s_mart: SMART/Java/Python/misc/RPlotter.py comparison

comparison SMART/Java/Python/misc/RPlotter.py @ 6:769e306b7933

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author	yufei-luo
date	Fri, 18 Jan 2013 04:54:14 -0500
parents
children	94ab73e8a190

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+:769e306b7933
+#
+# Copyright INRA-URGI 2009-2010
+#
+# This software is governed by the CeCILL license under French law and
+# abiding by the rules of distribution of free software. You can use,
+# modify and/ or redistribute the software under the terms of the CeCILL
+# license as circulated by CEA, CNRS and INRIA at the following URL
+# "http://www.cecill.info".
+#
+# As a counterpart to the access to the source code and rights to copy,
+# modify and redistribute granted by the license, users are provided only
+# with a limited warranty and the software's author, the holder of the
+# economic rights, and the successive licensors have only limited
+# liability.
+#
+# In this respect, the user's attention is drawn to the risks associated
+# with loading, using, modifying and/or developing or reproducing the
+# software by the user in light of its specific status of free software,
+# that may mean that it is complicated to manipulate, and that also
+# therefore means that it is reserved for developers and experienced
+# professionals having in-depth computer knowledge. Users are therefore
+# encouraged to load and test the software's suitability as regards their
+# requirements in conditions enabling the security of their systems and/or
+# data to be ensured and, more generally, to use and operate it in the
+# same conditions as regards security.
+#
+# The fact that you are presently reading this means that you have had
+# knowledge of the CeCILL license and that you accept its terms.
+#
+import os
+import subprocess
+import random
+import math
+minPositiveValue = 10e-6
+"""
+Plot simple curves in R
+"""
+class RPlotter(object):
+"""
+Plot some curves
+@ivar nbColors: number of different colors
+@type nbColors: int
+@ivar fileName: name of the file
+@type fileName: string
+@ivar lines: lines to be plotted
+@type lines: array of dict
+@ivar names: name of the lines
+@type names: array of strings
+@ivar colors: color of the lines
+@type colors: array of strings
+@ivar types: type of the lines (plain or dashed)
+@type types: array of strings
+@ivar format: format of the picture
+@type format: string
+@ivar lineWidth: width of the line in a xy-plot
+@type lineWidth: int
+@ivar xMin: minimum value taken on the x-axis
+@type xMin: int
+@ivar xMax: maximum value taken on the x-axis
+@type xMax: int
+@ivar yMin: minimum value taken on the y-axis
+@type yMin: int
+@ivar yMax: maximum value taken on the y-axis
+@type yMax: int
+@ivar minimumX: minimum value allowed on the x-axis
+@type minimumX: int
+@ivar maximumX: maximum value allowed on the x-axis
+@type maximumX: int
+@ivar minimumY: minimum value allowed on the y-axis
+@type minimumY: int
+@ivar maximumY: maximum value allowed on the y-axis
+@type maximumY: int
+@ivar leftMargin:  add some margin in the left part of the plot
+@type leftMargin:  float
+@ivar rightMargin: add some margin in the right part of the plot
+@type rightMargin: float
+@ivar downMargin:  add some margin at the top of the plot
+@type downMargin:  float
+@ivar upMargin:    add some margin at the bottom of the plot
+@type upMargin:    float
+@ivar logX: use log scale on the x-axis
+@type logX: boolean
+@ivar logY: use log scale on the y-axis
+@type logY: boolean
+@ivar logZ: use log scale on the z-axis (the color)
+@type logZ: boolean
+@ival fill: if a value is not given, fill it with given value
+@type fill: int
