hammock_plot
-        import pandas as pd
-        df = pd.read_csv('../examples/asthma/asth_all3_for_python.csv')
-        ```
-        Minimal example of a hammock plot:
-        ```python
-        var = ["hospitalizations","group","gender","comorbidities"]
-        hammock = hammock_plot.Hammock(data_df = df)
-        ax = hammock.plot(var=var)
-        ```
-        The ordering of the child-adolescent-adult variable is not in the desired order; adult should not be in the middle. We now specify a specific order, child-adolescent-adult.
-        ```python
-        var = ["hospitalizations","group","gender","comorbidities"]
-        group_dict= {1: "child", 2: "adolescent",3: "adult"}
-        value_order = {"group": group_dict}
-        hammock = hammock_plot.Hammock(data_df = df)
-        ax = hammock.plot(var=var, value_order=value_order )
-        ```
-        We highlight observations with comorbidities=0  in red:
-        ```python
-        ax = hammock.plot(var=var, value_order=value_order ,hi_var="comorbidities", hi_value=[0], color=["red"])
-        ```
-        ### Example Satisfaction scales for the diabetes data
-        We import the diabetes dataset:
-        ```python
-        import hammock_plot
-        import pandas as pd
-        df = pd.read_csv('../examples/diabetes_outlier/diabetes_for_python.csv')
-        ```
-        The three variables represent different ordinal scales for satisfaction. We are checking for missing values:
-        ```python
-        var = ["sataces","satcomm","satrate"]
-        hammock = hammock_plot.Hammock(data_df = df)
-        ax = hammock.plot(var=var,  default_color="blue", missing=True)
-        ```
-        The missing value category is shown at the bottom for each variable. We find missing values for all 3 variables, but fewest for the last one. We also see a phenomenon called "top coding", where
-        satisfied respondents simply choose the highest value.
-        ## API Reference
-        ```
-          hammock()
-        ```
-        | Category | Parameter | Type     | Description                |
-        | --- | :-------- | :------- | :-------------------------  |
-        | General |     `var` | `List[str]` | List of variables to display. |
-        | |             `value_order` | `Dict[str, Dict[int, str]]`  |  If specified, the order of the values in the plot follows the order of values in the list supplied in the dictionary. A specific value order is useful, for example, for ordered variables. The integer values affect spacing: for example the values 4,5,6 imply equal spacing between 4,5 and 5,6. The values 4,5,7 implies twice as much space between 5,7 as between 4,5.
-        | |             `missing` | `bool` | Whether or not to add a category for missing values at the bottom of the plot.  If False, observations that have a missing value for any variable in the data frame (even those not used in the hammock plot) are removed.  Default is False. |
-        | |             `label` | `bool` | Whether or not to display labels between the plotting segments |
-        | Highlighting | `hi_var` | `str` |  Variable to be highlighted. Default is none. |
-        | | `hi_value` | `List[str or int]` | List of values of `hi_var` to be highlighted. You can highlighted one or multiple values. |
-        | | `hi_missing` | `bool` | Whether or not missing values for `hi_var` should be highlighted. |
-        | | `color` | `List[str]` | List of colors corresponding to the list of values to be highlighted. Default highlight color list is ["red", "green", "yellow", "lightblue", "orange", "gray", "brown", "olive", "pink", "cyan", "magenta"] |
-        | | `default_color` | `str` |  Default color of plotting elements for boxes that are not highlighted. Default is "blue" |
-        | Manipulating Spacing and Layout |   `bar_width` | `float`  | Factor by which the default width is  increased or reduced. This allows reducing visual clutter. Default is 1.0. |
-        | |              `space` |  `float`  | Space left for the labels between the plotting elements. Default is 0.5 |
-        | |              `label_options` |  `Dict[str, Dict[str, Any]]`  | Manipulates the size and look of the labels. Args following the options in the website: https://matplotlib.org/stable/api/_as_gen/matplotlib.pyplot.text.html Example:{"ExampleVarname":{"fontsize":12,"fontstyle":"italic","fontweight":"black","color":"b"}}  Default is None. |
-        | |              `height` |  `float`  | Height of the plot in inches. Default is 10. |
-        | |              `width` |  `float`  |  Width of the plot in inches. Default is 15. Caution: Width too narrow may distort the plot. |
-        | Other options |              `shape` |  `str`  | Shape of the boxes. "rectangle" (default) or "parallelogram". |
-        | |              `same_scale` |  `List[str]`  | List of variables that have the same scale. Default is None. |
-        | |              `display_figure` |  `bool`  | Whether or not to display the figure. This can be useful if you just want to save the plots. Default is 'True'. |
-        | |              `save_path` |  `str`  |   If it is not None, the figure will be saved to the given path with given name and format. Default is None. |
-        ## Historical context
-        In 1898, Sankey diagrams were developed to visualize flows of energy and materials.
-        In 1985, Inselberg popularized parallel coordinates to visualize continuous variables only. The central contribution is the use of parallel axes.
-        In 2003, Schonlau proposed the hammock plot. This was the first plot to visualize categorical data (or mixed categorical continuous data) on parallel axes.
-        In 2010, Rosvall proposed alluvial plots to visualize network variables over time. Rather than using bars to connect axes, alluvial plots use rounded curves. Alluvial plots are now also used to visualize categorical data.
-        There are several additional variations that also visualize categorical data including Parallel Set plots (Bendix et al, 2005) and Right Angle plots (Hofmann and Vendettuoli, 2013).
-        ### References
-        Bendix, F., Kosara, R., & Hauser, H. (2005). Parallel sets: visual analysis of categorical data. In IEEE Symposium on Information Visualization, 2005. INFOVIS 2005. 133-140.
-        Hofmann, H., & Vendettuoli, M. (2013). Common angle plots as perception-true visualizations of categorical associations. IEEE transactions on visualization and computer graphics, 19(12), 2297-2305.
-        Inselberg, A., & Dimsdale, B. (2009). Parallel coordinates. Human-Machine Interactive Systems, 199-233.
-        Rosvall, Martin, & Bergstrom, C.T. (2010) "Mapping change in large networks." PloS one 5.1: e8694.
-        Sankey, H. (1898). Introductory note on the thermal efficiency of steam-engines. report of
-        the committee appointed on the 31st march, 1896, to consider and report to the council
-        upon the subject of the definition of a standard or standards of thermal efficiency for
-        steam-engines: With an introductory note. In Minutes of proceedings of the institution
-        of civil engineers, Volume 134, pp. 278–283.
-        Schonlau M.
-        *[Visualizing Categorical Data Arising in the Health Sciences Using Hammock Plots.](http://www.schonlau.net/publication/03jsm_hammockplot.pdf)*
-        In Proceedings of the Section on Statistical Graphics, American Statistical Association; 2003
-        ### Other implementations of the hammock plot
-        There is also a Stata implementation `hammock` (available from the Stata archive SSC) and an R implementation as part of the package `ggparallel`.
-        [![MIT License](https://img.shields.io/badge/License-MIT-green.svg)](https://choosealicense.com/licenses/mit/)
-        ## Authors
-        - Tiancheng Yang t77yang@uwaterloo.ca
-Platform: UNKNOWN
-Classifier: Programming Language :: Python :: 3
-Classifier: License :: OSI Approved :: MIT License
-Classifier: Operating System :: OS Independent
-Classifier: Intended Audience :: Science/Research
-Requires-Python: >=3.6
-Description-Content-Type: text/markdown

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