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@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

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

On Jun 16, 2017, at 4:35 PM, Hernán Morales Durand < 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@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 ^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;._,.;:~^~:;.

On Jun 15, 2017, at 1:16 AM, Hernán Morales Durand < 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 <Roassal.jpeg>_______________________________________________ Moose-dev mailing list Moose-dev@list.inf.unibe.ch https://www.list.inf.unibe.ch/listinfo/moose-dev

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