Merge pull request #2 from MSD-IRIMAS/aif/fix_read_me

[ENH-BUG] Refactoring README and fix the white axis bug with new version of matplotlib

Author: hadifawaz1999

.gitignore

@@ -14,6 +14,9 @@ __pycache__/
 !heatmap.png
 !heatline_vertical.png
 !heatline_horizontal.png
+!heatmap.pdf
+!heatline_horizontal.tex
+
 
 # Distribution / packaging
 .Python

MCM/MCM.py

@@ -553,6 +553,7 @@ def draw(
 
     plt.rcParams["figure.autolayout"] = True
     fig, ax = plt.subplots(1, 1, figsize=(figsize[0], figsize[1]))
+    ax.grid(False)
 
     _can_be_negative = False
     if colorbar_value is None or colorbar_value == "mean-difference":

README.md

@@ -12,7 +12,7 @@ The input format is in a ```.csv``` file containing the statistics of each class
 
 ## Usage of Code - Plot the MCM
 
-In order for the user to plot the MCM, first thing is to load the ```.csv``` file into a ```pandas``` dataframe and feed it to the ```compare``` function. The user should specify the ```fig_savename``` parameter in order to save the output figure in ```pdf``` and ```png``` formats.
+In order for the user to plot the MCM, first thing is to load the ```.csv``` file into a ```pandas``` dataframe and feed it to the ```compare``` function. The user should specify the ```pdf_savename```, ```png_savename```, ```csv_savename``` or ```tex_savename``` parameter in order to save the output figure in ```pdf```, ```png```, ```csv``` or ```tex``` formats respecively.
 
 ## Examples
 
@@ -29,8 +29,8 @@ output_dir = '/output/directory/desired'
 MCM.compare(
         output_dir=output_dir,
         df_results=df_results,
-        fig_savename='heatmap',
-        load_analysis=False
+        pdf_savename="heatmap",
+        png_savename="heatmap",
     )
 ```
 
@@ -52,8 +52,9 @@ MCM.compare(
         output_dir=output_dir,
         df_results=df_results,
         excluded_col_comparates=['clf1','clf3'],
-        fig_savename='heatline_vertical',
-        load_analysis=False
+        png_savename='heatline_vertical',
+        tex_savename='heatline_vertical',
+        include_ProbaWinTieLoss=True
     )
 ```
 
@@ -75,8 +76,8 @@ MCM.compare(
         output_dir=output_dir,
         df_results=df_results,
         excluded_row_comparates=['clf1','clf3'],
-        fig_savename='heatline_vertical',
-        load_analysis=False
+        png_savename='heatline_horizontal',
+        csv_savename='heatline_horizontal',
     )
 ```
 
@@ -88,8 +89,9 @@ MCM.compare(
 
 The following python packages are required for the usage of the module:
 
-1. ```numpy==1.23.5```
-2. ```pandas==1.5.2```
-3. ```matplotlib==3.6.2```
+1. ```numpy==1.24.4```
+2. ```pandas==2.0.3```
+3. ```matplotlib==3.7.4```
 4. ```scipy==1.10.0```
 5. ```baycomp==1.0```
+6. ```tqdm==4.66.1```

heatline_horizontal.png

@@ -0,0 +1,19 @@
+\documentclass[a4,12pt]{article}
+\usepackage{colortbl}
+\usepackage{pgfplots}
+\usepackage[margin=2cm]{geometry}
+\pgfplotsset{compat=newest}
+\begin{document}
+\begin{table}
+\footnotesize
+\sffamily
+\begin{center}
+\begin{tabular}{cccccc}
+Mean-Accuracy & \shortstack{clf1 \\ 0.5376} & \shortstack{clf3 \\ 0.5220} & \shortstack{clf2 \\ 0.5123} & \shortstack{clf4 \\ 0.4825} \\[1ex]
+\shortstack{clf2 \\ 0.5123} & \cellcolor[rgb]{0.6355,0.7567,0.9983}\shortstack{\rule{0em}{3ex} -0.0253 \\ 60 / 0 / 68 \\ 0.5162} & \cellcolor[rgb]{0.7867,0.8448,0.9398}\shortstack{\rule{0em}{3ex} -0.0097 \\ 64 / 0 / 64 \\ 0.8102} & \cellcolor[rgb]{0.8674,0.8644,0.8626}\shortstack{\rule{0em}{3ex} Mean-Difference \\ r$>$c / r=c / r$<$c \\ Wilcoxon p-value} & \cellcolor[rgb]{0.9649,0.6402,0.5198}\shortstack{\rule{0em}{3ex} 0.0298 \\ 72 / 0 / 56 \\ 0.3880} \\[1ex]
+\shortstack{clf4 \\ 0.4825} & \cellcolor[rgb]{0.3286,0.4397,0.8696}\shortstack{\rule{0em}{3ex} -0.0551 \\ 59 / 0 / 69 \\ 0.1018} & \cellcolor[rgb]{0.4839,0.622,0.9748}\shortstack{\rule{0em}{3ex} -0.0395 \\ 58 / 0 / 70 \\ 0.2835} & \cellcolor[rgb]{0.5869,0.7181,0.9989}\shortstack{\rule{0em}{3ex} -0.0298 \\ 56 / 0 / 72 \\ 0.3880} & \cellcolor[rgb]{0.8674,0.8644,0.8626}\shortstack{\rule{0em}{3ex} If in bold, then \\ p-value $<$ 0.05} \\[1ex]
+\end{tabular}\\
+\begin{tikzpicture}[baseline=(current bounding box.center)]\begin{axis}[hide axis,scale only axis,width=0sp,height=0sp,colorbar horizontal,colorbar style={width=0.25\linewidth,colormap={cm}{rgb255(1)=(83,112,221) rgb255(2)=(220,220,220) rgb255(3)=(209,73,62)},colorbar horizontal,point meta min=-0.07,point meta max=0.07,colorbar/width=1.0em,scaled x ticks=false,xticklabel style={/pgf/number format/fixed,/pgf/number format/precision=3},xlabel={Mean-Difference},}] \addplot[draw=none] {0};\end{axis}\end{tikzpicture}\end{center}
+\caption{[...] \textbf{If in bold, then p-value $<$ 0.05} [...]}
+\end{table}
+\end{document}

heatline_horizontal.tex

@@ -3,7 +3,7 @@
 from MCM import MCM
 
 if __name__ == "__main__":
-    path_res = "./results_example_no_data_column2.csv"
+    path_res = "./results_example.csv"
     output_dir = "./"
 
     df_results = pd.read_csv(path_res)
@@ -18,6 +18,7 @@
         df_results=df_results,
         excluded_col_comparates=["clf1", "clf3"],
         png_savename="heatline_vertical",
+        include_ProbaWinTieLoss=True
     )
 
     MCM.compare(