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authorArthur Centeno2021-04-09 20:38:21 +0000
committerArthur Centeno2021-04-09 20:38:21 +0000
commite2b04a322f26670782fe7f7c39bcebc508fdabdd (patch)
treea51c32bae4d544cc0beea19f455ccc52f0544a4c /wqflask/utility/Plot.py
parent187cd40bd3273b50d2813bfccf98bfadbb8c14ff (diff)
parentef51e08753defdfc7f3e67f8788cd1362d2cf631 (diff)
downloadgenenetwork2-e2b04a322f26670782fe7f7c39bcebc508fdabdd.tar.gz
Merge branch 'testing' of github.com:genenetwork/genenetwork2 into acenteno
Diffstat (limited to 'wqflask/utility/Plot.py')
-rw-r--r--wqflask/utility/Plot.py127
1 files changed, 80 insertions, 47 deletions
diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py
index cce8435d..61f408d2 100644
--- a/wqflask/utility/Plot.py
+++ b/wqflask/utility/Plot.py
@@ -24,32 +24,35 @@
#
# Last updated by GeneNetwork Core Team 2010/10/20
-from __future__ import print_function
-
-import piddle as pid
-from pprint import pformat as pf
+from PIL import ImageColor
+from PIL import ImageDraw
+from PIL import ImageFont
from math import *
-import random
-import sys, os
-from numarray import linear_algebra as la
-from numarray import ones, array, dot, swapaxes
-
-import reaper
-import webqtlUtil
-import corestats
+import utility.corestats as corestats
from base import webqtlConfig
-
+from utility.pillow_utils import draw_rotated_text
import utility.logger
logger = utility.logger.getLogger(__name__ )
+# ---- 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','.'):
+ while strD[-1] in ('0', '.'):
if strD[-1] == '0' and strD[-2] == '.' and len(strD) <= 4:
break
elif strD[-1] == '.':
@@ -77,7 +80,7 @@ def frange(start, end=None, inc=1.0):
# Need to adjust the count. AFAICT, it always comes up one short.
count += 1
L = [start] * count
- for i in xrange(1, count):
+ for i in range(1, count):
L[i] = start + i * inc
return L
@@ -88,7 +91,7 @@ def find_outliers(vals):
>>> 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])
+ >>> 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,
@@ -116,7 +119,8 @@ def find_outliers(vals):
# 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=pid.blue, axesColor=pid.black, labelColor=pid.black, XLabel=None, YLabel=None, title=None, offset= (60, 20, 40, 40), zoom = 1):
+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
@@ -152,7 +156,7 @@ def plotBar(canvas, data, barColor=pid.blue, axesColor=pid.black, labelColor=pid
j = int((item-xLow)/step)
Count[j] += 1
- yLow, yTop, stepY=detScale(0,max(Count))
+ yLow, yTop, stepY=detScale(0, max(Count))
#draw data
xScale = plotWidth/(xTop-xLow)
@@ -163,67 +167,91 @@ def plotBar(canvas, data, barColor=pid.blue, axesColor=pid.black, labelColor=pid
if count:
xc = (dataXY[i]-xLow)*xScale+xLeftOffset
yc =-(count-yLow)*yScale+yTopOffset+plotHeight
- canvas.drawRect(xc+2,yc,xc+barWidth-2,yTopOffset+plotHeight,edgeColor=barColor,fillColor=barColor)
+ im_drawer.rectangle(
+ xy=((xc+2, yc), (xc+barWidth-2, yTopOffset+plotHeight)),
+ outline=barColor, fill=barColor)
#draw drawing region
- canvas.drawRect(xLeftOffset, yTopOffset, xLeftOffset+plotWidth, yTopOffset+plotHeight)
+ im_drawer.rectangle(
+ xy=((xLeftOffset, yTopOffset), (xLeftOffset+plotWidth, yTopOffset+plotHeight))
