Sunday, September 5, 2010

The online box/violin/vio plot generator

It is our adage in our work for our online extreme solvers not to wait for a perfect implementation but rather to present quickly a working solver in order to be more productive with our precious time. Our solver is part of rplotpage, a page dedicated to using R to make quick statistical graphics for analysis.

Our solver is in R and we present the QP/QPY code, not to impress but to remind the developer to add more features to make the solver more useful, robust, fast and reliable.

"""
file    boxviolin.qpy
version 2010.09.01   0.0.1  first version
"""

__version__ = "0.0.1 2010.09.01"
__author__  = "ernesto.adorio@gmail.com"
__title__   = "Box-Violin Plots using R"
__file__    = "matrix.qpy"
__catalog__ = "BOXVIOLINPLOT-xxxx"
__url__     = "/solvers/rplotpage/box-violin/"


import time
import tempfile
import commands
import os

from   qp.fill.directory  import Directory
from   qp.fill.form       import Form, StringWidget, TextWidget,CheckboxWidget,SingleSelectWidget
from   qp.fill.css   import BASIC_FORM_CSS

from   qp.sites.extreme.lib.tmpfilesmanager import TmpFilesManager
from   qp.sites.extreme.lib.uicommon        import renderheader, renderfooter, processheader, processfooter
from   qp.pub.common                        import page
from   qp.sites.extreme.lib.checkinput      import checkInputs, getFormStrings
from   qp.sites.extreme.lib.qpyutils        import printRlines, showLogo
from   qp.sites.extreme.lib.webutils        import vecRead, GraphicsFile, as_R_cvector, as_R_vector, as_R_matrix, str2file,runRcode

from   qp.sites.extreme.lib import config

from   qp.sites.extreme.lib import getlists

def Solve(fields):
    # Get the fields.
    (gX, gY, orientation, notchedQ,  color, input, output, main, sub, data)= fields
    
    color = color.strip()
    # Start of R code.
    fname1    = GraphicsFile(str("png"))
    barefile1 = fname1.split(str("/"))[-1]

    if input == "lists":
       values, names = getlists.getlists(data)
    else:
       str2file(data, "%s.datR" % barefile1)       
    
    Rcode = """
library("UsingR")
library("vioplot")
png('%s', width=%s*72, height=%s*72)\n""" % (fname1,gX,gY)

    if input == "lists":
       Rcode += values
       Rcode += "%s(" % output  
       n = len(names)
       for i, name in enumerate(names):      
         if i == 0:
            Rcode += "%s" % name
         else:
            Rcode += ",%s"  % name
    else:
       if output != "vioplot": 
          Rcode += 'D<- read.table("%s.datR", header= %s)\n' %(barefile1, "T" if input == "dataframeh" else "F")
          Rcode += "%s(D" % output  
       else:
          return "Error: vioplot do not work with dataframes (will fix this later)." 

    Rcode += ",col=\"%s\"" % color 

    if output != "violinplot":
       Rcode += ",horizontal= %s" %("T" if (orientation== "horizontal") else "F")
    if output== "boxplot": 
       if notchedQ == "True":
          Rcode += ",notch=T"
       Rcode += ",main=\"%s\",sub=\"%s\"" % (main, sub)
    Rcode += ")\n"
    Rcode += """
graphics.off()
#img %s
    """ % (barefile1,)

    (status, output) = runRcode(Rcode)
    return output
    

class BoxviolinPage(Directory):
    def get_exports(self):
        yield ('', 'index', 'MatrixPlot', '')
           


    def index[html](self):
        form  = Form(enctype="multipart/form-data")  # enctype for file upload
        form.add(StringWidget, name="gX", title="gX", value = "6", size=3)
        form.add(StringWidget, name="gY", title="gY", value = "6", size=3)

        sample = """
    A =  [0.48277807, 0.55883118, 1.16229686, -2.46396356,  0.51974668,-0.01998613,
  -0.86259931, -1.06209308, -0.15671515,  0.38586572, -0.58470602,  0.31188390,
 -1.68227059,  0.23231185,  0.31535337, -0.26056577, -0.79349169, -0.94405202,
   0.24571925, -0.09696371, -0.23873567, -0.04282470, -1.14515572, -0.27451771,
  -0.34858889,  0.82800299, -0.95087183,  0.96757912, -0.15727265,  0.18871157,
 -0.86204394,  0.38754598,  1.50002723,  1.12436546,  0.61330870,  1.06893060,
  -1.41018422,  0.51767624, -0.45544199, -2.51855547, -0.77679863, -1.15285965,
   1.63166143,  0.65999935, -0.32582916,  1.56306037,  0.64053237,  0.01575183,
   0.46375195, -0.59255240,  0.10008879, -1.84196389, -1.52021625, -0.65748902,
   1.37202728,  1.02064967, -0.67488492, -0.60657784, -1.03975969, -0.33201024,
  -0.21770026, -0.35978620, -1.27524339, -0.98302583, -0.14502137,  0.54930432,
  -0.62277989,  0.30322268,  0.37256666, -0.32351923,  0.29565189, -0.18387578,
  -0.19855784, -1.15357907, -0.22684307, -1.45764974, -1.10523354, -0.04629259,
  0.36703816, -0.74684309, -1.61969633,  0.58941017,  -0.64764459,  0.11335716,
  -0.57165179, -0.02908054, -2.99190083, -0.13697042, -0.93464799, -0.09097572,
   0.77899241,  0.91366189, -0.36055108,  0.53784267, -2.15995157,  0.58759839,
  -2.36184597, -0.77934578,  0.80640923, -0.28747470]

