Trying to display local ancestry inference with Grapher

On Nov 18, 2015, at 8:49 PM, milton mamani <[hidden email]> wrote:

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.

<foo.png>

Cheers,

Milton

2015-11-18 17:15 GMT-04:00 Hernán Morales Durand <[hidden email]>:

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

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On Nov 18, 2015, at 6:15 PM, Hernán Morales Durand <[hidden email]> wrote:

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

<LocalAncestry.jpg><Grapher_Test1.png>_______________________________________________
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On Nov 19, 2015, at 11:18 AM, Hernán Morales Durand <[hidden email]> wrote:

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 <[hidden email]>:

Don’t you want to consider in moving to the last version of Roassal?

Alexandre

-- 
_,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:
Alexandre Bergel  http://www.bergel.eu
^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;.

On Nov 18, 2015, at 6:15 PM, Hernán Morales Durand <[hidden email]> wrote:

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

<LocalAncestry.jpg><Grapher_Test1.png>_______________________________________________
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[hidden email]
https://www.list.inf.unibe.ch/listinfo/moose-dev

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On Nov 23, 2015, at 3:28 PM, Hernán Morales Durand <[hidden email]> wrote:

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 <[hidden email]>:

Looks nice! :)

I will try it my data set.

Thank you Milton.

2015-11-18 20:49 GMT-03:00 milton mamani <[hidden email]>:

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.

<foo.png>

Cheers,

Milton

2015-11-18 17:15 GMT-04:00 Hernán Morales Durand <[hidden email]>:

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

_______________________________________________
Moose-dev mailing list
[hidden email]
https://www.list.inf.unibe.ch/listinfo/moose-dev

_______________________________________________
Moose-dev mailing list
[hidden email]
https://www.list.inf.unibe.ch/listinfo/moose-dev

_______________________________________________
Moose-dev mailing list
[hidden email]
https://www.list.inf.unibe.ch/listinfo/moose-dev