matplotlib Group boxplots

Question

Is there a way to group boxplots in matplotlib   Assume we have three groups  A    B   and  C  and for each we want to create a boxplot for both  apples  and  oranges   If a grouping is not possible directly  we can create all six combinations and place them linearly side by side  What would be to simplest way to visualize the groupings  I m trying to avoid setting the tick labels to something like  A   apples  since my scenario involves much longer names than  A

User · Answer

The accepted answer uses pylab and works for 2 groups. What if we have more?

Here is the flexible generic solution with matplotlib enter image description here

# --- Your data, e.g. results per algorithm:
data1 = [5,5,4,3,3,5]
data2 = [6,6,4,6,8,5]
data3 = [7,8,4,5,8,2]
data4 = [6,9,3,6,8,4]
data6 = [17,8,4,5,8,1]
data7 = [6,19,3,6,1,1]


# --- Combining your data:
data_group1 = [data1, data2, data6]
data_group2 = [data3, data4, data7]
data_group3 = [data1, data1, data1]
data_group4 = [data2, data2, data2]
data_group5 = [data2, data2, data2]

data_groups = [data_group1, data_group2, data_group3] #, data_group4] #, data_group5]

# --- Labels for your data:
labels_list = ['a','b', 'c']
width       = 0.3
xlocations  = [ x*((1+ len(data_groups))*width) for x in range(len(data_group1)) ]

symbol      = 'r+'
ymin        = min ( [ val  for dg in data_groups  for data in dg for val in data ] )
ymax        = max ( [ val  for dg in data_groups  for data in dg for val in data ])

ax = pl.gca()
ax.set_ylim(ymin,ymax)

ax.grid(True, linestyle='dotted')
ax.set_axisbelow(True)

pl.xlabel('X axis label')
pl.ylabel('Y axis label')
pl.title('title')

space = len(data_groups)/2
offset = len(data_groups)/2


ax.set_xticks( xlocations )
ax.set_xticklabels( labels_list, rotation=0 )
# --- Offset the positions per group:

group_positions = []
for num, dg in enumerate(data_groups):    
    _off = (0 - space + (0.5+num))
    print(_off)
    group_positions.append([x-_off*(width+0.01) for x in xlocations])

for dg, pos in zip(data_groups, group_positions):
    pl.boxplot(dg, 
                sym=symbol,
    #            labels=['']*len(labels_list),
                labels=['']*len(labels_list),           
                positions=pos, 
                widths=width, 
    #           notch=False,  
    #           vert=True, 
    #           whis=1.5,
    #           bootstrap=None, 
    #           usermedians=None, 
    #           conf_intervals=None,
    #           patch_artist=False,
                )



pl.show()

User · Answer

Here is my version  It stores data based on categories   import matplotlib pyplot as plt import numpy as np  data a     1 2 5    5 7 2 2 5    7 2 5   data b     6 4 2    1 2 5 3 2    2 3 5 1    ticks     A    B    C    def set box color bp  color       plt setp bp  boxes    color color      plt setp bp  whiskers    color color      plt setp bp  caps    color color      plt setp bp  medians    color color   plt figure    bpl   plt boxplot data a  positions np array xrange len data a    2 0-0 4  sym     widths 0 6  bpr   plt boxplot data b  positions np array xrange len data b    2 0 0 4  sym     widths 0 6  set box color bpl    D7191C     colors are from http   colorbrewer2 org  set box color bpr    2C7BB6      draw temporary red and blue lines and use them to create a legend plt plot     c   D7191C   label  Apples   plt plot     c   2C7BB6   label  Oranges   plt legend    plt xticks xrange 0  len ticks    2  2   ticks  plt xlim -2  len ticks  2  plt ylim 0  8  plt tight layout   plt savefig  boxcompare png     I am short of reputation so I cannot post an image to here  You can run it and see the result  Basically it s very similar to what Molly did   Note that  depending on the version of python you are using  you may need to replace xrange with range

