15 Jun
2017
15 Jun
'17
7:16 a.m.
Hi guys,
I am experiencing a problem visualizing histograms in Roassal with Pharo 5.
In the attached image you can observe the first bar shape starts from a
negative X axis value, where I want to start from 0. Besides, some bars are
gapped but I don't know why.
I am using with the following code:
| bins minPoint g ds |
bins := self groupedBySeqLengthDistribution: binNumber.
minPoint := ((bins reject: #isEmpty) detectMin: [ : c | c size ])
anyOne size.
" Build diagram "
g := RTGrapher new
extent: 500 @ 200;
minX: minPoint;
withoutOrigin;
yourself.
ds := RTData new
points: bins;
x: [ : c | c ifEmpty: [ minPoint ] ifNotEmpty: [ : d | d anyOne
size ] ];
y: #size.
ds barShape
borderColor: Color black;
color: aColor;
width: barWidth.
g add: ds.
" Configure axis settings "
g axisY
title: axixYLabel;
color: Color black;
noDecimal.
g axisX
noDecimal;
fromPoint: minPoint;
color: Color black;
title: axisXLabel.
" Open visualization in a new window "
g open.
Any idea what I am missing?
Cheers,
Hernán
16 Jun
16 Jun
3:40 p.m.
Hi Hernán,
I am not sure what exactly is the problematic situation you describe. Why you cannot
simply with with #minX: and #maxX: ?
For example, I tried to reuse the code you have provided. I can have:
bins := #(#(1 1 1 1 ) #(2 2 2) #(5 5 5 5 5)).
minPoint := ((bins reject: #isEmpty) detectMin: [ : c | c size ]) anyOne.
" Build diagram "
g := RTGrapher new
extent: 500 @ 200;
minX: 0;
maxX: 6;
withoutOrigin;
yourself.
ds := RTData new
points: bins;
x: [ : c | c ifEmpty: [ minPoint ] ifNotEmpty: [ : d | d anyOne ] ];
y: #size.
ds barShape
borderColor: Color black;
color: Color red trans;
width: 30.
g add: ds.
g
But you can have "minX: 1", which in that case, the first bar is above the
Y-Axis. This is what one would expect.
Which rendering do you wish to have? Can you provide a self-contained piece of code that I
can run on my machine?
Cheers,
Alexandre
--
_,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:
Alexandre Bergel http://www.bergel.eu
^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;.
On Jun 15, 2017, at 1:16 AM, Hernán Morales Durand
<hernan.morales(a)gmail.com> wrote:
Hi guys,
I am experiencing a problem visualizing histograms in Roassal with Pharo 5. In the
attached image you can observe the first bar shape starts from a negative X axis value,
where I want to start from 0. Besides, some bars are gapped but I don't know why.
I am using with the following code:
| bins minPoint g ds |
bins := self groupedBySeqLengthDistribution: binNumber.
minPoint := ((bins reject: #isEmpty) detectMin: [ : c | c size ]) anyOne size.
" Build diagram "
g := RTGrapher new
extent: 500 @ 200;
minX: minPoint;
withoutOrigin;
yourself.
ds := RTData new
points: bins;
x: [ : c | c ifEmpty: [ minPoint ] ifNotEmpty: [ : d | d anyOne size ] ];
y: #size.
ds barShape
borderColor: Color black;
color: aColor;
width: barWidth.
g add: ds.
" Configure axis settings "
g axisY
title: axixYLabel;
color: Color black;
noDecimal.
g axisX
noDecimal;
fromPoint: minPoint;
color: Color black;
title: axisXLabel.
" Open visualization in a new window "
g open.
Any idea what I am missing?
Cheers,
Hernán
<Roassal.jpeg>_______________________________________________
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4:35 p.m.
Hi Alex
I attached another screenshot which describes exactly the problem.
2017-06-16 10:40 GMT-03:00 Alexandre Bergel <alexandre.bergel(a)me.com>om>:
Hi Hernán,
I am not sure what exactly is the problematic situation you describe. Why
you cannot simply with with #minX: and #maxX: ?
My script actually sets minX: but it is wrongly drawn in the histogram
For example, I tried to reuse the code you have
provided. I can have:
bins := #(#(1 1 1 1 ) #(2 2 2) #(5 5 5 5 5)).
minPoint := ((bins reject: #isEmpty) detectMin: [ : c | c size ])
anyOne.
" Build diagram "
g := RTGrapher new
extent: 500 @ 200;
minX: 0;
maxX: 6;
withoutOrigin;
yourself.
ds := RTData new
points: bins;
x: [ : c | c ifEmpty: [ minPoint ] ifNotEmpty: [ : d | d anyOne ]
];
y: #size.
ds barShape
borderColor: Color black;
color: Color red trans;
width: 30.
g add: ds.
g
But you can have "minX: 1", which in that case, the first bar is above the
Y-Axis. This is what one would expect.
The problem is not positioning the bars above the Y-Axis, but positioning
them in the X-Axis.
Which rendering do you wish to have? Can you provide a
self-contained
piece of code that I can run on my machine?
If you have some time you could install BioSmalltalk in Pharo 5 (I haven't
tested Pharo 6 yet) and evaluate the problematic expression:
Metacello new
smalltalkhubUser: 'hernan' project: 'BioSmalltalk';
configuration: 'BioSmalltalk';
version: #bleedingEdge;
load
(BioParser parseMultiFastaFile: BioObject testFilesDirectoryName
asFileReference / 'ls_orchid.fasta')
plotHistogramBins: 20
xAxisLabel: 'Sequence lengths (bp)'
yAxisLabel: 'Count'
color: Color red
Cheers,
Hernán
Cheers,
Alexandre
--
_,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:
Alexandre Bergel http://www.bergel.eu
^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;.
On Jun 15, 2017, at 1:16 AM, Hernán Morales Durand <
hernan.morales(a)gmail.com> wrote:
Hi guys,
I am experiencing a problem visualizing histograms in Roassal with Pharo
5. In the attached image you can observe the first bar shape starts from a
negative X axis value, where I want to start from 0. Besides, some bars are
gapped but I don't know why.
I am using with the following code:
| bins minPoint g ds |
bins := self groupedBySeqLengthDistribution: binNumber.
minPoint := ((bins reject: #isEmpty) detectMin: [ : c | c size ])
anyOne size.
" Build diagram "
g := RTGrapher new
extent: 500 @ 200;
minX: minPoint;
withoutOrigin;
yourself.
ds := RTData new
points: bins;
x: [ : c | c ifEmpty: [ minPoint ] ifNotEmpty: [ : d | d anyOne
size ] ];
y: #size.
ds barShape
borderColor: Color black;
color: aColor;
width: barWidth.
g add: ds.
" Configure axis settings "
g axisY
title: axixYLabel;
color: Color black;
noDecimal.
g axisX
noDecimal;
fromPoint: minPoint;
color: Color black;
title: axisXLabel.
" Open visualization in a new window "
g open.
Any idea what I am missing?
Cheers,
Hernán
<Roassal.jpeg>_______________________________________________
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Moose-dev(a)list.inf.unibe.ch
https://www.list.inf.unibe.ch/listinfo/moose-dev
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https://www.list.inf.unibe.ch/listinfo/moose-dev
9 Jul
9 Jul
10:20 a.m.
Hi Hernán,
Sorry to reply to late.
Can you update Roassal and try:
-=-=-=-=-=-=-=-=-=
g := RTGrapher new.
ds := RTData new.
ds barShape.
ds points: #(1 2 3 -2).
ds maxX: 10.
g add: ds.
g configureForBarCharts.
g
-=-=-=-=-=-=-=-=-=
The call configureforBarCharts should do what you expect.
Cheers,
Alexandre
--
_,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:
Alexandre Bergel http://www.bergel.eu
^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;.
On Jun 16, 2017, at 4:35 PM, Hernán Morales Durand
<hernan.morales(a)gmail.com> wrote:
Hi Alex
I attached another screenshot which describes exactly the problem.
2017-06-16 10:40 GMT-03:00 Alexandre Bergel <alexandre.bergel(a)me.com>om>:
Hi Hernán,
I am not sure what exactly is the problematic situation you describe. Why you cannot
simply with with #minX: and #maxX: ?
My script actually sets minX: but it is wrongly drawn in the histogram
For example, I tried to reuse the code you have provided. I can have:
bins := #(#(1 1 1 1 ) #(2 2 2) #(5 5 5 5 5)).
minPoint := ((bins reject: #isEmpty) detectMin: [ : c | c size ]) anyOne.
