hammock-plot 0.3__tar.gz → 0.4__tar.gz

hammock_plot-0.4/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2023 Tiancheng Yang
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

{hammock_plot-0.3/hammock_plot.egg-info → hammock_plot-0.4}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
-Name: hammock-plot
-Version: 0.3
+Metadata-Version: 2.4
+Name: hammock_plot
+Version: 0.4
 Summary: Hammock - visualization of categorical or mixed categorical/continuous data
 Home-page: https://github.com/TianchengY/hammock_plot
 Author: Tiancheng Yang
@@ -11,16 +11,27 @@ Classifier: Operating System :: OS Independent
 Classifier: Intended Audience :: Science/Research
 Requires-Python: >=3.6
 Description-Content-Type: text/markdown
+License-File: LICENSE
 Requires-Dist: matplotlib
 Requires-Dist: numpy
 Requires-Dist: pandas
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license-file
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
 
 # Hammock plot
 
 
 ## Description
 
-    hammock draws a graph to visualize categorical data - though it also does fine with continuous data.
+    The hammock plot draws a graph to visualize categorical or mixed categorical / 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
@@ -64,6 +75,7 @@ var = ["hospitalizations","group","gender","comorbidities"]
 hammock = hammock_plot.Hammock(data_df = df)
 ax = hammock.plot(var=var)
 ```
+<img src="image/asthma_minimal.png" alt="Minimal example for a Hammock plot" width="600"/>
 
 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. 
 
@@ -75,12 +87,19 @@ hammock = hammock_plot.Hammock(data_df = df)
 ax = hammock.plot(var=var, value_order=value_order )
 ```
 
+<!--- to restrict image size, I am using a an html command, rather than the standard ![](image.png) --->
+<!---    ![Hammock plot ](image/asthma1.png)   --->
+<img src="image/asthma_value_order.png" alt="Hammock plot" width="600"/>
+
 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"])
 ```
 
+<!---   ![Hammock plot with highlighting](image/asthma_highlighting.png)    --->
+<img src="image/asthma_highlighting.png" alt="Hammock plot with highlighting" width="600"/>
+
 
 ### Example Satisfaction scales for the diabetes data
 
@@ -96,9 +115,11 @@ The three variables represent different ordinal scales for satisfaction. We are
 ```python
 var = ["sataces","satcomm","satrate"]
 hammock = hammock_plot.Hammock(data_df = df)
-ax = hammock.plot(var=var,  default_color="blue", missing=True) 
+ax = hammock.plot(var=var, missing=True) 
 ```
 
+<img src="image/diabetes.png" alt="Hammock plot for the Diabetes Data" width="600"/>
+
 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.
 
@@ -118,14 +139,16 @@ satisfied respondents simply choose the highest value.
 | |             `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_box` | `str` | Controls how highlighted values are displayed within category labels. Options are "vertical" for vertically stacked color segments or "horizontal" for horizontally split color segments. Default is "vertical".|
 | | `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"] |
+| | `color` | `List[str]` | List of colors corresponding to the list of values to be highlighted. Each color can be specified as a plain color name (e.g., `"red"`, `"yellow"`) or in the format `"color=alpha"` (e.g., `"red=0.5"`) to control transparency/intensity, where `alpha` is a decimal between 0 and 1. The 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. | 
+| |              `min_bar_width` | `float` | Minimal bar width. Bars representing only a tiny fraction of the data may be so narrow, that they are invivisible in a plot. The default value tries to ensure this does not happen.  Default is 0.07.
 | 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'. | 
@@ -142,7 +165,8 @@ In 2003, Schonlau proposed the hammock plot. This was the first plot to visualiz
 
 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).
+There are several additional variations that also visualize categorical data including Parallel Set plots (Bendix et al, 2005), Right Angle plots (Hofmann and Vendettuoli, 2013),
+and generalized parallel coordinate plots (GPCPs) (popularized by VanderPlas et al., 2023). 
 
 ### 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. 
@@ -163,7 +187,9 @@ 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
 
-
+VanderPlas, S., Ge, Y., Unwin, A., & Hofmann, H. (2023). 
+Penguins Go Parallel: a grammar of graphics framework for generalized parallel coordinate plots. 
+Journal of Computational and Graphical Statistics, 1-16. (online first)
 
 ### 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`.

hammock_plot-0.3/PKG-INFO → hammock_plot-0.4/README.md

@@ -1,26 +1,9 @@
-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.
+    The hammock plot draws a graph to visualize categorical or mixed categorical / 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
@@ -64,6 +47,7 @@ var = ["hospitalizations","group","gender","comorbidities"]
 hammock = hammock_plot.Hammock(data_df = df)
 ax = hammock.plot(var=var)
 ```
+<img src="image/asthma_minimal.png" alt="Minimal example for a Hammock plot" width="600"/>
 