+ )
#draw scale
- scaleFont=pid.Font(ttf="cour",size=11,bold=1)
+ scaleFont=ImageFont.truetype(font=COUR_FILE, size=11)
x=xLow
for i in range(int(stepX)+1):
xc=xLeftOffset+(x-xLow)*xScale
- canvas.drawLine(xc,yTopOffset+plotHeight,xc,yTopOffset+plotHeight+5, color=axesColor)
+ im_drawer.line(
+ xy=((xc, yTopOffset+plotHeight), (xc, yTopOffset+plotHeight+5)),
+ fill=axesColor)
strX = cformat(d=x, rank=0)
- canvas.drawString(strX,xc-canvas.stringWidth(strX,font=scaleFont)/2,yTopOffset+plotHeight+14,font=scaleFont)
+ 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
- canvas.drawLine(xLeftOffset,yc,xLeftOffset-5,yc, color=axesColor)
+ im_drawer.line(xy=((xLeftOffset, yc), (xLeftOffset-5, yc)), fill=axesColor)
strY = "%d" %y
- canvas.drawString(strY,xLeftOffset-canvas.stringWidth(strY,font=scaleFont)-6,yc+5,font=scaleFont)
+ 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=pid.Font(ttf="tahoma",size=17,bold=0)
+ labelFont=ImageFont.truetype(font=TAHOMA_FILE, size=17)
if XLabel:
- canvas.drawString(XLabel,xLeftOffset+(plotWidth-canvas.stringWidth(XLabel,font=labelFont))/2.0,
- yTopOffset+plotHeight+yBottomOffset-10,font=labelFont,color=labelColor)
+ 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:
- canvas.drawString(YLabel, 19, yTopOffset+plotHeight-(plotHeight-canvas.stringWidth(YLabel,font=labelFont))/2.0,
- font=labelFont,color=labelColor,angle=90)
-
- labelFont=pid.Font(ttf="verdana",size=16,bold=0)
+ 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:
- canvas.drawString(title,xLeftOffset+(plotWidth-canvas.stringWidth(title,font=labelFont))/2.0,
- 20,font=labelFont,color=labelColor)
+ 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):
+def detScaleOld(min, max):
if min>=max:
return None
elif min == -1.0 and max == 1.0:
- return [-1.2,1.2,12]
+ return [-1.2, 1.2, 12]
else:
a=max-min
b=floor(log10(a))
- c=pow(10.0,b)
+ 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)]
+ 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]
+ return [-1.2, 1.2, 12]
else:
a=max-min
if max != 0:
@@ -235,7 +263,7 @@ def detScale(min=0,max=0):
min -= 0.1*a
a=max-min
b=floor(log10(a))
- c=pow(10.0,b)
+ c=pow(10.0, b)
low=c*floor(min/c)
high=c*ceil(max/c)
n = round((high-low)/c)
@@ -253,7 +281,7 @@ def detScale(min=0,max=0):
high=c*ceil(max/c)
n = round((high-low)/c)
- return [low,high,n]
+ return [low, high, n]
def bluefunc(x):
return 1.0 / (1.0 + exp(-10*(x-0.6)))
@@ -262,21 +290,26 @@ 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)
+ return 1 - pow(redfunc(x+0.2), 2) - bluefunc(x-0.3)
def colorSpectrum(n=100):
multiple = 10
if n == 1:
- return [pid.Color(1,0,0)]
+ return [ImageColor.getrgb("rgb(100%,0%,0%)")]
elif n == 2:
- return [pid.Color(1,0,0),pid.Color(0,0,1)]
+ return [ImageColor.getrgb("100%,0%,0%)"),
+ ImageColor.getrgb("rgb(0%,0%,100%)")]
elif n == 3:
- return [pid.Color(1,0,0),pid.Color(0,1,0),pid.Color(0,0,1)]
+ 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] = pid.Color(redfunc(x), greenfunc(x), bluefunc(x));
+ 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
@@ -292,4 +325,4 @@ def _test():
if __name__=="__main__":
- _test() \ No newline at end of file
+ _test()