" Build diagram "
g := RTGrapher new
extent: 500 @ 200;
minX: 0;
maxX: 6;
withoutOrigin;
yourself.
ds := RTData new
points: bins;
x: [ : c | c ifEmpty: [ minPoint ] ifNotEmpty: [ : d | d anyOne ] ];
y: #size.
ds barShape
borderColor: Color black;
color: Color red trans;
width: 30.
g add: ds.
g
<Screenshot 2017-06-16 09.39.25.png>
But you can have "minX: 1", which in that case, the first bar is above the
Y-Axis. This is what one would expect.
The problem is not positioning the bars above the Y-Axis, but positioning them in the
X-Axis.
Which rendering do you wish to have? Can you provide a self-contained piece of code that
I can run on my machine?
If you have some time you could install BioSmalltalk in Pharo 5 (I haven't tested
Pharo 6 yet) and evaluate the problematic expression:
Metacello new
smalltalkhubUser: 'hernan' project: 'BioSmalltalk';
configuration: 'BioSmalltalk';
version: #bleedingEdge;
load
(BioParser parseMultiFastaFile: BioObject testFilesDirectoryName asFileReference /
'ls_orchid.fasta')
plotHistogramBins: 20
xAxisLabel: 'Sequence lengths (bp)'
yAxisLabel: 'Count'
color: Color red
Cheers,
Hernán
Cheers,
Alexandre
--
_,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:
Alexandre Bergel http://www.bergel.eu
^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;.
On Jun 15, 2017, at 1:16 AM, Hernán Morales
Durand <hernan.morales(a)gmail.com> wrote:
Hi guys,
I am experiencing a problem visualizing histograms in Roassal with Pharo 5. In the
attached image you can observe the first bar shape starts from a negative X axis value,
where I want to start from 0. Besides, some bars are gapped but I don't know why.
I am using with the following code:
| bins minPoint g ds |
bins := self groupedBySeqLengthDistribution: binNumber.
minPoint := ((bins reject: #isEmpty) detectMin: [ : c | c size ]) anyOne size.
" Build diagram "
g := RTGrapher new
extent: 500 @ 200;
minX: minPoint;
withoutOrigin;
yourself.
ds := RTData new
points: bins;
x: [ : c | c ifEmpty: [ minPoint ] ifNotEmpty: [ : d | d anyOne size ] ];
y: #size.
ds barShape
borderColor: Color black;
color: aColor;
width: barWidth.
g add: ds.
" Configure axis settings "
g axisY
title: axixYLabel;
color: Color black;
noDecimal.
g axisX
noDecimal;
fromPoint: minPoint;
color: Color black;
title: axisXLabel.
" Open visualization in a new window "
g open.
Any idea what I am missing?
Cheers,
Hernán
<Roassal.jpeg>_______________________________________________
Moose-dev mailing list
Moose-dev(a)list.inf.unibe.ch
https://www.list.inf.unibe.ch/listinfo/moose-dev
_______________________________________________
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Moose-dev(a)list.inf.unibe.ch
https://www.list.inf.unibe.ch/listinfo/moose-dev
<unnamed.jpg>_______________________________________________
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https://www.list.inf.unibe.ch/listinfo/moose-dev 
13 Jul
13 Jul
7:22 p.m.
Hi Alex,
Thank you for taking care of this issue.
The problem is partially fixed. I saw you implemented
>configureForBarCharts
self datasets do: #offsetForBarCharts.
self minX: 0.5.
self maxX: self getMaxNumberOfPoints.
self axisX noTick.
However, I want to display the ticks, so I borrowed the first 3 lines for
my plot method :
>plotHistogramBins: binNumber xAxisLabel: axisXLabel
yAxisLabel:
axixYLabel color: aColor barWidth: barWidth
| bins minPoint g ds |
bins := self groupedBySeqLengthDistribution: binNumber.
minPoint := ((bins reject: #isEmpty) detectMin: #size) anyOne size.
" Build diagram "
g := RTGrapher new
extent: 500 @ 200;
minX: minPoint;
withoutOrigin;
yourself.
ds := RTData new
points: bins;
x: [ : c | c ifEmpty: [ minPoint ] ifNotEmpty: [ : d | d anyOne
size ] ];
y: #size.
ds barShape
borderColor: Color black;
color: aColor;
width: barWidth.
g add: ds.
" Configure axis settings "
g axisY
title: axixYLabel;
color: Color black;
noDecimal.
g axisX
noDecimal;
fromPoint: minPoint;
color: Color black;
title: axisXLabel.
g datasets do: #offsetForBarCharts.
g minX: 0.
g maxX: g getMaxNumberOfPoints.
" Open visualization in a new window "
g open.
Now the shift problem is fixed, but I lost the sequence lengths in the X
axis. Please see the two attached screenshots.
Cheers,
Hernán
2017-07-09 5:20 GMT-03:00 Alexandre Bergel <alexandre.bergel(a)me.com>om>:
Hi Hernán,
Sorry to reply to late.
Can you update Roassal and try:
-=-=-=-=-=-=-=-=-=
g := RTGrapher new.
ds := RTData new.
ds barShape.
ds points: #(1 2 3 -2).
ds maxX: 10.
g add: ds.
g configureForBarCharts.
g
-=-=-=-=-=-=-=-=-=
The call configureforBarCharts should do what you expect.
Cheers,
Alexandre
--
_,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:
Alexandre Bergel http://www.bergel.eu
^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;.
On Jun 16, 2017, at 4:35 PM, Hernán Morales Durand <
hernan.morales(a)gmail.com> wrote:
Hi Alex
I attached another screenshot which describes exactly the problem.
2017-06-16 10:40 GMT-03:00 Alexandre Bergel <alexandre.bergel(a)me.com>om>:
Hi Hernán,
I am not sure what exactly is the problematic situation you describe. Why
you cannot simply with with #minX: and #maxX: ?
My script actually sets minX: but it is wrongly drawn in the histogram
For example, I tried to reuse the code you have provided. I can have:
bins := #(#(1 1 1 1 ) #(2 2 2) #(5 5 5 5 5)).
minPoint := ((bins reject: #isEmpty) detectMin: [ : c | c size ])
anyOne.
" Build diagram "
g := RTGrapher new
extent: 500 @ 200;
minX: 0;
maxX: 6;
withoutOrigin;
yourself.
ds := RTData new
points: bins;
x: [ : c | c ifEmpty: [ minPoint ] ifNotEmpty: [ : d | d anyOne ]
];
y: #size.
ds barShape
borderColor: Color black;
color: Color red trans;
width: 30.
g add: ds.
g
<Screenshot 2017-06-16 09.39.25.png>
But you can have "minX: 1", which in that case, the first bar is above the
Y-Axis. This is what one would expect.
The problem is not positioning the bars above the Y-Axis, but positioning
them in the X-Axis.
Which rendering do you wish to have? Can you provide a self-contained
piece of code that I can run on my machine?
If you have some time you could install BioSmalltalk in Pharo 5 (I haven't
tested Pharo 6 yet) and evaluate the problematic expression:
Metacello new
smalltalkhubUser: 'hernan' project: 'BioSmalltalk';
configuration: 'BioSmalltalk';
version: #bleedingEdge;
load
(BioParser parseMultiFastaFile: BioObject testFilesDirectoryName
asFileReference / 'ls_orchid.fasta')
plotHistogramBins: 20
xAxisLabel: 'Sequence lengths (bp)'
yAxisLabel: 'Count'
color: Color red
Cheers,
Hernán
Cheers,
Alexandre
--
_,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:
Alexandre Bergel http://www.bergel.eu
^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;.
On Jun 15, 2017, at 1:16 AM, Hernán Morales Durand <
hernan.morales(a)gmail.com> wrote:
Hi guys,
I am experiencing a problem visualizing histograms in Roassal with Pharo
5. In the attached image you can observe the first bar shape starts from a
negative X axis value, where I want to start from 0. Besides, some bars are
gapped but I don't know why.
I am using with the following code:
| bins minPoint g ds |
bins := self groupedBySeqLengthDistribution: binNumber.
minPoint := ((bins reject: #isEmpty) detectMin: [ : c | c size ])
anyOne size.
" Build diagram "
g := RTGrapher new
extent: 500 @ 200;
minX: minPoint;
withoutOrigin;
yourself.
ds := RTData new
points: bins;
x: [ : c | c ifEmpty: [ minPoint ] ifNotEmpty: [ : d | d anyOne
size ] ];
y: #size.
ds barShape
borderColor: Color black;
color: aColor;
width: barWidth.
g add: ds.
" Configure axis settings "
g axisY
title: axixYLabel;
color: Color black;
noDecimal.
g axisX
noDecimal;
fromPoint: minPoint;
color: Color black;
title: axisXLabel.