+@ival bucket: cluster the data into buckets of given size
+@type bucket: int
+@ival seed: a random number
+@type seed: int
+@ival regression: plot a linear regression
+@type regression: boolean
+@ival legend: set the legend
+@type legend: boolean
+@ival legendBySide: set the legend outside of the plot
+@type legendBySde: boolean
+@ival xLabel: label for the x-axis
+@type xLabel: string
+@ival yLabel: label for the y-axis
+@type yLabel: string
+@ival title: title of the plot
+@type title: string
+@ival barplot: use a barplot representation instead
+@type barplot: boolean
+@ival points: use a point cloud instead
+@type points: boolean
+@ival heatPoints: use a colored point cloud instead
+@type heatPoints: boolean
+@ival axesLabels: change the names of the axes
+@type axesLabels: vector of 2 int to string dict
+@ival rotateAxesLabels: rotate the axes labels
+@type rotateAxesLabels: dict of 2 boolean
+@ival verbosity: verbosity of the class
+@type verbosity: int
+@ival keep: keep temporary files
+@type keep: boolean
+"""
+def __init__(self, fileName, verbosity = 0, keep = False):
+"""
+Constructor
+@param fileName: name of the file to produce
+@type    fileName: string
+@param verbosity: verbosity
+@type    verbosity: int
+@param keep: keep temporary files
+@type keep: boolean
+"""
+self.nbColors = 9
+self.fileName = fileName
+self.verbosity = verbosity
+self.keep = keep
+self.format = "png"
+self.fill = None
+self.bucket = None
+self.lines = []
+self.names = []
+self.colors = []
+self.types = []
+self.lineWidth = 1
+self.xMin = None
+self.xMax = None
+self.yMin = None
+self.yMax = None
+self.seed = random.randint(0, 10000)
+self.minimumX = None
+self.maximumX = None
+self.minimumY = None
+self.maximumY = None
+self.leftMargin   = 0
+self.rightMargin  = 0
+self.topMargin    = 0
+self.bottomMargin = 0
+self.logX = False
+self.logY = False
+self.logZ = False
+self.regression = False
+self.width = 1000
+self.height = 500
+self.legend = False
+self.legendBySide = False
+self.xLabel = ""
+self.yLabel = ""
+self.title = None
+self.points = False
+self.heatPoints = False
+self.barplot = False
+self.axesLabels = {1: None, 2: None}
+self.rotateAxesLabels = {1: False, 2: False}
+self.linesToAddBox = ""
+def __del__(self):
+"""
+Destructor
+Remove tmp files
+"""
+if not self.keep:
+scriptFileName = "tmpScript-%d.R" % (self.seed)
+if os.path.exists(scriptFileName):
+os.remove(scriptFileName)
+outputFileName = "%sout" % (scriptFileName)
+if os.path.exists(outputFileName):
+os.remove(outputFileName)
+nbLines = len(self.lines) + (1 if self.heatPoints else 0)
+for i in range(nbLines):
+if os.path.exists("tmpData-%d-%d.dat" % (self.seed, i)):
+os.remove("tmpData-%d-%d.dat" % (self.seed, i))
+def setMinimumX(self, xMin):
+"""
+Set the minimum value on the x-axis
+@param xMin:minimum value on the x-axis
+@type xMin: int
+"""
+self.minimumX = xMin
+def setMaximumX(self, xMax):
+"""
+Set the maximum value on the x-axis
+@param xMax: maximum value on the x-axis
+@type xMax: int
+"""
+self.maximumX = xMax
+def setMinimumY(self, yMin):
+"""
+Set the minimum value on the y-axis
+@param yMin: minimum value on the y-axis
+@type yMin: int
+"""
+self.minimumY = yMin
+def setMaximumY(self, yMax):
+"""
+Set the maximum value on the y-axis
+@param yMax: maximum value on the y-axis
+@type xmax: int
+"""
+self.maximumY = yMax
+def setFill(self, fill):
+"""
+Fill empty data with given value
+@param fill: the value to fill with
+@type fill: int
+"""
+self.fill = fill
+def setBuckets(self, bucket):
+"""
+Cluster the data into buckets of given size
+@param bucket: the size of the buckets
+@type bucket: int
+"""
+self.bucket = bucket
+def setRegression(self, regression):
+"""
