18 Nov
2015
18 Nov
'15
10:15 p.m.
Hello,
I am using Roassal2 (StephanEggermont.40) in Pharo 4. The attached picture
displays a common visualization for inference of local ancestry in
population genetics, I have attached what I am getting now with Grapher.
Input data for such visualization is for example:
1:454 2:1488 1:2546 2:5711 1:14253 2:24411 1:31490 0:41585
(those are like Associations with key 0, 1 or 2 and value 454, 1488, ...
etc)
In the attached picture
Min X is 0 and
Max X is 41500
so the X axis (chromosome positions) is rendered in intervals between 10000.
This is what I am trying now (code is commented where I tried to configure
X axis interval)
| b intv |
intv := 0 to: 40000 by: 10000.
b := RTGrapher new.
ds := RTStackedDataSet new.
ds dotShape color: Color red.
ds
points: #(1 2 1 2 1 2 1 0);
x: intv. "????"
ds barShape width: 99; color: Color red.
"b
minX: 0;
maxX: 41500."
b add: ds.
b axisX noLabel; noTick. b axisY noDecimal.
b build.
I have some questions:
1) There is support to add an interval label to the X axis but preserving
the space relation with the real chromosome position (the X axis) for the
data (points in my example = 454 1488 2546 5711 14253 24411 31490 41585)?
2) How to clear the bar filling?
Any advice or help would be really nice.
Hernán
19 Nov
19 Nov
12:50 a.m.
New subject: Trying to display local ancestry inference with Grapher
Hi Hernan
Try the next piece of code and tell me what you think
| b data |
data := (0 to: 40000 by: 1000)
collect: [:n | n@ (Random new next * 3) floor].
b := RTGrapher new.
b extent: 1000@ 200.
ds := RTData new.
ds dotShape rectangle height: 1; width: 25; color: Color blue.
ds connectUsing: (RTLine new
color: (Color blue);
width: 1;
withHorizontalAttachPoint; yourself).
ds
points: data;
x: #x;
y: #y.
b add: ds.
b axisX.
b axisY title: 'alles Count'.
b build.
[image: Imágenes integradas 1]
Cheers,
Milton
2015-11-18 17:15 GMT-04:00 Hernán Morales Durand <hernan.morales(a)gmail.com>om>:
23 Nov
23 Nov
7:28 p.m.
New subject: Trying to display local ancestry inference with Grapher
Hi again,
Probably it's me but with my real data I cannot find an easy way to set the
extent in such way breakpoint lines are displayed vertically but not sloped.
Do you know what I'm missing?
| b data dataSet dataPoints win alleleCount breakPoints |
win := '11:85 00:301 01:493 00:639 11:1063 00:1458 11:1754 00:2110 11:2299
00:2705 11:2786 01:2998 11:3213 01:3388 00:3495 01:4004 00:4156 11:4249
00:4339 11:4462 01:4997 00:5585' lines.
dataPoints := (win first findTokens: Character space) collect: [ : dp | dp
findTokens: $: ].
breakPoints := (dataPoints collect: #second) collect: #asNumber.
alleleCount := dataPoints collect: [ : a | a first = '11' ifTrue: [ 2 ]
ifFalse: [ a first = '01' ifTrue: [ 1 ] ifFalse: [ 0 ] ] ].
data := breakPoints with: alleleCount collect: [ : bp : ac | bp @ ac ].
b := RTGrapher new.
b extent: 570 @ 200.
dataSet := RTDataSet new.
dataSet dotShape rectangle
height: 1;
width: 25;
color: Color blue.
dataSet connectUsing: (RTLine new
color: (Color blue);
width: 1;
withHorizontalAttachPoint; yourself).
dataSet
points: data;
x: #x;
y: #y.
b add: dataSet.
b axisX.
b axisY title: 'alleles Count'.
b build.
Hernán
2015-11-18 21:48 GMT-03:00 Hernán Morales Durand <hernan.morales(a)gmail.com>om>:
24 Nov
24 Nov
1:14 p.m.
New subject: Trying to display local ancestry inference with Grapher
Why do you need a width for the dot?
You can do:
win := '11:85 00:301 01:493 00:639 11:1063 00:1458 11:1754 00:2110 11:2299 00:2705
11:2786 01:2998 11:3213 01:3388 00:3495 01:4004 00:4156 11:4249 00:4339 11:4462 01:4997
00:5585' lines.
dataPoints := (win first findTokens: Character space) collect: [ : dp | dp findTokens: $:
].
breakPoints := (dataPoints collect: #second) collect: #asNumber.
alleleCount := dataPoints collect: [ : a | a first = '11' ifTrue: [ 2 ] ifFalse: [
a first = '01' ifTrue: [ 1 ] ifFalse: [ 0 ] ] ].
data := breakPoints with: alleleCount collect: [ : bp : ac | bp @ ac ].
b := RTGrapher new.
b extent: 570 @ 200.
dataSet := RTDataSet new.
dataSet dotShape
color: Color blue.
dataSet
connectUsing: ((RTMultiLine new withVerticallAttachPoint; orthoHorizontal)
color: (Color blue);
width: 1;
withHorizontalAttachPoint; yourself).
dataSet
points: data;
x: #x;
y: #y.
b add: dataSet.
b axisX.
b axisY title: 'alleles Count'.
b build.
Cheers,
Alexandre
--
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Alexandre Bergel http://www.bergel.eu
^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;.
4:25 p.m.
New subject: Trying to display local ancestry inference with Grapher
2015-11-24 9:14 GMT-03:00 Alexandre Bergel <alexandre.bergel(a)me.com>om>:
Why do you need a width for the dot?
Ahá! I didn't checked rectangle and multiline, I need more practice with
Roassal API :)
Thank you Alex,
Hernán
19 Nov
19 Nov
1:31 p.m.
New subject: Trying to display local ancestry inference with Grapher
Excellent example! I have added it in Roassal
Alexandre
--
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Alexandre Bergel http://www.bergel.eu
^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;.
1:32 p.m.
New subject: Trying to display local ancestry inference with Grapher
Don’t you want to consider in moving to the last version of Roassal?
Alexandre
--
_,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:
Alexandre Bergel http://www.bergel.eu
^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;.
3:18 p.m.
New subject: Trying to display local ancestry inference with Grapher
Hi Alex,
Yes but I just installed the version available in the Configuration
Browser. I thought it was the latest one, but then I've checked in Pharo 5
the Catalog Browser seems to install another more updated version.
Cheers,
Hernán
2015-11-19 9:31 GMT-03:00 Alexandre Bergel <alexandre.bergel(a)me.com>om>:
4:17 p.m.
New subject: Trying to display local ancestry inference with Grapher
Ah okay. Yes, version for Pharo 4 is not maintained at all.
Cheers,
Alexandre
--
_,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:
Alexandre Bergel http://www.bergel.eu
^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;.
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9 comments
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participants (3)
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Alexandre Bergel -
Hernán Morales Durand -
milton mamani