" Open visualization in a new window "
g open.
Any idea what I am missing?
Cheers,
Hernán
<Roassal.jpeg>_______________________________________________
Moose-dev mailing list
Moose-dev(a)list.inf.unibe.ch
https://www.list.inf.unibe.ch/listinfo/moose-dev
_______________________________________________
Moose-dev mailing list
Moose-dev(a)list.inf.unibe.ch
https://www.list.inf.unibe.ch/listinfo/moose-dev
<unnamed.jpg>_______________________________________________
Moose-dev mailing list
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_______________________________________________
Moose-dev mailing list
Moose-dev(a)list.inf.unibe.ch
https://www.list.inf.unibe.ch/listinfo/moose-dev
9:44 p.m.
Consider the example:
-=-=-=-=-=-=-=-=-=
g := RTGrapher new.
ds := RTData new.
ds barShape.
ds points: #(1 2 3 -2).
ds maxX: 10.
g add: ds.
g configureForBarCharts.
g axisX
numberOfLabels: 4;
labelConversion: [ :value | value + 500 ].
g
-=-=-=-=-=-=-=-=-=
Does this solve your problem?
Cheers,
Alexandre
--
_,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:
Alexandre Bergel http://www.bergel.eu
^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;.
On Jul 13, 2017, at 7:22 PM, Hernán Morales Durand
<hernan.morales(a)gmail.com> wrote:
Hi Alex,
Thank you for taking care of this issue.
The problem is partially fixed. I saw you implemented
>configureForBarCharts
self datasets do: #offsetForBarCharts.
self minX: 0.5.
self maxX: self getMaxNumberOfPoints.
self axisX noTick.
However, I want to display the ticks, so I borrowed the first 3 lines for my plot method
:
>plotHistogramBins: binNumber xAxisLabel:
axisXLabel yAxisLabel: axixYLabel color: aColor barWidth: barWidth
| bins minPoint g ds |
bins := self groupedBySeqLengthDistribution: binNumber.
minPoint := ((bins reject: #isEmpty) detectMin: #size) anyOne size.
" Build diagram "
g := RTGrapher new
extent: 500 @ 200;
minX: minPoint;
withoutOrigin;
yourself.
ds := RTData new
points: bins;
x: [ : c | c ifEmpty: [ minPoint ] ifNotEmpty: [ : d | d anyOne size ] ];
y: #size.
ds barShape
borderColor: Color black;
color: aColor;
width: barWidth.
g add: ds.
" Configure axis settings "
g axisY
title: axixYLabel;
color: Color black;
noDecimal.
g axisX
noDecimal;
fromPoint: minPoint;
color: Color black;
title: axisXLabel.
g datasets do: #offsetForBarCharts.
g minX: 0.
g maxX: g getMaxNumberOfPoints.
" Open visualization in a new window "
g open.
Now the shift problem is fixed, but I lost the sequence lengths in the X axis. Please see
the two attached screenshots.
Cheers,
Hernán
2017-07-09 5:20 GMT-03:00 Alexandre Bergel <alexandre.bergel(a)me.com>om>:
Hi Hernán,
Sorry to reply to late.
Can you update Roassal and try:
-=-=-=-=-=-=-=-=-=
g := RTGrapher new.
ds := RTData new.
ds barShape.
ds points: #(1 2 3 -2).
ds maxX: 10.
g add: ds.
g configureForBarCharts.
g
-=-=-=-=-=-=-=-=-=
The call configureforBarCharts should do what you expect.
Cheers,
Alexandre
<Screenshot 2017-07-09 10.20.26.png>
--
_,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:
Alexandre Bergel http://www.bergel.eu
^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;.
On Jun 16, 2017, at 4:35 PM, Hernán Morales
Durand <hernan.morales(a)gmail.com> wrote:
Hi Alex
I attached another screenshot which describes exactly the problem.
2017-06-16 10:40 GMT-03:00 Alexandre Bergel <alexandre.bergel(a)me.com>om>:
Hi Hernán,
I am not sure what exactly is the problematic situation you describe. Why you cannot
simply with with #minX: and #maxX: ?
My script actually sets minX: but it is wrongly drawn in the histogram
For example, I tried to reuse the code you have provided. I can have:
bins := #(#(1 1 1 1 ) #(2 2 2) #(5 5 5 5 5)).
minPoint := ((bins reject: #isEmpty) detectMin: [ : c | c size ]) anyOne.
" Build diagram "
g := RTGrapher new
extent: 500 @ 200;
minX: 0;
maxX: 6;
withoutOrigin;
yourself.
ds := RTData new
points: bins;
x: [ : c | c ifEmpty: [ minPoint ] ifNotEmpty: [ : d | d anyOne ] ];
y: #size.
ds barShape
borderColor: Color black;
color: Color red trans;
width: 30.
g add: ds.
g
<Screenshot 2017-06-16 09.39.25.png>
But you can have "minX: 1", which in that case, the first bar is above the
Y-Axis. This is what one would expect.
The problem is not positioning the bars above the Y-Axis, but positioning them in the
X-Axis.
Which rendering do you wish to have? Can you provide a self-contained piece of code that
I can run on my machine?
If you have some time you could install BioSmalltalk in Pharo 5 (I haven't tested
Pharo 6 yet) and evaluate the problematic expression:
Metacello new
smalltalkhubUser: 'hernan' project: 'BioSmalltalk';
configuration: 'BioSmalltalk';
version: #bleedingEdge;
load
(BioParser parseMultiFastaFile: BioObject testFilesDirectoryName asFileReference /
'ls_orchid.fasta')
plotHistogramBins: 20
xAxisLabel: 'Sequence lengths (bp)'
yAxisLabel: 'Count'
color: Color red
Cheers,
Hernán
Cheers,
Alexandre
--
_,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:
Alexandre Bergel http://www.bergel.eu
^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;.
_______________________________________________
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<Grapher1.jpg><Grapher2.jpg>_______________________________________________
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Moose-dev(a)list.inf.unibe.ch
https://www.list.inf.unibe.ch/listinfo/moose-dev On Jun 15, 2017, at 1:16 AM, Hernán Morales
Durand <hernan.morales(a)gmail.com> wrote:
Hi guys,
I am experiencing a problem visualizing histograms in Roassal with Pharo 5. In the
attached image you can observe the first bar shape starts from a negative X axis value,
where I want to start from 0. Besides, some bars are gapped but I don't know why.
I am using with the following code:
| bins minPoint g ds |
bins := self groupedBySeqLengthDistribution: binNumber.
minPoint := ((bins reject: #isEmpty) detectMin: [ : c | c size ]) anyOne size.
" Build diagram "
g := RTGrapher new
extent: 500 @ 200;
minX: minPoint;
withoutOrigin;
yourself.
ds := RTData new
points: bins;
x: [ : c | c ifEmpty: [ minPoint ] ifNotEmpty: [ : d | d anyOne size ] ];
y: #size.
ds barShape
borderColor: Color black;
color: aColor;
width: barWidth.
g add: ds.
" Configure axis settings "
g axisY
title: axixYLabel;
color: Color black;
noDecimal.
g axisX
noDecimal;
fromPoint: minPoint;
color: Color black;
title: axisXLabel.
" Open visualization in a new window "
g open.
Any idea what I am missing?
Cheers,
Hernán
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15 Jul
15 Jul
7:24 a.m.
Hi Alex,
Unfortunately those messages didn't helped me. I have been stepping inside
RTGrapher.
I have a question: If I have already configured #minX and #maxX in my
grapher to specific Numbers (as in my case). Why do you perform
#datasetComputeMinAndMax in RTGrapher>>renderIn: ?
If I manually set RTAbstractData>>computeMinAndMaxForX
..
minX := self builder minX.
maxX := self builder maxX.
...
then nothing is displayed.
Cheers,
Hernán
2017-07-13 16:44 GMT-03:00 Alexandre Bergel <alexandre.bergel(a)me.com>om>:
Consider the example:
-=-=-=-=-=-=-=-=-=
g := RTGrapher new.
ds := RTData new.
ds barShape.
ds points: #(1 2 3 -2).
ds maxX: 10.
g add: ds.
g configureForBarCharts.
g axisX
numberOfLabels: 4;
labelConversion: [ :value | value + 500 ].
g
-=-=-=-=-=-=-=-=-=
Does this solve your problem?
Cheers,
Alexandre
--
_,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:
Alexandre Bergel http://www.bergel.eu
^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;.