+Plot a linear regression line
+@param regression: whether to plot the regression
+@type  regression: bool
+"""
+self.regression = regression
+def setFormat(self, format):
+"""
+Set the format of the picture
+@param format: the format
+@type format: string
+"""
+if format not in ("png", "pdf", "jpeg", "bmp", "tiff"):
+raise Exception("Format '%s' is not supported by RPlotter" % (format))
+self.format = format
+def setWidth(self, width):
+"""
+Set the dimensions of the image produced
+@param width: width of the image
+@type width: int
+"""
+self.width = width
+def setHeight(self, height):
+"""
+Set the dimensions of the image produced
+@param height: heigth of the image
+@type height: int
+"""
+self.height = height
+def setImageSize(self, width, height):
+"""
+Set the dimensions of the image produced
+@param width: width of the image
+@type width: int
+@param height: heigth of the image
+@type height: int
+"""
+self.setWidth(width)
+self.setHeight(height)
+def setLegend(self, legend, bySide = False):
+"""
+Print a legend or not
+@param legend: print a legend
+@type  legend: boolean
+@param bySide: put the legend outside of the plot
+@type  bySide: boolean
+"""
+self.legend       = legend
+self.legendBySide = bySide
+def setXLabel(self, label):
+"""
+Print a label for the x-axis
+@param label: the label
+@type label: string
+"""
+self.xLabel = label
+if self.xLabel != None:
+self.xLabel = self.xLabel.replace("_", " ")
+def setYLabel(self, label):
+"""
+Print a label for the y-axis
+@param label: the label
+@type label: string
+"""
+self.yLabel = label
+if self.yLabel != None:
+self.yLabel = self.yLabel.replace("_", " ")
+def addLeftMargin(self, margin):
+"""
+Increase the size of the space on the left part of the graph
+@param margin: the space added
+@type  margin: float
+"""
+self.leftMargin = margin
+def addRightMargin(self, margin):
+"""
+Increase the size of the space on the right part of the graph
+@param margin: the space added
+@type  margin: float
+"""
+self.rightMargin = margin
+def addTopMargin(self, margin):
+"""
+Increase the size of the space at the top of the graph
+TopMargin is a percentage if 0 < TopMargin < 1.
+TopMargin is a value if TopMargin >= 1.
+@param margin: the space added
+@type  margin: float
+"""
+self.topMargin = margin
+def addBottomMargin(self, margin):
+"""
+Increase the size of the space at the bottom of the graph
+@param margin: the space added
+@type  margin: float
+"""
+self.bottomMargin = margin
+def getNewYMaxWithTopMargin(self):
+"""
+Return new xMin coordinate with left margin
+@param xMin: coordinate
+@type  xMin: float
+"""
+yMax = self.yMax
+if 0 < self.topMargin and self.topMargin < 1:
+topMargin = self.topMargin * self.yMax
+yMax = self.yMax + topMargin
+elif self.topMargin >= 1:
+yMax = self.yMax + self.topMargin
+return yMax
+def setTitle(self, title):
+"""
+Print a title for graph
+@param title: a title
+@type title: string
+"""
+self.title = title
+if self.title != None:
+self.title = self.title.replace("_", " ")
+def setAxisLabel(self, i, labels):
+"""
+Change x- or y-labels
+@param i: x for x-label, y for y-label
+@type  i: string
+@param labels: new labels
+@type  labels: int to string dict
+"""
+i = i.lower()
+if i not in ("x", "y"):
+raise Exception("Label name '" + i + "' should by 'x' or 'y' while changing axis labels.")
+self.axesLabels[{"x": 1, "y": 2}[i]] = labels
+def rotateAxisLabel(self, i, b = True):
+"""
+Rotate x- or y-labels
+@param i: x for x-label, y for y-label
+@type  i: string
+@param b: whether the labels should be rotated
+@type  b: boolean
+"""
+i = i.lower()
+if i not in ("x", "y"):
+raise Exception("Label name '" + i + "' should by 'x' or 'y' while rotating axis labels.")