 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. 
 
@@ -75,12 +59,19 @@ hammock = hammock_plot.Hammock(data_df = df)
 ax = hammock.plot(var=var, value_order=value_order )
 ```
 
+<!--- to restrict image size, I am using a an html command, rather than the standard ![](image.png) --->
+<!---    ![Hammock plot ](image/asthma1.png)   --->
+<img src="image/asthma_value_order.png" alt="Hammock plot" width="600"/>
+
 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"])
 ```
 
+<!---   ![Hammock plot with highlighting](image/asthma_highlighting.png)    --->
+<img src="image/asthma_highlighting.png" alt="Hammock plot with highlighting" width="600"/>
+
 
 ### Example Satisfaction scales for the diabetes data
 
@@ -96,9 +87,11 @@ The three variables represent different ordinal scales for satisfaction. We are
 ```python
 var = ["sataces","satcomm","satrate"]
 hammock = hammock_plot.Hammock(data_df = df)
-ax = hammock.plot(var=var,  default_color="blue", missing=True) 
+ax = hammock.plot(var=var, missing=True) 
 ```
 
+<img src="image/diabetes.png" alt="Hammock plot for the Diabetes Data" width="600"/>
+
 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.
 
@@ -118,14 +111,16 @@ satisfied respondents simply choose the highest value.
 | |             `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_box` | `str` | Controls how highlighted values are displayed within category labels. Options are "vertical" for vertically stacked color segments or "horizontal" for horizontally split color segments. Default is "vertical".|
 | | `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"] |
+| | `color` | `List[str]` | List of colors corresponding to the list of values to be highlighted. Each color can be specified as a plain color name (e.g., `"red"`, `"yellow"`) or in the format `"color=alpha"` (e.g., `"red=0.5"`) to control transparency/intensity, where `alpha` is a decimal between 0 and 1. The 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. | 
+| |              `min_bar_width` | `float` | Minimal bar width. Bars representing only a tiny fraction of the data may be so narrow, that they are invivisible in a plot. The default value tries to ensure this does not happen.  Default is 0.07.
 | 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'. | 
@@ -142,7 +137,8 @@ In 2003, Schonlau proposed the hammock plot. This was the first plot to visualiz
 
 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).
+There are several additional variations that also visualize categorical data including Parallel Set plots (Bendix et al, 2005), Right Angle plots (Hofmann and Vendettuoli, 2013),
+and generalized parallel coordinate plots (GPCPs) (popularized by VanderPlas et al., 2023). 
 
 ### 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. 
@@ -163,7 +159,9 @@ 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
 
-
+VanderPlas, S., Ge, Y., Unwin, A., & Hofmann, H. (2023). 
+Penguins Go Parallel: a grammar of graphics framework for generalized parallel coordinate plots. 
+Journal of Computational and Graphical Statistics, 1-16. (online first)
 
 ### 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`.

{hammock_plot-0.3 → hammock_plot-0.4}/hammock_plot/__init__.py

@@ -1,4 +1,4 @@
-from .hammock_plot import Hammock
-
-__author__ = "Tiancheng Yang"
-__author_email__ = "t77yang@uwaterloo.ca"
+from .hammock_plot import Hammock
+
+__author__ = "Tiancheng Yang"
+__author_email__ = "t77yang@uwaterloo.ca"