On Jul 13, 2017, at 7:22 PM, Hernán Morales Durand <
hernan.morales(a)gmail.com> wrote:
Hi Alex,
Thank you for taking care of this issue.
The problem is partially fixed. I saw you implemented
>configureForBarCharts
self datasets do: #offsetForBarCharts.
self minX: 0.5.
self maxX: self getMaxNumberOfPoints.
self axisX noTick.
However, I want to display the ticks, so I borrowed the first 3 lines for
my plot method :
>plotHistogramBins: binNumber xAxisLabel:
axisXLabel yAxisLabel:
axixYLabel color: aColor barWidth: barWidth
| bins minPoint g ds |
bins := self groupedBySeqLengthDistribution: binNumber.
minPoint := ((bins reject: #isEmpty) detectMin: #size) anyOne size.
" Build diagram "
g := RTGrapher new
extent: 500 @ 200;
minX: minPoint;
withoutOrigin;
yourself.
ds := RTData new
points: bins;
x: [ : c | c ifEmpty: [ minPoint ] ifNotEmpty: [ : d | d anyOne
size ] ];
y: #size.
ds barShape
borderColor: Color black;
color: aColor;
width: barWidth.
g add: ds.
" Configure axis settings "
g axisY
title: axixYLabel;
color: Color black;
noDecimal.
g axisX
noDecimal;
fromPoint: minPoint;
color: Color black;
title: axisXLabel.
g datasets do: #offsetForBarCharts.
g minX: 0.
g maxX: g getMaxNumberOfPoints.
" Open visualization in a new window "
g open.
Now the shift problem is fixed, but I lost the sequence lengths in the X
axis. Please see the two attached screenshots.
Cheers,
Hernán
2017-07-09 5:20 GMT-03:00 Alexandre Bergel <alexandre.bergel(a)me.com>om>:
Hi Hernán,
Sorry to reply to late.
Can you update Roassal and try:
-=-=-=-=-=-=-=-=-=
g := RTGrapher new.
ds := RTData new.
ds barShape.
ds points: #(1 2 3 -2).
ds maxX: 10.
g add: ds.
g configureForBarCharts.
g
-=-=-=-=-=-=-=-=-=
The call configureforBarCharts should do what you expect.
Cheers,
Alexandre
<Screenshot 2017-07-09 10.20.26.png>
--
_,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:
Alexandre Bergel http://www.bergel.eu
^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;.
On Jun 16, 2017, at 4:35 PM, Hernán Morales Durand <
hernan.morales(a)gmail.com> wrote:
Hi Alex
I attached another screenshot which describes exactly the problem.
2017-06-16 10:40 GMT-03:00 Alexandre Bergel <alexandre.bergel(a)me.com>om>:
Hi Hernán,
I am not sure what exactly is the problematic situation you describe. Why
you cannot simply with with #minX: and #maxX: ?
My script actually sets minX: but it is wrongly drawn in the histogram
For example, I tried to reuse the code you have provided. I can have:
bins := #(#(1 1 1 1 ) #(2 2 2) #(5 5 5 5 5)).
minPoint := ((bins reject: #isEmpty) detectMin: [ : c | c size ])
anyOne.
" Build diagram "
g := RTGrapher new
extent: 500 @ 200;
minX: 0;
maxX: 6;
withoutOrigin;
yourself.
ds := RTData new
points: bins;
x: [ : c | c ifEmpty: [ minPoint ] ifNotEmpty: [ : d | d anyOne ]
];
y: #size.
ds barShape
borderColor: Color black;
color: Color red trans;
width: 30.
g add: ds.
g
<Screenshot 2017-06-16 09.39.25.png>
But you can have "minX: 1", which in that case, the first bar is above the
Y-Axis. This is what one would expect.
The problem is not positioning the bars above the Y-Axis, but positioning
them in the X-Axis.
Which rendering do you wish to have? Can you provide a self-contained
piece of code that I can run on my machine?
If you have some time you could install BioSmalltalk in Pharo 5 (I haven't
tested Pharo 6 yet) and evaluate the problematic expression:
Metacello new
smalltalkhubUser: 'hernan' project: 'BioSmalltalk';
configuration: 'BioSmalltalk';
version: #bleedingEdge;
load
(BioParser parseMultiFastaFile: BioObject testFilesDirectoryName
asFileReference / 'ls_orchid.fasta')
plotHistogramBins: 20
xAxisLabel: 'Sequence lengths (bp)'
yAxisLabel: 'Count'
color: Color red
Cheers,
Hernán
Cheers,
Alexandre
--
_,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:
Alexandre Bergel http://www.bergel.eu
^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;.
On Jun 15, 2017, at 1:16 AM, Hernán Morales Durand <
hernan.morales(a)gmail.com> wrote:
Hi guys,
I am experiencing a problem visualizing histograms in Roassal with Pharo
5. In the attached image you can observe the first bar shape starts from a
negative X axis value, where I want to start from 0. Besides, some bars are
gapped but I don't know why.
I am using with the following code:
| bins minPoint g ds |
bins := self groupedBySeqLengthDistribution: binNumber.
minPoint := ((bins reject: #isEmpty) detectMin: [ : c | c size ])
anyOne size.
" Build diagram "
g := RTGrapher new
extent: 500 @ 200;
minX: minPoint;
withoutOrigin;
yourself.
ds := RTData new
points: bins;
x: [ : c | c ifEmpty: [ minPoint ] ifNotEmpty: [ : d | d anyOne
size ] ];
y: #size.
ds barShape
borderColor: Color black;
color: aColor;
width: barWidth.
g add: ds.
" Configure axis settings "
g axisY
title: axixYLabel;
color: Color black;
noDecimal.
g axisX
noDecimal;
fromPoint: minPoint;
color: Color black;
title: axisXLabel.
" Open visualization in a new window "
g open.
Any idea what I am missing?
Cheers,
Hernán
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21 Jul
21 Jul
8:47 p.m.
I have a question: If I have already configured #minX
and #maxX in my grapher to specific Numbers (as in my case). Why do you perform
#datasetComputeMinAndMax in RTGrapher>>renderIn: ?
Because you could have different data sets with different min and max values. These data
sets have to be homogenized to fit within one graph.
If I manually set
RTAbstractData>>computeMinAndMaxForX
..
minX := self builder minX.
maxX := self builder maxX.
...
then nothing is displayed.
Can you provide a simple examples that I can reproduce on my computer ? :-)
Cheers,
Alexandre
2017-07-13 16:44 GMT-03:00 Alexandre Bergel <alexandre.bergel(a)me.com
<mailto:alexandre.bergel@me.com>>:
Consider the example:
-=-=-=-=-=-=-=-=-=
g := RTGrapher new.
ds := RTData new.
ds barShape.
ds points: #(1 2 3 -2).
ds maxX: 10.
g add: ds.
g configureForBarCharts.
g axisX
numberOfLabels: 4;
labelConversion: [ :value | value + 500 ].
g
-=-=-=-=-=-=-=-=-=
<Screenshot 2017-07-13 21.44.20.png>
Does this solve your problem?
Cheers,
Alexandre
--
_,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:
Alexandre Bergel http://www.bergel.eu <http://www.bergel.eu/>
^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;.
On Jul 13, 2017, at 7:22 PM, Hernán Morales
Durand <hernan.morales(a)gmail.com <mailto:hernan.morales@gmail.com>> wrote:
Hi Alex,
Thank you for taking care of this issue.
The problem is partially fixed. I saw you implemented
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https://www.list.inf.unibe.ch/listinfo/moose-dev >configureForBarCharts
self datasets do: #offsetForBarCharts.
self minX: 0.5.
self maxX: self getMaxNumberOfPoints.
self axisX noTick.
However, I want to display the ticks, so I borrowed the first 3 lines for my plot method
:
>plotHistogramBins: binNumber xAxisLabel:
axisXLabel yAxisLabel: axixYLabel color: aColor barWidth: barWidth
| bins minPoint g ds |
bins := self groupedBySeqLengthDistribution: binNumber.
minPoint := ((bins reject: #isEmpty) detectMin: #size) anyOne size.
" Build diagram "
g := RTGrapher new
extent: 500 @ 200;
minX: minPoint;
withoutOrigin;
yourself.
ds := RTData new
points: bins;
x: [ : c | c ifEmpty: [ minPoint ] ifNotEmpty: [ : d | d anyOne size ] ];
y: #size.
ds barShape
borderColor: Color black;
color: aColor;
width: barWidth.
g add: ds.
" Configure axis settings "
g axisY
title: axixYLabel;
color: Color black;
noDecimal.
g axisX
noDecimal;
fromPoint: minPoint;
color: Color black;
title: axisXLabel.
g datasets do: #offsetForBarCharts.
g minX: 0.
g maxX: g getMaxNumberOfPoints.
