Mercurial > repos > mzytnicki > s_mart
changeset 140:a7825a22f239 draft
Uploaded
| author | mzytnicki |
|---|---|
| date | Tue, 05 Nov 2013 05:52:22 -0500 |
| parents | bb9b82438c90 |
| children | ff6607328942 |
| files | SMART/Java/Python/misc/RPlotter.py SMART/Java/Python/ncList/__init__.pyc commons/__init__.pyc commons/core/LoggerFactory.pyc commons/core/__init__.pyc commons/core/checker/RepetException.pyc commons/core/checker/__init__.pyc commons/core/coord/Align.pyc commons/core/coord/Map.pyc commons/core/coord/Range.pyc commons/core/coord/__init__.pyc commons/core/parsing/AxtParser.pyc commons/core/parsing/BamParser.pyc commons/core/parsing/BedParser.pyc commons/core/parsing/BlastParser.pyc commons/core/parsing/BowtieParser.pyc commons/core/parsing/CoordsParser.pyc commons/core/parsing/ElandParser.pyc commons/core/parsing/ExoParser.pyc commons/core/parsing/FastaParser.pyc commons/core/parsing/FastqParser.pyc commons/core/parsing/GffParser.pyc commons/core/parsing/GtfParser.pyc commons/core/parsing/MapParser.pyc commons/core/parsing/MapperParser.pyc commons/core/parsing/MaqParser.pyc commons/core/parsing/NCListParser.pyc commons/core/parsing/ParserChooser.pyc commons/core/parsing/PklParser.pyc commons/core/parsing/PslParser.pyc commons/core/parsing/RmapParser.pyc commons/core/parsing/SamParser.pyc commons/core/parsing/SeqmapParser.pyc commons/core/parsing/SequenceListParser.pyc commons/core/parsing/ShrimpParser.pyc commons/core/parsing/Soap2Parser.pyc commons/core/parsing/SoapParser.pyc commons/core/parsing/TranscriptListParser.pyc commons/core/parsing/WigParser.pyc commons/core/parsing/__init__.pyc commons/core/seq/Bioseq.pyc commons/core/seq/__init__.pyc commons/core/utils/RepetOptionParser.pyc commons/core/utils/__init__.pyc commons/core/writer/BedWriter.pyc commons/core/writer/CsvWriter.pyc commons/core/writer/EmblWriter.pyc commons/core/writer/FastaWriter.pyc commons/core/writer/FastqWriter.pyc commons/core/writer/GbWriter.pyc commons/core/writer/Gff2Writer.pyc commons/core/writer/Gff3Writer.pyc commons/core/writer/GtfWriter.pyc commons/core/writer/MapWriter.pyc commons/core/writer/MySqlTranscriptWriter.pyc commons/core/writer/SamWriter.pyc commons/core/writer/SequenceListWriter.pyc commons/core/writer/TranscriptListWriter.pyc commons/core/writer/UcscWriter.pyc commons/core/writer/WigWriter.pyc commons/core/writer/WriterChooser.pyc commons/core/writer/__init__.pyc |
| diffstat | 62 files changed, 754 insertions(+), 722 deletions(-) [+] |
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--- a/SMART/Java/Python/misc/RPlotter.py Tue Nov 05 05:49:09 2013 -0500 +++ b/SMART/Java/Python/misc/RPlotter.py Tue Nov 05 05:52:22 2013 -0500 @@ -40,782 +40,814 @@ """ 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 - """ + """ + 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 pointShapes: shape of the points + @type pointShapes: array of int + @ivar types: type of the lines (plain or dashed) + @type types: array of strings + @ivar legendNames: name of the lines printed in the legend + @type legendNames: array of strings + @ivar legendColors: color of the lines printed in the legend + @type legendColors: array of strings + @ivar legendTypes: type of the lines (plain or dashed) printed in the legend + @type legendTypes: array of strings + @ivar legendShapes: shape of points printed in the legend + @type legendShapes: array of int + @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 + @ival sizeLegend: size of the police for the legend + @type sizeLegend: float + """ - 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 __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.nbUsedColors = 0 + 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.pointShapes = [] + self.types = [] + self.legendNames = [] + self.legendColors = [] + self.legendTypes = [] + self.legendShapes = [] + 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 setBarplot(self, barplot): - """ - Use barplot representation instead - @param barplot: barplot representation - @type barplot: boolean - """ - self.barplot = barplot - + 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 setPoints(self, points): - """ - Use points cloud representation instead - @param points: points cloud representation - @type points: boolean - """ - self.points = points - + def setSizePoliceLegend(self, sizeLegend): + """ + Modify the size of the police for the legend only + @param size: a size + @type size: float + """ + self.sizeLegend = sizeLegend - 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 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) + def