diff options
Diffstat (limited to 'wqflask/utility')
| -rw-r--r-- | wqflask/utility/Plot.py | 134 | ||||
| -rw-r--r-- | wqflask/utility/corestats.py | 99 |
2 files changed, 100 insertions, 133 deletions
diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py index d60e2bb2..3a8b8dd5 100644 --- a/wqflask/utility/Plot.py +++ b/wqflask/utility/Plot.py @@ -36,11 +36,10 @@ from numarray import linear_algebra as la from numarray import ones, array, dot, swapaxes import reaper -# sys.path.append("..") Never in a running webserver -from basicStatistics import corestats import svg import webqtlUtil +import corestats from base import webqtlConfig import utility.logger @@ -315,137 +314,6 @@ def find_outliers(vals): logger.debug(pf(locals())) return upper_bound, lower_bound - -def plotBoxPlot(canvas, data, offset= (40, 40, 40, 40), XLabel="Category", YLabel="Value"): - xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset - plotWidth = canvas.size[0] - xLeftOffset - xRightOffset - plotHeight = canvas.size[1] - yTopOffset - yBottomOffset - iValues = [] - for item in data: - for item2 in item[1]: - try: - iValues.append(item2[1]) - except: - iValues.append(item2) - - #draw frame - max_Y = max(iValues) - min_Y = min(iValues) - scaleY = detScale(min_Y, max_Y) - Yll = scaleY[0] - Yur = scaleY[1] - nStep = scaleY[2] - stepY = (Yur - Yll)/nStep - stepYPixel = plotHeight/(nStep) - canvas.drawRect(plotWidth+xLeftOffset, plotHeight + yTopOffset, xLeftOffset, yTopOffset) - - ##draw Y Scale - YYY = Yll - YCoord = plotHeight + yTopOffset - scaleFont=pid.Font(ttf="cour",size=11,bold=1) - for i in range(nStep+1): - strY = cformat(d=YYY, rank=0) - YCoord = max(YCoord, yTopOffset) - canvas.drawLine(xLeftOffset,YCoord,xLeftOffset-5,YCoord) - canvas.drawString(strY, xLeftOffset -30,YCoord +5,font=scaleFont) - YYY += stepY - YCoord -= stepYPixel - - ##draw X Scale - stepX = plotWidth/len(data) - XCoord = xLeftOffset + 0.5*stepX - YCoord = plotHeight + yTopOffset - scaleFont = pid.Font(ttf="tahoma",size=12,bold=0) - labelFont = pid.Font(ttf="tahoma",size=13,bold=0) - for item in data: - itemname, itemvalue = item - canvas.drawLine(XCoord, YCoord,XCoord, YCoord+5, color=pid.black) - canvas.drawString(itemname, XCoord - canvas.stringWidth(itemname,font=labelFont)/2.0,\ - YCoord +20,font=labelFont) - - nValue = len(itemvalue) - catValue = [] - for item2 in itemvalue: - try: - tstrain, tvalue = item2 - except: - tvalue = item2 - if nValue <= 4: - canvas.drawCross(XCoord, plotHeight + yTopOffset - (tvalue-Yll)*plotHeight/(Yur - Yll), color=pid.red,size=5) - else: - catValue.append(tvalue) - if catValue != []: - catMean = gmean(catValue) - catMedian = gmedian(catValue) - lowHinge = gpercentile(catValue, 25) - upHinge = gpercentile(catValue, 75) - Hstep = 1.5*(upHinge - lowHinge) - - outlier = [] - extrem = [] - - upperAdj = None - for item in catValue: - if item >= upHinge + 2*Hstep: - extrem.append(item) - elif item >= upHinge + Hstep: - outlier.append(item) - elif item > upHinge and item < upHinge + Hstep: - if upperAdj == None or item > upperAdj: - upperAdj = item - else: - pass - lowerAdj = None - for item in catValue: - if item <= lowHinge - 2*Hstep: - extrem.append(item) - elif item <= lowHinge - Hstep: - outlier.append(item) - if item < lowHinge and item > lowHinge - Hstep: - if lowerAdj == None or item < lowerAdj: - lowerAdj = item - else: - pass - canvas.drawRect(XCoord-20, plotHeight + yTopOffset - (lowHinge-Yll)*plotHeight/(Yur - Yll), \ - XCoord+20, plotHeight + yTopOffset - (upHinge-Yll)*plotHeight/(Yur - Yll)) - canvas.drawLine(XCoord-20, plotHeight + yTopOffset - (catMedian-Yll)*plotHeight/(Yur - Yll), \ - XCoord+20, plotHeight + yTopOffset - (catMedian-Yll)*plotHeight/(Yur - Yll)) - if upperAdj != None: - canvas.drawLine(XCoord, plotHeight + yTopOffset - (upHinge-Yll)*plotHeight/(Yur - Yll), \ - XCoord, plotHeight + yTopOffset - (upperAdj-Yll)*plotHeight/(Yur - Yll)) - canvas.drawLine(XCoord-20, plotHeight + yTopOffset - (upperAdj-Yll)*plotHeight/(Yur - Yll), \ - XCoord+20, plotHeight + yTopOffset - (upperAdj-Yll)*plotHeight/(Yur - Yll)) - if lowerAdj != None: - canvas.drawLine(XCoord, plotHeight + yTopOffset - (lowHinge-Yll)*plotHeight/(Yur - Yll), \ - XCoord, plotHeight + yTopOffset - (lowerAdj-Yll)*plotHeight/(Yur - Yll)) - canvas.drawLine(XCoord-20, plotHeight + yTopOffset - (lowerAdj-Yll)*plotHeight/(Yur - Yll), \ - XCoord+20, plotHeight + yTopOffset - (lowerAdj-Yll)*plotHeight/(Yur - Yll)) - - outlierFont = pid.Font(ttf="cour",size=12,bold=0) - if outlier != []: - for item in outlier: - yc = plotHeight + yTopOffset - (item-Yll)*plotHeight/(Yur - Yll) - #canvas.drawEllipse(XCoord-3, yc-3, XCoord+3, yc+3) - canvas.drawString('o', XCoord-3, yc+5, font=outlierFont, color=pid.orange) - if extrem != []: - for item in extrem: - yc = plotHeight + yTopOffset - (item-Yll)*plotHeight/(Yur - Yll) - #canvas.drawEllipse(XCoord-3, yc-3, XCoord+3, yc+3) - canvas.drawString('*', XCoord-3, yc+6, font=outlierFont, color=pid.red) - - canvas.drawCross(XCoord, plotHeight + yTopOffset - (catMean-Yll)*plotHeight/(Yur - Yll), \ - color=pid.blue,size=3) - #print(catMean, catMedian, cat25per, cat75per) - pass - - XCoord += stepX - - labelFont=pid.Font(ttf="verdana",size=18,bold=0) - canvas.drawString(XLabel, xLeftOffset + (plotWidth -canvas.stringWidth(XLabel,font=labelFont))/2.0, \ - YCoord +40, font=labelFont) - canvas.drawString(YLabel,xLeftOffset-40, YCoord-(plotHeight -canvas.stringWidth(YLabel,font=labelFont))/2.0,\ - font=labelFont, angle =90) - def plotSecurity(canvas, text="12345"): if not text: return diff --git a/wqflask/utility/corestats.py b/wqflask/utility/corestats.py new file mode 100644 index 00000000..c48183ed --- /dev/null +++ b/wqflask/utility/corestats.py @@ -0,0 +1,99 @@ +#!/usr/bin/env python + +# corestats.py (COREy STATS) +# Copyright (c) 2006-2007, Corey Goldberg (corey@goldb.org) +# +# statistical calculation class +# for processing numeric sequences +# +# license: GNU LGPL +# +# This library is free software; you can redistribute it and/or +# modify it under the terms of the GNU Lesser General Public +# License as published by the Free Software Foundation; either +# version 2.1 of the License, or (at your option) any later version. + +import sys + +#ZS: Should switch to using some third party library for this; maybe scipy has an equivalent +class Stats: + + def __init__(self, sequence): + # sequence of numbers we will process + # convert all items to floats for numerical processing + self.sequence = [float(item) for item in sequence] + + + def sum(self): + if len(self.sequence) < 1: + return None + else: + return sum(self.sequence) + + + def count(self): + return len(self.sequence) + + + def min(self): + if len(self.sequence) < 1: + return None + else: + return min(self.sequence) + + + def max(self): + if len(self.sequence) < 1: + return None + else: + return max(self.sequence) + + + def avg(self): + if len(self.sequence) < 1: + return None + else: + return sum(self.sequence) / len(self.sequence) + + + def median(self): + if len(self.sequence) < 1: + return None + else: + self.sequence.sort() + return self.sequence[len(self.sequence) // 2] + + + def stdev(self): + if len(self.sequence) < 1: + return None + else: + avg = self.avg() + sdsq = sum([(i - avg) ** 2 for i in self.sequence]) + stdev = (sdsq / (len(self.sequence) - 1)) ** .5 + return stdev + + + def percentile(self, percentile): + if len(self.sequence) < 1: + value = None + elif (percentile >= 100): + sys.stderr.write('ERROR: percentile must be < 100. you supplied: %s\n'% percentile) + value = None + else: + element_idx = int(len(self.sequence) * (percentile / 100.0)) + self.sequence.sort() + value = self.sequence[element_idx] + return value + + +# Sample script using this class: +# ------------------------------------------- +# #!/usr/bin/env python +# import corestats +# +# sequence = [1, 2.5, 7, 13.4, 8.0] +# stats = corestats.Stats(sequence) +# print stats.avg() +# print stats.percentile(90) +# -------------------------------------------
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