" Open visualization in a new window "
g open.
Now the shift problem is fixed, but I lost the sequence lengths in the X axis. Please see
the two attached screenshots.
Cheers,
Hernán
2017-07-09 5:20 GMT-03:00 Alexandre Bergel <alexandre.bergel(a)me.com
<mailto:alexandre.bergel@me.com>>:
Hi Hernán,
Sorry to reply to late.
Can you update Roassal and try:
-=-=-=-=-=-=-=-=-=
g := RTGrapher new.
ds := RTData new.
ds barShape.
ds points: #(1 2 3 -2).
ds maxX: 10.
g add: ds.
g configureForBarCharts.
g
-=-=-=-=-=-=-=-=-=
The call configureforBarCharts should do what you expect.
Cheers,
Alexandre
<Screenshot 2017-07-09 10.20.26.png>
--
_,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:
Alexandre Bergel http://www.bergel.eu <http://www.bergel.eu/>
^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;.
On Jun 16, 2017, at 4:35 PM, Hernán Morales
Durand <hernan.morales(a)gmail.com <mailto:hernan.morales@gmail.com>> wrote:
Hi Alex
I attached another screenshot which describes exactly the problem.
2017-06-16 10:40 GMT-03:00 Alexandre Bergel <alexandre.bergel(a)me.com
<mailto:alexandre.bergel@me.com>>:
Hi Hernán,
I am not sure what exactly is the problematic situation you describe. Why you cannot
simply with with #minX: and #maxX: ?
My script actually sets minX: but it is wrongly drawn in the histogram
For example, I tried to reuse the code you have provided. I can have:
bins := #(#(1 1 1 1 ) #(2 2 2) #(5 5 5 5 5)).
minPoint := ((bins reject: #isEmpty) detectMin: [ : c | c size ]) anyOne.
" Build diagram "
g := RTGrapher new
extent: 500 @ 200;
minX: 0;
maxX: 6;
withoutOrigin;
yourself.
ds := RTData new
points: bins;
x: [ : c | c ifEmpty: [ minPoint ] ifNotEmpty: [ : d | d anyOne ] ];
y: #size.
ds barShape
borderColor: Color black;
color: Color red trans;
width: 30.
g add: ds.
g
<Screenshot 2017-06-16 09.39.25.png>
But you can have "minX: 1", which in that case, the first bar is above the
Y-Axis. This is what one would expect.
The problem is not positioning the bars above the Y-Axis, but positioning them in the
X-Axis.
Which rendering do you wish to have? Can you provide a self-contained piece of code that
I can run on my machine?
If you have some time you could install BioSmalltalk in Pharo 5 (I haven't tested
Pharo 6 yet) and evaluate the problematic expression:
Metacello new
smalltalkhubUser: 'hernan' project: 'BioSmalltalk';
configuration: 'BioSmalltalk';
version: #bleedingEdge;
load
(BioParser parseMultiFastaFile: BioObject testFilesDirectoryName asFileReference /
'ls_orchid.fasta')
plotHistogramBins: 20
xAxisLabel: 'Sequence lengths (bp)'
yAxisLabel: 'Count'
color: Color red
Cheers,
Hernán
Cheers,
Alexandre
--
_,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:
Alexandre Bergel http://www.bergel.eu <http://www.bergel.eu/>
^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;.
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<https://www.list.inf.unibe.ch/listinfo/moose-dev> On Jun 15, 2017, at 1:16 AM, Hernán Morales
Durand <hernan.morales(a)gmail.com <mailto:hernan.morales@gmail.com>> wrote:
Hi guys,
I am experiencing a problem visualizing histograms in Roassal with Pharo 5. In the
attached image you can observe the first bar shape starts from a negative X axis value,
where I want to start from 0. Besides, some bars are gapped but I don't know why.
I am using with the following code:
| bins minPoint g ds |
bins := self groupedBySeqLengthDistribution: binNumber.
minPoint := ((bins reject: #isEmpty) detectMin: [ : c | c size ]) anyOne size.
" Build diagram "
g := RTGrapher new
extent: 500 @ 200;
minX: minPoint;
withoutOrigin;
yourself.
ds := RTData new
points: bins;
x: [ : c | c ifEmpty: [ minPoint ] ifNotEmpty: [ : d | d anyOne size ] ];
y: #size.
ds barShape
borderColor: Color black;
color: aColor;
width: barWidth.
g add: ds.
" Configure axis settings "
g axisY
title: axixYLabel;
color: Color black;
noDecimal.
g axisX
noDecimal;
fromPoint: minPoint;
color: Color black;
title: axisXLabel.
" Open visualization in a new window "
g open.
Any idea what I am missing?
Cheers,
Hernán
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26 Jul
26 Jul
7:35 a.m.
Hi Alex,
2017-07-21 15:47 GMT-03:00 Alexandre Bergel <alexandre.bergel(a)me.com>om>:
I have a question: If I have already configured #minX and #maxX in my
grapher to specific Numbers (as in my case). Why do you perform
#datasetComputeMinAndMax in RTGrapher>>renderIn: ?
Because you could have different data sets with different min and max
values. These data sets have to be homogenized to fit within one graph.
I don't want to criticize the design decisions behind Roassal, my goal
is to have this histogram rendered as I have seen in other libraries.
I understand that you have modeled a generic class (RTGrapher) which
could handle 1..n data sets and that sounds reasonable. In the case of
having >= 2 data sets, adjusting the min and max is not only desirable
but necessary because as you said, they possibly don't fit.
But in the case of having just one data set, and I specifically
configured the min and max, could you trust my min and max values by
not adjusting by #datasetComputeMinAndMax ?
Maybe we could get faster rendering times as a plus?
Does it makes sense?
If I manually set
RTAbstractData>>computeMinAndMaxForX
..
minX := self builder minX.
maxX := self builder maxX.
...
then nothing is displayed.
Can you provide a simple examples that I can reproduce on my computer ? :-)
I prepared a BioSmalltalk image with the script ready to be evaluated:
https://www.dropbox.com/s/v1un45w15xypnbj/BioSmalltalk_image.zip?dl=0
Let me know any issue.
Cheers,
Hernán
Cheers,
Alexandre
2017-07-13 16:44 GMT-03:00 Alexandre Bergel <alexandre.bergel(a)me.com>om>:
Consider the example:
-=-=-=-=-=-=-=-=-=
g := RTGrapher new.
ds := RTData new.
ds barShape.
ds points: #(1 2 3 -2).
ds maxX: 10.
g add: ds.
g configureForBarCharts.
g axisX
numberOfLabels: 4;
labelConversion: [ :value | value + 500 ].
g
-=-=-=-=-=-=-=-=-=
<Screenshot 2017-07-13 21.44.20.png>
Does this solve your problem?
Cheers,
Alexandre
--
_,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:
Alexandre Bergel http://www.bergel.eu
^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;.
On Jul 13, 2017, at 7:22 PM, Hernán Morales Durand
<hernan.morales(a)gmail.com> wrote:
Hi Alex,
Thank you for taking care of this issue.
The problem is partially fixed. I saw you implemented
_______________________________________________
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>configureForBarCharts
self datasets do: #offsetForBarCharts.
self minX: 0.5.
self maxX: self getMaxNumberOfPoints.
self axisX noTick.
However, I want to display the ticks, so I borrowed the first 3 lines for
my plot method :
>plotHistogramBins: binNumber xAxisLabel:
axisXLabel yAxisLabel:
> axixYLabel color: aColor barWidth: barWidth
| bins minPoint g ds |
bins := self groupedBySeqLengthDistribution: binNumber.
minPoint := ((bins reject: #isEmpty) detectMin: #size) anyOne size.
" Build diagram "
g := RTGrapher new
extent: 500 @ 200;
minX: minPoint;
withoutOrigin;
yourself.
ds := RTData new
points: bins;
x: [ : c | c ifEmpty: [ minPoint ] ifNotEmpty: [ : d | d anyOne
size ] ];
y: #size.
ds barShape
borderColor: Color black;
color: aColor;
width: barWidth.
g add: ds.
" Configure axis settings "
g axisY
title: axixYLabel;
color: Color black;
noDecimal.
g axisX
noDecimal;
fromPoint: minPoint;
color: Color black;
title: axisXLabel.
g datasets do: #offsetForBarCharts.
g minX: 0.
g maxX: g getMaxNumberOfPoints.
" Open visualization in a new window "
g open.
Now the shift problem is fixed, but I lost the sequence lengths in the X
axis. Please see the two attached screenshots.