+self.rotateAxesLabels[{"x": 1, "y": 2}[i]] = b
+def setLineWidth(self, width):
+"""
+Set the line width in a xy-plot
+@param width: the new line width
+@type  width: int
+"""
+self.lineWidth = width
+def setLog(self, log):
+"""
+Use log-scale for axes
+@param log: use log scale
+@type log: boolean
+"""
+self.logX = ("x" in log)
+self.logY = ("y" in log)
+self.logZ = ("z" in log)
+def setBarplot(self, barplot):
+"""
+Use barplot representation instead
+@param barplot: barplot representation
+@type barplot: boolean
+"""
+self.barplot = barplot
+def setPoints(self, points):
+"""
+Use points cloud representation instead
+@param points: points cloud representation
+@type points: boolean
+"""
+self.points = points
+def setHeatPoints(self, heatPoints):
+"""
+Use points cloud representation with color representing another variable instead
+@param points: colored points cloud representation
+@type points: boolean
+"""
+self.heatPoints = heatPoints
+def addBox(self, lXCoordList, minY, maxY):
+for lXCoord in lXCoordList:
+self.linesToAddBox += "rect(%s,%s,%s,%s,density=50, col='grey',border='transparent')\n" % (lXCoord[0], minY, lXCoord[1], maxY)
+def addLine(self, line, name = "", color = None):
+"""
+Add a line
+@param line: a line to plot
+@type line: dict
+"""
+# prepare data
+plot = []
+if self.points or self.heatPoints:
+values = line.values()
+elif self.fill == None:
+values = sorted(line.keys())
+else:
+values = range(min(line.keys()), max(line.keys()) + 1)
+for element in values:
+if self.points or self.heatPoints:
+x = element[0]
+y = element[1]
+else:
+x = element
+if x not in line:
+y = self.fill
+else:
+y = line[x]
+if self.minimumX != None and x < self.minimumX:
+continue
+if self.maximumX != None and x > self.maximumX:
+continue
+if x == None:
+raise Exception("Problem! x is None. Aborting...")
+if y == None:
+raise Exception("Problem! y is None. Aborting...")
+if x == 0 and self.logX:
+x = minPositiveValue
+if y == 0 and self.logY:
+y = minPositiveValue
+if self.xMin == None:
+if not self.logX or x != 0:
+self.xMin = x
+else:
+if not self.logX or x != 0:
+self.xMin = min(self.xMin, x)
+if self.xMax == None:
+self.xMax = x
+else:
+self.xMax = max(self.xMax, x)
+if self.yMin == None:
+if not self.logY or y != 0:
+self.yMin = y
+else:
+if not self.logY or y != 0:
+if y != "NA":
+self.yMin = min(self.yMin, y)
+if self.yMax == None:
+self.yMax = y
+else:
+if y != "NA":
+self.yMax = max(self.yMax, y)
+plot.append((x, y))
+# cluster the data into buckets
+if self.bucket != None:
+buckets = dict([((int(value) / int(self.bucket)) * self.bucket, 0) for value in xrange(min(line.keys()), max(line.keys())+1)])
+for distance, nb in line.iteritems():
+buckets[(int(distance) / int(self.bucket)) * self.bucket] += nb
+self.yMax = max(buckets.values())
+plot = []
+for x, y in buckets.iteritems():
+plot.append((x, y))
+# write file
+dataFileName = "tmpData-%d-%d.dat" % (self.seed, len(self.lines))
+dataHandle = open(dataFileName, "w")
+if not self.heatPoints:
+plot.sort()
+for (x, y) in plot:
+if y != "NA":
+dataHandle.write("%f\t%f\n" % (x, y))
+else:
+dataHandle.write("%f\t%s\n" % (x, y))
+dataHandle.close()
+self.lines.append(line)
+self.names.append(name)
+if color == None:
+colorNumber = len(self.colors) % (self.nbColors - 1) + 1
+type = "solid"
+if len(self.colors) >= self.nbColors:
+type = "dashed"
+color = "colorPanel[%d]" % (colorNumber)
+else:
+color = "\"%s\"" % (color)
+type = "solid"
+self.colors.append(color)
+self.types.append(type)
+def addHeatLine(self, line, name = "", color = None):
+"""
+Add the heat line
+@param line: the line which gives the color of the points
+@type    line: dict
+"""
+if not self.heatPoints:
+raise Exception("Error! Trying to add a heat point whereas not mentioned to earlier! Aborting.")
