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Diffstat (limited to 'gn2/utility/Plot.py')
| -rw-r--r-- | gn2/utility/Plot.py | 343 |
1 files changed, 343 insertions, 0 deletions
diff --git a/gn2/utility/Plot.py b/gn2/utility/Plot.py new file mode 100644 index 00000000..ace954e4 --- /dev/null +++ b/gn2/utility/Plot.py @@ -0,0 +1,343 @@ +# Copyright (C) University of Tennessee Health Science Center, Memphis, TN. +# +# This program is free software: you can redistribute it and/or modify it +# under the terms of the GNU Affero General Public License +# as published by the Free Software Foundation, either version 3 of the +# License, or (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. +# See the GNU Affero General Public License for more details. +# +# This program is available from Source Forge: at GeneNetwork Project +# (sourceforge.net/projects/genenetwork/). +# +# Contact Drs. Robert W. Williams and Xiaodong Zhou (2010) +# at rwilliams@uthsc.edu and xzhou15@uthsc.edu +# +# +# +# This module is used by GeneNetwork project (www.genenetwork.org) +# +# Created by GeneNetwork Core Team 2010/08/10 +# +# Last updated by GeneNetwork Core Team 2010/10/20 + +from PIL import ImageColor +from PIL import ImageDraw +from PIL import ImageFont + +from math import * + +import gn2.utility.corestats as corestats +from gn2.base import webqtlConfig +from gn2.utility.pillow_utils import draw_rotated_text + + +# ---- Define common colours ---- # +BLUE = ImageColor.getrgb("blue") +BLACK = ImageColor.getrgb("black") +# ---- END: Define common colours ---- # + +# ---- FONT FILES ---- # +VERDANA_FILE = "./wqflask/static/fonts/verdana.ttf" +COUR_FILE = "./wqflask/static/fonts/courbd.ttf" +TAHOMA_FILE = "./wqflask/static/fonts/tahoma.ttf" +# ---- END: FONT FILES ---- # + + +def cformat(d, rank=0): + 'custom string format' + strD = "%2.6f" % d + + if rank == 0: + while strD[-1] in ('0', '.'): + if strD[-1] == '0' and strD[-2] == '.' and len(strD) <= 4: + break + elif strD[-1] == '.': + strD = strD[:-1] + break + else: + strD = strD[:-1] + + else: + strD = strD.split(".")[0] + + if strD == '-0.0': + strD = '0.0' + return strD + + +def frange(start, end=None, inc=1.0): + "A faster range-like function that does accept float increments..." + if end == None: + end = start + 0.0 + start = 0.0 + else: + start += 0.0 # force it to be a float + count = int((end - start) / inc) + if start + count * inc != end: + # Need to adjust the count. AFAICT, it always comes up one short. + count += 1 + L = [start] * count + for i in range(1, count): + L[i] = start + i * inc + return L + + +def find_outliers(vals): + """Calculates the upper and lower bounds of a set of sample/case values + + + >>> find_outliers([3.504, 5.234, 6.123, 7.234, 3.542, 5.341, 7.852, 4.555, 12.537]) + (11.252500000000001, 0.5364999999999993) + + >>> find_outliers([9,12,15,17,31,50,7,5,6,8]) + (32.0, -8.0) + + If there are no vals, returns None for the upper and lower bounds, + which code that calls it will have to deal with. + >>> find_outliers([]) + (None, None) + + """ + + if vals: + stats = corestats.Stats(vals) + low_hinge = stats.percentile(25) + up_hinge = stats.percentile(75) + hstep = 1.5 * (up_hinge - low_hinge) + + upper_bound = up_hinge + hstep + lower_bound = low_hinge - hstep + + else: + upper_bound = None + lower_bound = None + + return upper_bound, lower_bound + +# parameter: data is either object returned by reaper permutation function (called by MarkerRegressionPage.py) +# or the first object returned by direct (pair-scan) permu function (called by DirectPlotPage.py) + + +def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLabel=None, YLabel=None, title=None, offset=(60, 20, 40, 40), zoom=1): + im_drawer = ImageDraw.Draw(canvas) + xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset + + plotWidth = canvas.size[0] - xLeftOffset - xRightOffset + plotHeight = canvas.size[1] - yTopOffset - yBottomOffset + if plotHeight <= 0 or plotWidth <= 0: + return + + if len(data) < 2: + return + + max_D = max(data) + min_D = min(data) + # add by NL 06-20-2011: fix the error: when max_D is infinite, log function in detScale will go wrong + if (max_D == float('inf') or max_D > webqtlConfig.MAXLRS) and min_D < webqtlConfig.MAXLRS: + max_D = webqtlConfig.MAXLRS # maximum LRS value + + xLow, xTop, stepX = detScale(min_D, max_D) + + # reduce data + # ZS: Used to determine number of bins for permutation output + step = ceil((xTop - xLow) / 50.0) + j = xLow + dataXY = [] + Count = [] + while j <= xTop: + dataXY.append(j) + Count.append(0) + j += step + + for i, item in enumerate(data): + if (item == float('inf') or item > webqtlConfig.MAXLRS) and min_D < webqtlConfig.MAXLRS: + item = webqtlConfig.MAXLRS # maximum LRS value + j = int((item - xLow) / step) + Count[j] += 1 + + yLow, yTop, stepY = detScale(0, max(Count)) + + # draw data + xScale = plotWidth / (xTop - xLow) + yScale = plotHeight / (yTop - yLow) + barWidth = xScale * step + + for i, count in enumerate(Count): + if count: + xc = (dataXY[i] - xLow) * xScale + xLeftOffset + yc = -(count - yLow) * yScale + yTopOffset + plotHeight + im_drawer.rectangle( + xy=((xc + 2, yc), (xc + barWidth - 2, yTopOffset + plotHeight)), + outline=barColor, fill=barColor) + + # draw drawing region + im_drawer.rectangle( + xy=((xLeftOffset, yTopOffset), + (xLeftOffset + plotWidth, yTopOffset + plotHeight)) + ) + + # draw scale + scaleFont = ImageFont.truetype(font=COUR_FILE, size=11) + x = xLow + for i in range(int(stepX) + 1): + xc = xLeftOffset + (x - xLow) * xScale + im_drawer.line( + xy=((xc, yTopOffset + plotHeight), + (xc, yTopOffset + plotHeight + 5)), + fill=axesColor) + strX = cformat(d=x, rank=0) + im_drawer.text( + text=strX, + xy=(xc - im_drawer.textsize(strX, font=scaleFont)[0] / 2, + yTopOffset + plotHeight + 14), font=scaleFont) + x += (xTop - xLow) / stepX + + y = yLow + for i in range(int(stepY) + 1): + yc = yTopOffset + plotHeight - (y - yLow) * yScale + im_drawer.line( + xy=((xLeftOffset, yc), (xLeftOffset - 5, yc)), fill=axesColor) + strY = "%d" % y + im_drawer.text( + text=strY, + xy=(xLeftOffset - im_drawer.textsize(strY, + font=scaleFont)[0] - 6, yc + 5), + font=scaleFont) + y += (yTop - yLow) / stepY + + # draw label + labelFont = ImageFont.truetype(font=TAHOMA_FILE, size=17) + if XLabel: + im_drawer.text( + text=XLabel, + xy=(xLeftOffset + ( + plotWidth - im_drawer.textsize(XLabel, font=labelFont)[0]) / 2.0, + yTopOffset + plotHeight + yBottomOffset - 10), + font=labelFont, fill=labelColor) + + if YLabel: + draw_rotated_text(canvas, text=YLabel, + xy=(19, + yTopOffset + plotHeight - ( + plotHeight - im_drawer.textsize( + YLabel, font=labelFont)[0]) / 2.0), + font=labelFont, fill=labelColor, angle=90) + + labelFont = ImageFont.truetype(font=VERDANA_FILE, size=16) + if title: + im_drawer.text( + text=title, + xy=(xLeftOffset + (plotWidth - im_drawer.textsize( + title, font=labelFont)[0]) / 2.0, + 20), + font=labelFont, fill=labelColor) + +# This function determines the scale of the plot + + +def detScaleOld(min, max): + if min >= max: + return None + elif min == -1.0 and max == 1.0: + return [-1.2, 1.2, 12] + else: + a = max - min + b = floor(log10(a)) + c = pow(10.0, b) + if a < c * 5.0: + c /= 2.0 + # print a,b,c + low = c * floor(min / c) + high = c * ceil(max / c) + return [low, high, round((high - low) / c)] + + +def detScale(min=0, max=0): + + if min >= max: + return None + elif min == -1.0 and max == 1.0: + return [-1.2, 1.2, 12] + else: + a = max - min + if max != 0: + max += 0.1 * a + if min != 0: + if min > 0 and min < 0.1 * a: + min = 0.0 + else: + min -= 0.1 * a + a = max - min + b = floor(log10(a)) + c = pow(10.0, b) + low = c * floor(min / c) + high = c * ceil(max / c) + n = round((high - low) / c) + div = 2.0 + while n < 5 or n > 15: + if n < 5: + c /= div + else: + c *= div + if div == 2.0: + div = 5.0 + else: + div = 2.0 + low = c * floor(min / c) + high = c * ceil(max / c) + n = round((high - low) / c) + + return [low, high, n] + + +def bluefunc(x): + return 1.0 / (1.0 + exp(-10 * (x - 0.6))) + + +def redfunc(x): + return 1.0 / (1.0 + exp(10 * (x - 0.5))) + + +def greenfunc(x): + return 1 - pow(redfunc(x + 0.2), 2) - bluefunc(x - 0.3) + + +def colorSpectrum(n=100): + multiple = 10 + if n == 1: + return [ImageColor.getrgb("rgb(100%,0%,0%)")] + elif n == 2: + return [ImageColor.getrgb("100%,0%,0%)"), + ImageColor.getrgb("rgb(0%,0%,100%)")] + elif n == 3: + return [ImageColor.getrgb("rgb(100%,0%,0%)"), + ImageColor.getrgb("rgb(0%,100%,0%)"), + ImageColor.getrgb("rgb(0%,0%,100%)")] + N = n * multiple + out = [None] * N + for i in range(N): + x = float(i) / N + out[i] = ImageColor.getrgb("rgb({}%,{}%,{}%".format( + *[int(i * 100) for i in ( + redfunc(x), greenfunc(x), bluefunc(x))])) + out2 = [out[0]] + step = N / float(n - 1) + j = 0 + for i in range(n - 2): + j += step + out2.append(out[int(j)]) + out2.append(out[-1]) + return out2 + + +def _test(): + import doctest + doctest.testmod() + + +if __name__ == "__main__": + _test() |