Cheers,
Hernán
2017-07-09 5:20 GMT-03:00 Alexandre Bergel <alexandre.bergel(a)me.com>om>:
Hi Hernán,
Sorry to reply to late.
Can you update Roassal and try:
-=-=-=-=-=-=-=-=-=
g := RTGrapher new.
ds := RTData new.
ds barShape.
ds points: #(1 2 3 -2).
ds maxX: 10.
g add: ds.
g configureForBarCharts.
g
-=-=-=-=-=-=-=-=-=
The call configureforBarCharts should do what you expect.
Cheers,
Alexandre
<Screenshot 2017-07-09 10.20.26.png>
--
_,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:
Alexandre Bergel http://www.bergel.eu
^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;.
On Jun 16, 2017, at 4:35 PM, Hernán Morales Durand
<hernan.morales(a)gmail.com> wrote:
Hi Alex
I attached another screenshot which describes exactly the problem.
2017-06-16 10:40 GMT-03:00 Alexandre Bergel <alexandre.bergel(a)me.com>om>:
Hi Hernán,
I am not sure what exactly is the problematic situation you describe. Why
you cannot simply with with #minX: and #maxX: ?
My script actually sets minX: but it is wrongly drawn in the histogram
For example, I tried to reuse the code you have provided. I can have:
bins := #(#(1 1 1 1 ) #(2 2 2) #(5 5 5 5 5)).
minPoint := ((bins reject: #isEmpty) detectMin: [ : c | c size ])
anyOne.
" Build diagram "
g := RTGrapher new
extent: 500 @ 200;
minX: 0;
maxX: 6;
withoutOrigin;
yourself.
ds := RTData new
points: bins;
x: [ : c | c ifEmpty: [ minPoint ] ifNotEmpty: [ : d | d anyOne ]
];
y: #size.
ds barShape
borderColor: Color black;
color: Color red trans;
width: 30.
g add: ds.
g
<Screenshot 2017-06-16 09.39.25.png>
But you can have "minX: 1", which in that case, the first bar is above the
Y-Axis. This is what one would expect.
The problem is not positioning the bars above the Y-Axis, but positioning
them in the X-Axis.
Which rendering do you wish to have? Can you provide a self-contained
piece of code that I can run on my machine?
If you have some time you could install BioSmalltalk in Pharo 5 (I haven't
tested Pharo 6 yet) and evaluate the problematic expression:
Metacello new
smalltalkhubUser: 'hernan' project: 'BioSmalltalk';
configuration: 'BioSmalltalk';
version: #bleedingEdge;
load
(BioParser parseMultiFastaFile: BioObject testFilesDirectoryName
asFileReference / 'ls_orchid.fasta')
plotHistogramBins: 20
xAxisLabel: 'Sequence lengths (bp)'
yAxisLabel: 'Count'
color: Color red
Cheers,
Hernán
Cheers,
Alexandre
--
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^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;.
On Jun 15, 2017, at 1:16 AM, Hernán Morales Durand
<hernan.morales(a)gmail.com> wrote:
Hi guys,
I am experiencing a problem visualizing histograms in Roassal with Pharo
5. In the attached image you can observe the first bar shape starts from a
negative X axis value, where I want to start from 0. Besides, some bars are
gapped but I don't know why.
I am using with the following code:
| bins minPoint g ds |
bins := self groupedBySeqLengthDistribution: binNumber.
minPoint := ((bins reject: #isEmpty) detectMin: [ : c | c size ])
anyOne size.
" Build diagram "
g := RTGrapher new
extent: 500 @ 200;
minX: minPoint;
withoutOrigin;
yourself.
ds := RTData new
points: bins;
x: [ : c | c ifEmpty: [ minPoint ] ifNotEmpty: [ : d | d anyOne
size ] ];
y: #size.
ds barShape
borderColor: Color black;
color: aColor;
width: barWidth.
g add: ds.
" Configure axis settings "
g axisY
title: axixYLabel;
color: Color black;
noDecimal.
g axisX
noDecimal;
fromPoint: minPoint;
color: Color black;
title: axisXLabel.
" Open visualization in a new window "
g open.
Any idea what I am missing?
Cheers,
Hernán
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27 Jul
27 Jul
1:27 a.m.
Hi Hernán,
I understand your point.
I am still figuring out what exactly the problem you are facing.
I cannot open the image you provide. Which VM do you need for it? Which version of pharo
are you using? I tried different VMs, including Cog from April 2013.
Alexandre
On Jul 26, 2017, at 1:35 AM, Hernán Morales Durand
<hernan.morales(a)gmail.com> wrote:
Hi Alex,
2017-07-21 15:47 GMT-03:00 Alexandre Bergel <alexandre.bergel(a)me.com>om>:
--
_,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:
Alexandre Bergel http://www.bergel.eu
^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;.
I have a question: If I have already configured #minX and #maxX in my
grapher to specific Numbers (as in my case). Why do you perform
#datasetComputeMinAndMax in RTGrapher>>renderIn: ?
Because you could have different data sets with different min and max
values. These data sets have to be homogenized to fit within one graph.
I don't want to criticize the design decisions behind Roassal, my goal
is to have this histogram rendered as I have seen in other libraries.
I understand that you have modeled a generic class (RTGrapher) which
could handle 1..n data sets and that sounds reasonable. In the case of
having >= 2 data sets, adjusting the min and max is not only desirable
but necessary because as you said, they possibly don't fit.
But in the case of having just one data set, and I specifically
configured the min and max, could you trust my min and max values by
not adjusting by #datasetComputeMinAndMax ?
Maybe we could get faster rendering times as a plus?
Does it makes sense?
If I manually set
RTAbstractData>>computeMinAndMaxForX
..
minX := self builder minX.
maxX := self builder maxX.
...
then nothing is displayed.
Can you provide a simple examples that I can reproduce on my computer ? :-)
I prepared a BioSmalltalk image with the script ready to be evaluated:
https://www.dropbox.com/s/v1un45w15xypnbj/BioSmalltalk_image.zip?dl=0
Let me know any issue.
Cheers,
Hernán
Cheers,
Alexandre
2017-07-13 16:44 GMT-03:00 Alexandre Bergel <alexandre.bergel(a)me.com>om>:
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Consider the example:
-=-=-=-=-=-=-=-=-=
g := RTGrapher new.
ds := RTData new.
ds barShape.
ds points: #(1 2 3 -2).
ds maxX: 10.
g add: ds.
g configureForBarCharts.
g axisX
numberOfLabels: 4;
labelConversion: [ :value | value + 500 ].
g
-=-=-=-=-=-=-=-=-=
<Screenshot 2017-07-13 21.44.20.png>
Does this solve your problem?
Cheers,
Alexandre
--
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^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;.
On Jul 13, 2017, at 7:22 PM, Hernán Morales Durand
<hernan.morales(a)gmail.com> wrote:
Hi Alex,
Thank you for taking care of this issue.
The problem is partially fixed. I saw you implemented
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> configureForBarCharts
self datasets do: #offsetForBarCharts.
self minX: 0.5.
self maxX: self getMaxNumberOfPoints.
self axisX noTick.
However, I want to display the ticks, so I borrowed the first 3 lines for
my plot method :
> plotHistogramBins: binNumber xAxisLabel:
axisXLabel yAxisLabel:
> axixYLabel color: aColor barWidth: barWidth
| bins minPoint g ds |
bins := self groupedBySeqLengthDistribution: binNumber.
minPoint := ((bins reject: #isEmpty) detectMin: #size) anyOne size.
" Build diagram "
g := RTGrapher new
extent: 500 @ 200;
minX: minPoint;
withoutOrigin;
yourself.
ds := RTData new
points: bins;
x: [ : c | c ifEmpty: [ minPoint ] ifNotEmpty: [ : d | d anyOne
size ] ];
y: #size.
ds barShape
borderColor: Color black;
color: aColor;
width: barWidth.
g add: ds.
" Configure axis settings "
g axisY
title: axixYLabel;
color: Color black;
noDecimal.
g axisX
noDecimal;
fromPoint: minPoint;
color: Color black;
title: axisXLabel.
g datasets do: #offsetForBarCharts.
g minX: 0.
g maxX: g getMaxNumberOfPoints.
" Open visualization in a new window "
g open.
Now the shift problem is fixed, but I lost the sequence lengths in the X
axis. Please see the two attached screenshots.
Cheers,
Hernán
2017-07-09 5:20 GMT-03:00 Alexandre Bergel <alexandre.bergel(a)me.com>om>:
Hi Hernán,
Sorry to reply to late.
