Roassal histogram bars left shifted
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Roassal histogram bars left shifted
 
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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 _______________________________________________ Moose-dev mailing list [hidden email] https://www.list.inf.unibe.ch/listinfo/moose-dev |
Roassal.jpeg (24K)
Re: Roassal histogram bars left shifted
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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 ^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;.
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Re: Roassal histogram bars left shifted
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Hi Alex I attached another screenshot which describes exactly the problem.2017-06-16 10:40 GMT-03:00 Alexandre Bergel <[hidden email]>:
My script actually sets minX: but it is wrongly drawn in the histogram
The problem is not positioning the bars above the Y-Axis, but positioning them in the X-Axis.
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
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Re: Roassal histogram bars left shifted
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Re: Roassal histogram bars left shifted
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Re: Roassal histogram bars left shifted
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In reply to this post by hernanmd
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 <[hidden email]> wrote: _______________________________________________ Moose-dev mailing list [hidden email] https://www.list.inf.unibe.ch/listinfo/moose-dev |
Re: Roassal histogram bars left shifted
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Hi Alex, Thank you for taking care of this issue.>>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 <[hidden email]>:
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Re: Roassal histogram bars left shifted
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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 -=-=-=-=-=-=-=-=-=  Does this solve your problem? Cheers, Alexandre -- _,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;: Alexandre Bergel http://www.bergel.eu ^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;. On Jul 13, 2017, at 7:22 PM, Hernán Morales Durand <[hidden email]> wrote: _______________________________________________ Moose-dev mailing list [hidden email] https://www.list.inf.unibe.ch/listinfo/moose-dev |
Re: Roassal histogram bars left shifted
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Hi Alex, Unfortunately those messages didn't helped me. I have been stepping inside RTGrapher... minX := self builder minX. maxX := self builder maxX. ... then nothing is displayed. Cheers, Hernán 2017-07-13 16:44 GMT-03:00 Alexandre Bergel <[hidden email]>:
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Re: Roassal histogram bars left shifted
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Re: Roassal histogram bars left shifted
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Re: Roassal histogram bars left shifted
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Re: Roassal histogram bars left shifted
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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 <[hidden email]>: > 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 <[hidden email]> wrote: >> >> Hi Alex, >> >> 2017-07-21 15:47 GMT-03:00 Alexandre Bergel <[hidden email]>: >>> >>> 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 <[hidden email]>: >>>> >>>> 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 >>>> <[hidden email]> 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 <[hidden email]>: >>>> 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 >>>> <[hidden email]> wrote: >>>> >>>> Hi Alex >>>> >>>> I attached another screenshot which describes exactly the problem. >>>> >>>> 2017-06-16 10:40 GMT-03:00 Alexandre Bergel <[hidden email]>: >>>> 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 >>>> <[hidden email]> 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 >>>> [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 >>>> >>>> >>>> <unnamed.jpg>_______________________________________________ >>>> 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 >>>> >>>> >>>> >>>> <Grapher1.jpg><Grapher2.jpg>_______________________________________________ >>>> 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 >>> >>> >>> >>> _______________________________________________ >>> 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 > > -- > _,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;: > Alexandre Bergel http://www.bergel.eu > ^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;. > > > > _______________________________________________ > 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 |
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