User · Answer

Here s a function I wrote that takes Molly s code and some other code I ve found on the internet to make slightly fancier grouped boxplots   import numpy as np import matplotlib pyplot as plt  def custom legend colors  labels  linestyles None           Creates a list of matplotlib Patch objects that can be passed to the legend      function to create a custom         legend        param colors  A list of colors  one for each entry in the legend  You can also include a linestyle  for example   k--       param labels   A list of labels  one for each entry in the legend               if linestyles is not None          assert len linestyles     len colors    Length of linestyles must match length of colors        h   list       for k  c l  in enumerate zip colors  labels            clr   c         ls    solid          if linestyles is not None              ls   linestyles k          patch   patches Patch color clr  label l  linestyle ls          h append patch      return h   def grouped boxplot data  group names None  subgroup names None  ax None  subgroup colors None                      box width 0 6  box spacing 1 0           Draws a grouped boxplot  The data should be organized in a hierarchy  where there are multiple         subgroups for each main group        param data  A dictionary of length equal to the number of the groups  The key should be the                 group name  the value should be a list of arrays  The length of the list should be                 equal to the number of subgroups       param group names   Optional  The group names  should be the same as data keys    but can be ordered       param subgroup names   Optional  Names of the subgroups       param subgroup colors  A list specifying the plot color for each subgroup       param ax   Optional  The axis to plot on               if group names is None          group names   data keys        if ax is None          ax   plt gca       plt sca ax       nsubgroups   np array  len v  for v in data values         assert len np unique nsubgroups      1   Number of subgroups for each property differ       nsubgroups   nsubgroups 0       if subgroup colors is None          subgroup colors   list           for k in range nsubgroups               subgroup colors append np random rand 3       else          assert len subgroup colors     nsubgroups   subgroup colors length must match number of subgroups   d     nsubgroups      def  decorate box  bp   d           plt setp  bp  boxes    lw 0  color  k           plt setp  bp  whiskers    lw 3 0  color  k              fill in each box with a color         assert len  bp  boxes       nsubgroups         for  k  box in enumerate  bp  boxes                  boxX   list                boxY   list               for  j in range 5                    boxX append  box get xdata    j                    boxY append  box get ydata    j                boxCoords   zip  boxX   boxY               boxPolygon   plt Polygon  boxCoords  facecolor subgroup colors  k               ax add patch  boxPolygon             draw a black line for the median         for  k  med in enumerate  bp  medians                  medianX   list                medianY   list               for  j in range 2                    medianX append  med get xdata    j                    medianY append  med get ydata    j                   plt plot  medianX   medianY   k   linewidth 3 0                 draw a black asterisk for the mean             plt plot  np mean  med get xdata       np mean  d  k     color  w   marker                            markeredgecolor  k   markersize 12       cpos   1     label pos   list       for k in group names          d   data k          nsubgroups   len d          pos   np arange nsubgroups    cpos         label pos append pos mean            bp   plt boxplot d  positions pos  widths box width           decorate box bp  d          cpos    nsubgroups   box spacing      plt xlim 0  cpos-1      plt xticks label pos  group names       if subgroup names is not None          leg   custom legend subgroup colors  subgroup names          plt legend handles leg    You can use the function s  like this   data      A   np random randn 100   np random randn 100    5             B   np random randn 100  1  np random randn 100    9             C   np random randn 100 -3  np random randn 100  -5            grouped boxplot data  group names   A    B    C    subgroup names   Apples    Oranges    subgroup colors    D02D2E     D67700    plt show

User · Answer

Just to add to the conversation  I have found a more elegant way to change the color of the box plot by iterating over the dictionary of the object itself  import numpy as np import matplotlib pyplot as plt  def color box bp  color          Define the elements to color  You can also add medians  fliers and means     elements     boxes   caps   whiskers          Iterate over each of the elements changing the color     for elem in elements           plt setp bp elem  idx   color color  for idx in xrange len bp elem         return  a   np random uniform 0 10  100 5        bp   plt boxplot a  color box bp   red         Cheers