Can you update Roassal and try:
-=-=-=-=-=-=-=-=-=
g := RTGrapher new.
ds := RTData new.
ds barShape.
ds points: #(1 2 3 -2).
ds maxX: 10.
g add: ds.
g configureForBarCharts.
g
-=-=-=-=-=-=-=-=-=
The call configureforBarCharts should do what you expect.
Cheers,
Alexandre
<Screenshot 2017-07-09 10.20.26.png>
--
_,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:
Alexandre Bergel http://www.bergel.eu
^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;.
On Jun 16, 2017, at 4:35 PM, Hernán Morales Durand
<hernan.morales(a)gmail.com> wrote:
Hi Alex
I attached another screenshot which describes exactly the problem.
2017-06-16 10:40 GMT-03:00 Alexandre Bergel <alexandre.bergel(a)me.com>om>:
Hi Hernán,
I am not sure what exactly is the problematic situation you describe. Why
you cannot simply with with #minX: and #maxX: ?
My script actually sets minX: but it is wrongly drawn in the histogram
For example, I tried to reuse the code you have provided. I can have:
bins := #(#(1 1 1 1 ) #(2 2 2) #(5 5 5 5 5)).
minPoint := ((bins reject: #isEmpty) detectMin: [ : c | c size ])
anyOne.
" Build diagram "
g := RTGrapher new
extent: 500 @ 200;
minX: 0;
maxX: 6;
withoutOrigin;
yourself.
ds := RTData new
points: bins;
x: [ : c | c ifEmpty: [ minPoint ] ifNotEmpty: [ : d | d anyOne ]
];
y: #size.
ds barShape
borderColor: Color black;
color: Color red trans;
width: 30.
g add: ds.
g
<Screenshot 2017-06-16 09.39.25.png>
But you can have "minX: 1", which in that case, the first bar is above the
Y-Axis. This is what one would expect.
The problem is not positioning the bars above the Y-Axis, but positioning
them in the X-Axis.
Which rendering do you wish to have? Can you provide a self-contained
piece of code that I can run on my machine?
If you have some time you could install BioSmalltalk in Pharo 5 (I haven't
tested Pharo 6 yet) and evaluate the problematic expression:
Metacello new
smalltalkhubUser: 'hernan' project: 'BioSmalltalk';
configuration: 'BioSmalltalk';
version: #bleedingEdge;
load
(BioParser parseMultiFastaFile: BioObject testFilesDirectoryName
asFileReference / 'ls_orchid.fasta')
plotHistogramBins: 20
xAxisLabel: 'Sequence lengths (bp)'
yAxisLabel: 'Count'
color: Color red
Cheers,
Hernán
Cheers,
Alexandre
--
_,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:
Alexandre Bergel http://www.bergel.eu
^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;.
On Jun 15, 2017, at 1:16 AM, Hernán Morales Durand
<hernan.morales(a)gmail.com> wrote:
Hi guys,
I am experiencing a problem visualizing histograms in Roassal with Pharo
5. In the attached image you can observe the first bar shape starts from a
negative X axis value, where I want to start from 0. Besides, some bars are
gapped but I don't know why.
I am using with the following code:
| bins minPoint g ds |
bins := self groupedBySeqLengthDistribution: binNumber.
minPoint := ((bins reject: #isEmpty) detectMin: [ : c | c size ])
anyOne size.
" Build diagram "
g := RTGrapher new
extent: 500 @ 200;
minX: minPoint;
withoutOrigin;
yourself.
ds := RTData new
points: bins;
x: [ : c | c ifEmpty: [ minPoint ] ifNotEmpty: [ : d | d anyOne
size ] ];
y: #size.
ds barShape
borderColor: Color black;
color: aColor;
width: barWidth.
g add: ds.
" Configure axis settings "
g axisY
title: axixYLabel;
color: Color black;
noDecimal.
g axisX
noDecimal;
fromPoint: minPoint;
color: Color black;
title: axisXLabel.
" Open visualization in a new window "
g open.
Any idea what I am missing?
Cheers,
Hernán
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6:34 a.m.
Hi Alex,
I forgot to mention, it is a Pharo 5.0 standard image saved in Win
8.1, Cog Spur VM 5.0 (release) from May 4, 2016
Compiler gcc 4.6.2, downloaded using
wget -O- get.pharo.org/50+vm | bash -
Anyway, I launched my hackintosh OS X Mavericks and could open the
image after changing the permissions
chmod 644 Pharo.image Pharo.changes
../MacOS/Pharo Pharo.image
Do you get an error message?
Cheers,
Hernán
2017-07-26 20:27 GMT-03:00 Alexandre Bergel <alexandre.bergel(a)me.com>om>:
Hi Hernán,
I understand your point.
I am still figuring out what exactly the problem you are facing.
I cannot open the image you provide. Which VM do you need for it? Which version of pharo
are you using? I tried different VMs, including Cog from April 2013.
Alexandre
On Jul 26, 2017, at 1:35 AM, Hernán Morales
Durand <hernan.morales(a)gmail.com> wrote:
Hi Alex,
2017-07-21 15:47 GMT-03:00 Alexandre Bergel <alexandre.bergel(a)me.com>om>:
--
_,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:
Alexandre Bergel http://www.bergel.eu
^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;.
_______________________________________________
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I have a question: If I have already configured #minX and #maxX in my
grapher to specific Numbers (as in my case). Why do you perform
#datasetComputeMinAndMax in RTGrapher>>renderIn: ?
Because you could have different data sets with different min and max
values. These data sets have to be homogenized to fit within one graph.
I don't want to criticize the design decisions behind Roassal, my goal
is to have this histogram rendered as I have seen in other libraries.
I understand that you have modeled a generic class (RTGrapher) which
could handle 1..n data sets and that sounds reasonable. In the case of
having >= 2 data sets, adjusting the min and max is not only desirable
but necessary because as you said, they possibly don't fit.
But in the case of having just one data set, and I specifically
configured the min and max, could you trust my min and max values by
not adjusting by #datasetComputeMinAndMax ?
Maybe we could get faster rendering times as a plus?
Does it makes sense?
If I manually set
RTAbstractData>>computeMinAndMaxForX
..
minX := self builder minX.
maxX := self builder maxX.
...
then nothing is displayed.
Can you provide a simple examples that I can reproduce on my computer ? :-)
I prepared a BioSmalltalk image with the script ready to be evaluated:
https://www.dropbox.com/s/v1un45w15xypnbj/BioSmalltalk_image.zip?dl=0
Let me know any issue.
Cheers,
Hernán
Cheers,
Alexandre
2017-07-13 16:44 GMT-03:00 Alexandre Bergel <alexandre.bergel(a)me.com>om>:
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Consider the example:
-=-=-=-=-=-=-=-=-=
g := RTGrapher new.
ds := RTData new.
ds barShape.
ds points: #(1 2 3 -2).
ds maxX: 10.
g add: ds.
g configureForBarCharts.
g axisX
numberOfLabels: 4;
labelConversion: [ :value | value + 500 ].
g
-=-=-=-=-=-=-=-=-=
<Screenshot 2017-07-13 21.44.20.png>
Does this solve your problem?
Cheers,
Alexandre
--
_,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:
Alexandre Bergel http://www.bergel.eu
^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;.
On Jul 13, 2017, at 7:22 PM, Hernán Morales Durand
<hernan.morales(a)gmail.com> wrote:
Hi Alex,
Thank you for taking care of this issue.
The problem is partially fixed. I saw you implemented
>> configureForBarCharts
self datasets do: #offsetForBarCharts.
self minX: 0.5.
self maxX: self getMaxNumberOfPoints.
self axisX noTick.
However, I want to display the ticks, so I borrowed the first 3 lines for
my plot method :
>> plotHistogramBins: binNumber xAxisLabel: axisXLabel yAxisLabel:
>> axixYLabel color: aColor barWidth: barWidth
| bins minPoint g ds |
bins := self groupedBySeqLengthDistribution: binNumber.
minPoint := ((bins reject: #isEmpty) detectMin: #size) anyOne size.
" Build diagram "
g := RTGrapher new
extent: 500 @ 200;
minX: minPoint;
withoutOrigin;
yourself.
ds := RTData new
points: bins;
x: [ : c | c ifEmpty: [ minPoint ] ifNotEmpty: [ : d | d anyOne
size ] ];
y: #size.
ds barShape
borderColor: Color black;
color: aColor;
width: barWidth.
g add: ds.
" Configure axis settings "
g axisY
title: axixYLabel;
color: Color black;
noDecimal.
g axisX
noDecimal;
fromPoint: minPoint;
color: Color black;
title: axisXLabel.
g datasets do: #offsetForBarCharts.
g minX: 0.
g maxX: g getMaxNumberOfPoints.
