merge changes

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diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py
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index df7156b4..00000000
--- a/wqflask/utility/Plot.py
+++ /dev/null
@@ -1,343 +0,0 @@
-# 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 utility.corestats as corestats
-from base import webqtlConfig
-from 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()