+dataFileName = "tmpData-%d-%d.dat" % (self.seed, len(self.lines))
+dataHandle = open(dataFileName, "w")
+minimumHeat = min(line.values())
+maximumHeat = max(line.values())
+minLogValue = 0.00001
+log = self.logZ
+if log:
+if minimumHeat == 0:
+for element in line:
+line[element] += minLogValue
+minimumHeat += minLogValue
+maximumHeat += minLogValue
+minimumHeat = math.log10(minimumHeat)
+maximumHeat = math.log10(maximumHeat)
+coeff = 255.0 / (maximumHeat - minimumHeat)
+for element in line:
+value = line[element]
+if log:
+value = math.log10(max(minLogValue, value))
+dataHandle.write("\"#%02X%02X00\"\n" % (int((value - minimumHeat) * coeff), 255 - int((value - minimumHeat) * coeff)))
+dataHandle.close()
+self.names.append(name)
+if color == None:
+colorNumber = len(self.colors) % (self.nbColors - 1) + 1
+type = "solid"
+if len(self.colors) >= self.nbColors:
+type = "dashed"
+color = "colorPanel[%d]" % (colorNumber)
+else:
+color = "\"%s\"" % (color)
+type = "solid"
+self.colors.append(color)
+self.types.append(type)
+def getScript(self):
+"""
+Write (unfinished) R script
+"""
+script = ""
+xMin = self.xMin - self.leftMargin
+if self.minimumX != None:
+xMin = max(xMin, self.minimumX)
+xMax = self.xMax + self.rightMargin
+if self.maximumX != None:
+xMax = min(xMax, self.maximumX)
+yMin = self.yMin - self.bottomMargin
+if self.minimumY != None:
+yMin = self.minimumY
+yMax = self.getNewYMaxWithTopMargin()
+if self.maximumY != None:
+yMax = self.maximumY
+log = ""
+if self.logX:
+log += "x"
+if self.logY:
+log += "y"
+if log != "":
+log = ", log=\"%s\"" % (log)
+title = ""
+if self.title != None:
+title = ", main = \"%s\"" % (self.title)
+if self.legend and self.legendBySide:
+script += "layout(matrix(c(1,2), 1, 2), widths=c(5,1))\n"
+if self.rotateAxesLabels[2]:
+script += "par(mar=c(5,12,4,2))\n"
+else:
+script += "par(mar=c(5,5,4,2))\n"
+addAxes = True
+if self.barplot:
+script += "data = scan(\"tmpData-%d-0.dat\", list(x = -666, y = -666))\n" % (self.seed)
+if len(self.lines) == 1:
+script += "barplot(data$y, name = data$x, xlab=\"%s\", ylab=\"%s\", ylim = c(%f, %f), cex.axis = 2, cex.names = 2, cex.lab = 2%s%s)\n" % (self.xLabel, self.yLabel, yMin, yMax, title, log)
+addAxes = False
+else:
+script += "data1 = scan(\"tmpData-%d-1.dat\", list(x = -666, y = -666))\n" % (self.seed)
+script += "barplot(rbind(data$y, data1$y), name = data$x, xlab=\"%s\", ylab=\"%s\", cex.axis = 2, cex.names = 2, cex.lab = 2%s, beside = TRUE, space=c(-1,0), axes = FALSE%s)\n" % (self.xLabel, self.yLabel, title, log)
+elif self.points:
+script += "data = scan(\"tmpData-%d-0.dat\", list(x = -666, y = -666))\n" % (self.seed)
+script += "plot(data$x, data$y, xlab=\"%s\", ylab=\"%s\", cex.axis = 2, cex.lab = 2, axes = FALSE%s%s)\n" % (self.xLabel, self.yLabel, title, log)
+if self.regression:
+x = "log10(data$x)" if self.logX else "data$x"
+y = "log10(data$y)" if self.logY else "data$y"
+script += "abline(lm(%s ~ %s))\n" % (y, x)
+elif self.heatPoints:
+if len(self.lines) != 1:
+raise Exception("Error! Bad number of input data! Aborting...")