" Open visualization in a new window "
g open.
Now the shift problem is fixed, but I lost the sequence lengths in the X
axis. Please see the two attached screenshots.
Cheers,
Hernán
2017-07-09 5:20 GMT-03:00 Alexandre Bergel <alexandre.bergel(a)me.com>om>:
Hi Hernán,
Sorry to reply to late.
Can you update Roassal and try:
-=-=-=-=-=-=-=-=-=
g := RTGrapher new.
ds := RTData new.
ds barShape.
ds points: #(1 2 3 -2).
ds maxX: 10.
g add: ds.
g configureForBarCharts.
g
-=-=-=-=-=-=-=-=-=
The call configureforBarCharts should do what you expect.
Cheers,
Alexandre
<Screenshot 2017-07-09 10.20.26.png>
--
_,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:
Alexandre Bergel http://www.bergel.eu
^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;.
On Jun 16, 2017, at 4:35 PM, Hernán Morales Durand
<hernan.morales(a)gmail.com> wrote:
Hi Alex
I attached another screenshot which describes exactly the problem.
2017-06-16 10:40 GMT-03:00 Alexandre Bergel <alexandre.bergel(a)me.com>om>:
Hi Hernán,
I am not sure what exactly is the problematic situation you describe. Why
you cannot simply with with #minX: and #maxX: ?
My script actually sets minX: but it is wrongly drawn in the histogram
For example, I tried to reuse the code you have provided. I can have:
bins := #(#(1 1 1 1 ) #(2 2 2) #(5 5 5 5 5)).
minPoint := ((bins reject: #isEmpty) detectMin: [ : c | c size ])
anyOne.
" Build diagram "
g := RTGrapher new
extent: 500 @ 200;
minX: 0;
maxX: 6;
withoutOrigin;
yourself.
ds := RTData new
points: bins;
x: [ : c | c ifEmpty: [ minPoint ] ifNotEmpty: [ : d | d anyOne ]
];
y: #size.
ds barShape
borderColor: Color black;
color: Color red trans;
width: 30.
g add: ds.
g
<Screenshot 2017-06-16 09.39.25.png>
But you can have "minX: 1", which in that case, the first bar is above the
Y-Axis. This is what one would expect.
The problem is not positioning the bars above the Y-Axis, but positioning
them in the X-Axis.
Which rendering do you wish to have? Can you provide a self-contained
piece of code that I can run on my machine?
If you have some time you could install BioSmalltalk in Pharo 5 (I haven't
tested Pharo 6 yet) and evaluate the problematic expression:
Metacello new
smalltalkhubUser: 'hernan' project: 'BioSmalltalk';
configuration: 'BioSmalltalk';
version: #bleedingEdge;
load
(BioParser parseMultiFastaFile: BioObject testFilesDirectoryName
asFileReference / 'ls_orchid.fasta')
plotHistogramBins: 20
xAxisLabel: 'Sequence lengths (bp)'
yAxisLabel: 'Count'
color: Color red
Cheers,
Hernán
Cheers,
Alexandre
--
_,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:
Alexandre Bergel http://www.bergel.eu
^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;.
On Jun 15, 2017, at 1:16 AM, Hernán Morales Durand
<hernan.morales(a)gmail.com> wrote:
Hi guys,
I am experiencing a problem visualizing histograms in Roassal with Pharo
5. In the attached image you can observe the first bar shape starts from a
negative X axis value, where I want to start from 0. Besides, some bars are
gapped but I don't know why.
I am using with the following code:
| bins minPoint g ds |
bins := self groupedBySeqLengthDistribution: binNumber.
minPoint := ((bins reject: #isEmpty) detectMin: [ : c | c size ])
anyOne size.
" Build diagram "
g := RTGrapher new
extent: 500 @ 200;
minX: minPoint;
withoutOrigin;
yourself.
ds := RTData new
points: bins;
x: [ : c | c ifEmpty: [ minPoint ] ifNotEmpty: [ : d | d anyOne
size ] ];
y: #size.
ds barShape
borderColor: Color black;
color: aColor;
width: barWidth.
g add: ds.
" Configure axis settings "
g axisY
title: axixYLabel;
color: Color black;
noDecimal.
g axisX
noDecimal;
fromPoint: minPoint;
color: Color black;
title: axisXLabel.
" Open visualization in a new window "
g open.
Any idea what I am missing?
Cheers,
Hernán
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16 Jun
16 Jun
7:06 p.m.
Hi,
I suspect your issue I want a bug per se. Your x axis starts at the first
bar x location. The bars are going to be centered on the point - meaning it
will overlap to the left (or negative) side.
As for the gaps I suspect that has to do with the data. The bars have a
width and the space between each point is very small - so there will be
overlap. And space for x values that aren't in your data (giving you the
gaps).
Did you want instead each bar next to the next and individually labbeled?
On Jun 14, 2017 10:16 PM, "Hernán Morales Durand"
<hernan.morales(a)gmail.com>
wrote:
Hi guys,
I am experiencing a problem visualizing histograms in Roassal with Pharo
5. In the attached image you can observe the first bar shape starts from a
negative X axis value, where I want to start from 0. Besides, some bars are
gapped but I don't know why.
I am using with the following code:
| bins minPoint g ds |
bins := self groupedBySeqLengthDistribution: binNumber.
minPoint := ((bins reject: #isEmpty) detectMin: [ : c | c size ])
anyOne size.
" Build diagram "
g := RTGrapher new
extent: 500 @ 200;
minX: minPoint;
withoutOrigin;
yourself.
ds := RTData new
points: bins;
x: [ : c | c ifEmpty: [ minPoint ] ifNotEmpty: [ : d | d anyOne
size ] ];
y: #size.
ds barShape
borderColor: Color black;
color: aColor;
width: barWidth.
g add: ds.
" Configure axis settings "
g axisY
title: axixYLabel;
color: Color black;
noDecimal.
g axisX
noDecimal;
fromPoint: minPoint;
color: Color black;
title: axisXLabel.
" Open visualization in a new window "
g open.
Any idea what I am missing?
Cheers,
Hernán
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17 Jun
17 Jun
6:16 a.m.
Hi Chris,
2017-06-16 14:06 GMT-03:00 Chris Cunningham <cunningham.cb(a)gmail.com>om>:
Hi,
I suspect your issue I want a bug per se.
I didn't understood that.
Your x axis starts at the first bar x location. The
bars are going to be
centered on the point - meaning it will overlap to the left (or negative)
side.
So my Axis X starts at 572.
My minPoint is 592.
So why the first bar is shifted to the left?
Anyway, I had to manually substract to adjust the minPoint:
minPoint := ((bins reject: #isEmpty) detectMin: #size) anyOne size - 28.
As for the gaps I suspect that has to do with the data. The bars have a
width and the space between each point is very small - so there will be
overlap. And space for x values that aren't in your data (giving you the
gaps).
Did you want instead each bar next to the next and individually labbeled?
I want each bar next to the next, I think I never saw a histogram with
overlapped bars.
Somehow matplotlib got this right:
http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc295
Cheers,
Hernán
On Jun 14, 2017 10:16 PM, "Hernán Morales Durand"
<hernan.morales(a)gmail.com>
wrote:
Hi guys,
I am experiencing a problem visualizing histograms in Roassal with Pharo
5. In the attached image you can observe the first bar shape starts from a
negative X axis value, where I want to start from 0. Besides, some bars are
gapped but I don't know why.
I am using with the following code:
| bins minPoint g ds |
bins := self groupedBySeqLengthDistribution: binNumber.
minPoint := ((bins reject: #isEmpty) detectMin: [ : c | c size ])
anyOne size.
" Build diagram "
g := RTGrapher new
extent: 500 @ 200;
minX: minPoint;
withoutOrigin;
yourself.
ds := RTData new
points: bins;
x: [ : c | c ifEmpty: [ minPoint ] ifNotEmpty: [ : d | d anyOne
size ] ];
y: #size.
ds barShape
borderColor: Color black;
color: aColor;
width: barWidth.
g add: ds.
" Configure axis settings "
g axisY
title: axixYLabel;
color: Color black;
noDecimal.
g axisX
noDecimal;
fromPoint: minPoint;
color: Color black;
title: axisXLabel.
" Open visualization in a new window "
g open.
Any idea what I am missing?
Cheers,
Hernán
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2465
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days old
12 comments
3 participants
participants (3)
-
Alexandre Bergel -
Chris Cunningham -
Hernán Morales Durand