# 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 2024/09/11
import os
from pathlib import Path
from PIL import ImageColor
from PIL import ImageDraw
from PIL import ImageFont
from math import *
from flask import current_app as app
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 ---- #
REPO_ROOT = Path(__file__).parent.parent
FONTS_DIR = REPO_ROOT.joinpath("wqflask/static/fonts")
VERDANA_FILE = f"{FONTS_DIR.joinpath('verdana.ttf')}"
COUR_FILE = f"{FONTS_DIR.joinpath('courbd.ttf')}"
TAHOMA_FILE = f"{FONTS_DIR.joinpath('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
app.logger.debug("Font file path: %s", os.path.abspath(COUR_FILE))
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()