+script += "data = scan(\"tmpData-%d-0.dat\", list(x = -666, y = -666))\n" % (self.seed)
+script += "heatData = scan(\"tmpData-%d-1.dat\", list(x = \"\"))\n" % (self.seed)
+script += "plot(data$x, data$y, col=heatData$x, xlab=\"%s\", ylab=\"%s\", cex.axis = 2, cex.lab = 2, axes = FALSE%s%s)\n" % (self.xLabel, self.yLabel, title, log)
+if self.regression:
+x = "log10(data$x)" if self.logX else "data$x"
+y = "log10(data$y)" if self.logY else "data$y"
+script += "abline(lm(%s ~ %s))\n" % (y, x)
+else:
+script += "plot(x = NA, y = NA, panel.first = grid(lwd = 1.0), xlab=\"%s\", ylab=\"%s\", xlim = c(%f, %f), ylim = c(%f, %f), cex.axis = 2, cex.lab = 2, axes = FALSE%s%s)\n" % (self.xLabel, self.yLabel, xMin, xMax, yMin, yMax, title, log)
+for i in range(0, len(self.lines)):
+script += "data = scan(\"tmpData-%d-%d.dat\", list(x = -666.666, y = -666.666))\n" % (self.seed, i)
+script += "lines(x = data$x, y = data$y, col = %s, lty = \"%s\", lwd = %d)\n" % (self.colors[i], self.types[i], self.lineWidth)
+script += self.linesToAddBox
+if addAxes:
+for i in self.axesLabels:
+rotation = ", las = 2" if self.rotateAxesLabels[i] else ""
+if self.axesLabels[i] == None:
+script += "axis(%d, cex.axis = 2, cex.lab = 2%s)\n" % (i, rotation)
+else:
+oldKeys = ", ".join(["%d" % (key) for key in sorted(self.axesLabels[i].keys())])
+newKeys = ", ".join(["\"%s\"" % (self.axesLabels[i][key]) for key in sorted(self.axesLabels[i].keys())])
+script += "axis(%d, at=c(%s), lab=c(%s), cex.axis = 2, cex.lab = 2%s)\n" % (i, oldKeys, newKeys, rotation)
+script += "box()\n"
+if self.legend:
+if self.legendBySide:
+script += "plot.new()\n"
+script += "par(mar=c(0,0,0,0))\n"
+script += "plot.window(c(0,1), c(0,1))\n"
+script += "legends   = c(%s)\n" % ", ".join(["\"%s\"" % name  for name  in self.names])
+script += "colors    = c(%s)\n" % ", ".join(["%s" %     color for color in self.colors])
+script += "lineTypes = c(%s)\n" % ", ".join(["\"%s\"" % type  for type  in self.types])
+if self.legendBySide:
+script += "legend(0, 1, legend = legends, xjust = 0, yjust = 1, col = colors, lty = lineTypes, lwd = %d, cex = 1.5, ncol = 1, bg = \"white\")\n" % (self.lineWidth)
+else:
+script += "legend(\"topright\", legend = legends, xjust = 0, yjust = 1, col = colors, lty = lineTypes, lwd = %d, cex = 1.5, ncol = 1, bg = \"white\")\n" % (self.lineWidth)
+return script
+def plot(self):
+"""
+Plot the lines
+"""
+scriptFileName = "tmpScript-%d.R" % (self.seed)
+scriptHandle = open(scriptFileName, "w")
+scriptHandle.write("library(RColorBrewer)\n")
+scriptHandle.write("colorPanel = brewer.pal(n=%d, name=\"Set1\")\n" % (self.nbColors))
+scriptHandle.write("%s(%s = \"%s\", width = %d, height = %d, bg = \"white\")\n" % (self.format, "filename" if self.format != "pdf" else "file", self.fileName, self.width, self.height))