B = [28.833158, 25.579569, 24.135939, 22.743252, 29.847344, 25.390941, 26.578796,
 28.889899, 26.165342, 33.802780, 22.116170, 15.447919, 20.142984, 25.902806,
 19.445479, 28.119898, 26.801888, 29.305805, 30.587547, 34.293373, 28.956599,
 28.371756, 30.963548, 16.572734, 35.695663, 32.681236, 25.234438, 19.401117,
 23.782763, 26.520000, 39.802655, 21.715052, 25.242914, 21.716478, 26.979986,
 25.078014,  9.517322, 27.996393, 35.096322, 30.132288, 33.942315, 26.993927,
 27.792392, 15.718047, 36.352729, 28.949376, 20.445088, 29.874274, 29.586799,
 33.060320, 28.655216, 27.505567, 26.661354, 29.419386, 27.377346, 23.985406,
 15.868329, 17.621934, 35.456224, 26.697508, 28.179293, 27.151317, 28.227135,
 23.882481, 45.793041, 22.712121, 29.222936, 27.619567, 28.854152, 23.744545,
 23.856285, 34.919047, 40.032500, 32.566862, 34.253867, 31.959225, 29.008039,
 29.965751, 20.319337, 39.284185, 29.676313, 34.686862, 22.103798, 38.521644,
 30.967211, 18.150335, 21.622198, 24.717461, 29.424366, 34.169033, 27.881900,
 28.577999, 29.547534, 35.179072, 27.350809, 35.940215, 31.848857, 23.747476,
 27.135937, 29.275092]
        """
        form.add(TextWidget, name = "data",   title="Input", rows="25", cols = "90", value = sample)

        form.add(SingleSelectWidget, name= "input", title="Input", value = "lists", options=
           [ ("lists",      "R or Python lists"),
             ("dataframeh", "dataframe with headers"),
             ("dataframe",  "dataframe without headers")
           ])

        form.add(SingleSelectWidget, name="orientation", title="Orientation", value = "vertical", options= 
             [("vertical",   "vertical"), 
              ("horizontal", "horizontal")])

        form.add(CheckboxWidget, name="notched?", title="Notched?",value = True)

        form.add(SingleSelectWidget, name= "output", title="Output Graph ", value="boxplot", options=
           [("boxplot",     "Box plot"),
            ("violinplot",  "Violin plot"),  
            ("vioplot",     "Vioplot")
            # ("violinbox",   "Violin with boxplot"),
            # ("viobox",      "Vioplot with boxplot")
           ])

        form.add(StringWidget,  name = "color",  title="color", size = 35, value = "blue")
        form.add(StringWidget,  name = "main", title="Main Title",    size = 35, value = "Box plot")
        form.add(StringWidget,  name = "sub", title="Sub Title",     size = 35, value = "Extreme Computing")
          

        form.add_hidden("time",   value = time.time())
        form.add_submit("submit", "submit")

        def render [html] ():
            renderheader(__title__)

            """
            





%s %s%s %s %s
%s %s%s%s
%s
""" % (form.get_widget("gX").render(),
form.get_widget("gY").render(),
form.get_widget("orientation").render(),
form.get_widget("notched?").render(),
form.get_widget("color").render(),

form.get_widget("input").render(),
form.get_widget("output").render(),
form.get_widget("main").render(),
form.get_widget("sub").render(),
form.get_widget("data").render())
"""
Notched?, Main title and subtitle only works for boxplot.
Orientation only works for both box and vioplot.
"""

renderfooter(form, __version__, __catalog__, __author__)


if not form.is_submitted():
return page('Box Violin Plot page', render(), style= BASIC_FORM_CSS)

def process [html] ():
processheader(__title__)
calctime_start = time.time()

# Get the problem parameters
(gX, gY,orientation, notchedQ, color, input, output, main, sub, data) = getFormStrings(form,
[
"gX", "gY", "orientation", "notched?", "color",
"input", "output", "main", "sub",
"data"
])


output=Solve((gX, gY, orientation, notchedQ, color, input, output, main, sub, data))
"
"
            printRlines(output)
            "
"
showLogo("Rlogo.jpg")
processfooter(form, calctime_start, "./", __url__)
process()

Currently the box|violin|vio plot will only plot one of these types for each list.
The vioplot cannot be drawn for a dataframe and does not accept a main and a sub title.See previous posting on these topics.


Sep. 10: Vioplot can now process dataframes, by rewriting the code to draw the columns. If D is a dataframe with 3 columns for example, the code to draw a vioplot for this set is is vioplot(D[[1]], D[[2]], D[[3]]).




We will remove some of the limitation in a future version.

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