User · Answer

How about using colors to differentiate between  apples  and  oranges  and spacing to separate  A    B  and  C      Something like this   from pylab import plot  show  savefig  xlim  figure                    hold  ylim  legend  boxplot  setp  axes    function for setting the colors of the box plots pairs def setBoxColors bp       setp bp  boxes   0   color  blue       setp bp  caps   0   color  blue       setp bp  caps   1   color  blue       setp bp  whiskers   0   color  blue       setp bp  whiskers   1   color  blue       setp bp  fliers   0   color  blue       setp bp  fliers   1   color  blue       setp bp  medians   0   color  blue        setp bp  boxes   1   color  red       setp bp  caps   2   color  red       setp bp  caps   3   color  red       setp bp  whiskers   2   color  red       setp bp  whiskers   3   color  red       setp bp  fliers   2   color  red       setp bp  fliers   3   color  red       setp bp  medians   1   color  red      Some fake data to plot A    1  2  5      7  2   B     5  7  2  2  5    7  2  5   C     3 2 5 7    6  7  3    fig   figure   ax   axes   hold True     first boxplot pair bp   boxplot A  positions    1  2   widths   0 6  setBoxColors bp     second boxplot pair bp   boxplot B  positions    4  5   widths   0 6  setBoxColors bp     thrid boxplot pair bp   boxplot C  positions    7  8   widths   0 6  setBoxColors bp     set axes limits and labels xlim 0 9  ylim 0 9  ax set xticklabels   A    B    C    ax set xticks  1 5  4 5  7 5      draw temporary red and blue lines and use them to create a legend hB    plot  1 1   b-   hR    plot  1 1   r-   legend  hB  hR    Apples    Oranges    hB set visible False  hR set visible False   savefig  boxcompare png   show

User · Answer

Grouped boxplots  towards subtle academic publication styling     source    Left  Python 2 7 12 Matplotlib v1 5 3   Right  Python 3 7 3  Matplotlib v3 1 0      Code   import numpy as np import matplotlib pyplot as plt    --- Your data  e g  results per algorithm  data1    5 5 4 3 3 5  data2    6 6 4 6 8 5  data3    7 8 4 5 8 2  data4    6 9 3 6 8 4     --- Combining your data  data group1    data1  data2  data group2    data3  data4     --- Labels for your data  labels list     a   b   xlocations    range len data group1   width         0 3 symbol         r   ymin          0 ymax          10  ax   plt gca   ax set ylim ymin ymax  ax set xticklabels  labels list  rotation 0   ax grid True  linestyle  dotted   ax set axisbelow True  ax set xticks xlocations  plt xlabel  X axis label   plt ylabel  Y axis label   plt title  title      --- Offset the positions per group  positions group1    x- width 0 01  for x in xlocations  positions group2   xlocations  plt boxplot data group1               sym symbol              labels      len labels list               positions positions group1               widths width               notch False                vert True               whis 1 5              bootstrap None               usermedians None               conf intervals None              patch artist False                 plt boxplot data group2               labels labels list              sym symbol              positions positions group2               widths width               notch False                vert True               whis 1 5              bootstrap None               usermedians None               conf intervals None              patch artist False                 plt savefig  boxplot grouped png     plt savefig  boxplot grouped pdf        when publishing  use high quality PDFs  plt show                       uncomment to show the plot

User · Answer

A simple way would be to use pandas  I adapted an example from the plotting documentation   In  1   import pandas as pd  numpy as np  In  2   df   pd DataFrame np random rand 12 2   columns   Apples    Oranges      In  3   df  Categories     pd Series list  AAAABBBBCCCC     In  4   pd options display mpl style    default   In  5   df boxplot by  Categories   Out 5    array   lt matplotlib axes AxesSubplot object at 0x51a5190 gt           lt matplotlib axes AxesSubplot object at 0x53fddd0 gt    dtype object

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Mock data   df   pd DataFrame   Group    A   A   A   B   C   B   B   C   A   C                        Apple  np random rand 10   Orange  np random rand 10    df   df   Group   Apple   Orange             Group    Apple     Orange     0      A  0 465636  0 537723     1      A  0 560537  0 727238     2      A  0 268154  0 648927     3      B  0 722644  0 115550     4      C  0 586346  0 042896     5      B  0 562881  0 369686     6      B  0 395236  0 672477     7      C  0 577949  0 358801     8      A  0 764069  0 642724     9      C  0 731076  0 302369   You can use the Seaborn library for these plots  First melt the dataframe to format data and then create the boxplot of your choice   import pandas as pd import matplotlib pyplot as plt import seaborn as sns dd pd melt df id vars   Group   value vars   Apple   Orange   var name  fruits   sns boxplot x  Group  y  value  data dd hue  fruits

[python] matplotlib: Group boxplots

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