+scriptHandle.write(self.getScript())
+scriptHandle.write("dev.off()\n")
+scriptHandle.close()
+rCommand = "R"
+if "SMARTRPATH" in os.environ:
+rCommand = os.environ["SMARTRPATH"]
+command = "\"%s\" CMD BATCH %s" % (rCommand, scriptFileName)
+status = subprocess.call(command, shell=True)
+if status != 0:
+self.keep = True
+raise Exception("Problem with the execution of script file %s, status is: %s" % (scriptFileName, status))
+def getCorrelationData(self):
+if not self.regression:
+return ""
+scriptFileName = "tmpScript-%d.R" % (self.seed)
+rScript = open(scriptFileName, "w")
+rScript.write("data = scan(\"tmpData-%d-0.dat\", list(x = -0.000000, y = -0.000000))\n" % (self.seed))
+x = "log10(data$x)" if self.logX else "data$x"
+y = "log10(data$y)" if self.logY else "data$y"
+rScript.write("summary(lm(%s ~ %s))\n" % (y, x))
+rScript.close()
+rCommand = "R"
+if "SMARTRPATH" in os.environ:
+rCommand = os.environ["SMARTRPATH"]
+command = "\"%s\" CMD BATCH %s" % (rCommand, scriptFileName)
+status = subprocess.call(command, shell=True)
+if status != 0:
+self.keep = True
+raise Exception("Problem with the execution of script file %s computing the correlation, status is: %s" % (scriptFileName, status))
+outputRFile = open("%sout" % (scriptFileName))
+output      = ""
+start       = False
+end         = False
+for line in outputRFile:
+if start and "> " in line:
+end = True
+if start and not end:
+output += line
+if "summary" in line:
+start = True
+return output
+def getSpearmanRho(self):
+"""
+Get the Spearman rho correlation using R
+"""
+return None
+if not self.points and not self.barplot and not self.heatPoints:
+raise Exception("Cannot compute Spearman rho correlation whereas not in 'points' or 'bar' mode.")
+scriptFileName = "tmpScript-%d.R" % (self.seed)
+rScript = open(scriptFileName, "w")
+rScript.write("library(Hmisc)\n")
+rScript.write("data = scan(\"tmpData-%d-0.dat\", list(x = -0.000000, y = -0.000000))\n" % (self.seed))
+rScript.write("spearman(data$x, data$y)\n")
+rScript.close()
+rCommand = "R"
+if "SMARTRPATH" in os.environ:
+rCommand = os.environ["SMARTRPATH"]
+command = "\"%s\" CMD BATCH %s" % (rCommand, scriptFileName)
+status = subprocess.call(command, shell=True)
+if status != 0:
+self.keep = True
+raise Exception("Problem with the execution of script file %s, status is: %s" % (scriptFileName, status))
+outputRFile = open("%sout" % (scriptFileName))
+nextLine = False
+for line in outputRFile:
+line = line.strip()
+if nextLine:
+if line == "NA":
+return None
+return float(line)
+nextLine = False
+if line == "rho":
+nextLine = True
+return None

Mercurial > repos > yufei-luo > s_mart

comparison SMART/Java/Python/misc/RPlotter.py @ 6:769e306b7933