addColor(self, name, color): + if name == "" or name not in self.names: + if color == None: + colorNumber = self.nbUsedColors % (self.nbColors - 1) + 1 + type = "solid" if len(self.colors) < self.nbColors else "dashed" + color = "colorPanel[%d]" % (colorNumber) + self.nbUsedColors += 1 + else: + color = "\"%s\"" % (color) + type = "solid" + shape = 0 if not self.pointShapes else self.pointShapes[-1]+1 + self.legendNames.append(name) + self.legendColors.append(color) + self.legendTypes.append(type) + self.legendShapes.append(shape) + else: + index = self.names.index(name) + color = self.colors[index] + type = self.types[index] + shape = self.pointShapes[index] + self.colors.append(color) + self.types.append(type) + self.pointShapes.append(shape) + + def addLine(self, line, name = "", color = None): + """ + Add a line + @param line: a line to plot + @type line: dict + """ + # prepare data + plot = [] + if type(line[line.keys()[0]]) is dict: + 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 element is list: + 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)) + 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)) - # 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.addColor(name, color) + self.lines.append(line) + self.names.append(name) - # 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() + 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) - self.lines.append(line) - self.names.append(name) + 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))) - 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) + dataHandle.close() + self.addColor(name, color) + self.names.append(name) - 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) + 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() + yMax += min(1, yMax / 100.0) + 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 - 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))) + 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$x, xlab=\"%s\", ylab=\"%s\", cex.axis = 2, cex.names = 2, cex.lab = 2%s, beside = TRUE, space=c(-1,0), axes = FALSE%s)\n" % (self.xLabel, self.yLabel, title, log) + elif self.points: + script += "plot(x = NA, y = NA, panel.first = grid(lwd = 1.0), xlab=\"%s\", ylab=\"%s\", xlim = c(%f, %f), ylim = c(%f, %f), cex.axis = 2, cex.lab = 2, axes = FALSE%s%s)\n" % (self.xLabel, self.yLabel, xMin, xMax, yMin, yMax, title, log) + for i in range(0, len(self.lines)): + script += "data = scan(\"tmpData-%d-%d.dat\", list(x = -666.666, y = -666.666))\n" % (self.seed, i) + script += "points(x = data$x, y = data$y, col = %s, pch=%d, lwd = %d)\n" % (self.colors[i], self.pointShapes[i], self.lineWidth) + if self.regression: + if len(self.lines) != 1: + raise Exception("Error! Cannot compute regression with multiple data sets...") + x = "log10(data$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" - 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) + 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.legendNames]) + script += "colors = c(%s)\n" % ", ".join(["%s" % color for color in self.legendColors]) + script += "lineTypes = c(%s)\n" % ", ".join((["NA"] * len(self.legendTypes)) if self.points else (["\"%s\"" % type for type in self.legendTypes])) + if self.points: + script += "pointShapes = c(%s)\n" % ", ".join(["%d" % shape for shape in self.legendShapes]) + shape = ", pch = pointShapes" if self.points else "" + pos = "0, 1" if self.legendBySide else "\"topright\"" + script += "legend(%s, legend = legends, xjust = 0, yjust = 1, col = colors, lty = lineTypes, lwd = %d, cex = %f, ncol = 1, bg = \"white\"%s)\n" % (pos, self.lineWidth, self.sizeLegend, shape) + + return script + - 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() - yMax += min(1, yMax / 100.0) - if self.maximumY != None: - yMax = self.maximumY + 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) - 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 status != 0: + self.keep = True + raise Exception("Problem with the execution of script file %s, status is: %s" % (scriptFileName, status)) + - 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 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 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 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() - 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 + 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 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() + 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 - 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 + return None