gviz data track (heatmap) and title panel questions
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@martin-rijlaarsdam-6043
Last seen 9.6 years ago
Dear Sirs, Thank you very much for Gviz! I have been using it for a while now but I have two issues that I cannot seem to figure out. Both are pretty trivial settings, so my apologies in advance. Please see the attached image as an example. 1) I would like to rotate the text in the title panel for some of the tracks (HMM, ALL, DHP) so that the text is horizontal. 2) I would like to remove the color bar and it's legend from the heatmap. Ik can remove the color gradient, but the legend (20,40,60,80) remains visible. I want to remove it because the current presentation suggests a relation between the tumor types presented. Thanks in advance for any suggestions that you might have. Kind regards, Martin -- M.A. (Martin) Rijlaarsdam MSc. MD Erasmus MC - University Medical Center Rotterdam Department of Pathology Room Be-432b Shipping adress: P.O. Box 2040, 3000 CA Rotterdam, The Netherlands Visiting adress: Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands Email: m.a.rijlaarsdam at gmail.com Mobile: +31 6 45408508 Telephone (work): +31 10 7033409 Fax +31 10 7044365 Website: http://www.martinrijlaarsdam.nl -------------- next part -------------- A non-text attachment was scrubbed... Name: overlap_SE_DGvstype.I.TE_hypermethy.in_type.I.TE_details_chr6-32 128829-32139638.png Type: image/png Size: 399004 bytes Desc: not available URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20140501="" 138e8f18="" attachment.png="">
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@martin-rijlaarsdam-6043
Last seen 9.6 years ago
PS I know about the showAxis=F settings, but if I do that, my sample names disappear as well... Best, Martin -- M.A. (Martin) Rijlaarsdam MSc. MD Erasmus MC - University Medical Center Rotterdam Department of Pathology Room Be-432b Shipping adress: P.O. Box 2040, 3000 CA Rotterdam, The Netherlands Visiting adress: Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands Email: m.a.rijlaarsdam@gmail.com Mobile: +31 6 45408508 Telephone (work): +31 10 7033409 Fax +31 10 7044365 Website: http://www.martinrijlaarsdam.nl On Thu, May 1, 2014 at 11:33 AM, Martin Rijlaarsdam < m.a.rijlaarsdam@gmail.com> wrote: > Dear Sirs, > > Thank you very much for Gviz! > > I have been using it for a while now but I have two issues that I cannot > seem to figure out. Both are pretty trivial settings, so my apologies in > advance. Please see the attached image as an example. > > 1) I would like to rotate the text in the title panel for some of the > tracks (HMM, ALL, DHP) so that the text is horizontal. > 2) I would like to remove the color bar and it's legend from the heatmap. > Ik can remove the color gradient, but the legend (20,40,60,80) remains > visible. I want to remove it because the current presentation suggests a > relation between the tumor types presented. > > Thanks in advance for any suggestions that you might have. > > Kind regards, > Martin > > -- > M.A. (Martin) Rijlaarsdam MSc. MD > Erasmus MC - University Medical Center Rotterdam > Department of Pathology > Room Be-432b > Shipping adress: P.O. Box 2040, 3000 CA Rotterdam, The Netherlands > Visiting adress: Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands > > Email: m.a.rijlaarsdam@gmail.com > Mobile: +31 6 45408508 > Telephone (work): +31 10 7033409 > Fax +31 10 7044365 > Website: http://www.martinrijlaarsdam.nl > [[alternative HTML version deleted]]
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@florianhahnenovartiscom-3784
Last seen 5.6 years ago
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Hi Martin, You can control the rotation of the title text using the rotate.title parameter. Please note that this will not automatically adjust the width of the title panel, so you may want to decrease the font size, (cex.title) or increase the title panel width (title.width), or maybe both. I will have to re-work the while process of setting up the title panels for this to work automatically. With respect to the color bar: try the showColorBar and showSampleNames parameters, they should do exactly what you ask for. Florian On 01/05/14 11:33, "Martin Rijlaarsdam" <m.a.rijlaarsdam at="" gmail.com=""> wrote: >Dear Sirs, > >Thank you very much for Gviz! > >I have been using it for a while now but I have two issues that I cannot >seem to figure out. Both are pretty trivial settings, so my apologies in >advance. Please see the attached image as an example. > >1) I would like to rotate the text in the title panel for some of the >tracks (HMM, ALL, DHP) so that the text is horizontal. >2) I would like to remove the color bar and it's legend from the heatmap. >Ik can remove the color gradient, but the legend (20,40,60,80) remains >visible. I want to remove it because the current presentation suggests a >relation between the tumor types presented. > >Thanks in advance for any suggestions that you might have. > >Kind regards, >Martin > >-- >M.A. (Martin) Rijlaarsdam MSc. MD >Erasmus MC - University Medical Center Rotterdam >Department of Pathology >Room Be-432b >Shipping adress: P.O. Box 2040, 3000 CA Rotterdam, The Netherlands >Visiting adress: Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands > >Email: m.a.rijlaarsdam at gmail.com >Mobile: +31 6 45408508 >Telephone (work): +31 10 7033409 >Fax +31 10 7044365 >Website: http://www.martinrijlaarsdam.nl
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Hi, Thanks a lot. Turns out I was using an outdated version of Gviz without that feature. Best, Martin -- M.A. (Martin) Rijlaarsdam MSc. MD Erasmus MC - University Medical Center Rotterdam Department of Pathology Room Be-432b Shipping adress: P.O. Box 2040, 3000 CA Rotterdam, The Netherlands Visiting adress: Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands Email: m.a.rijlaarsdam@gmail.com Mobile: +31 6 45408508 Telephone (work): +31 10 7033409 Fax +31 10 7044365 Website: http://www.martinrijlaarsdam.nl On Mon, May 12, 2014 at 1:54 PM, Hahne, Florian <florian.hahne@novartis.com>wrote: > Hi Martin, > You can control the rotation of the title text using the rotate.title > parameter. Please note that this will not automatically adjust the width > of the title panel, so you may want to decrease the font size, (cex.title) > or increase the title panel width (title.width), or maybe both. I will > have to re-work the while process of setting up the title panels for this > to work automatically. > With respect to the color bar: try the showColorBar and showSampleNames > parameters, they should do exactly what you ask for. > Florian > > > > On 01/05/14 11:33, "Martin Rijlaarsdam" <m.a.rijlaarsdam@gmail.com> wrote: > > >Dear Sirs, > > > >Thank you very much for Gviz! > > > >I have been using it for a while now but I have two issues that I cannot > >seem to figure out. Both are pretty trivial settings, so my apologies in > >advance. Please see the attached image as an example. > > > >1) I would like to rotate the text in the title panel for some of the > >tracks (HMM, ALL, DHP) so that the text is horizontal. > >2) I would like to remove the color bar and it's legend from the heatmap. > >Ik can remove the color gradient, but the legend (20,40,60,80) remains > >visible. I want to remove it because the current presentation suggests a > >relation between the tumor types presented. > > > >Thanks in advance for any suggestions that you might have. > > > >Kind regards, > >Martin > > > >-- > >M.A. (Martin) Rijlaarsdam MSc. MD > >Erasmus MC - University Medical Center Rotterdam > >Department of Pathology > >Room Be-432b > >Shipping adress: P.O. Box 2040, 3000 CA Rotterdam, The Netherlands > >Visiting adress: Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands > > > >Email: m.a.rijlaarsdam@gmail.com > >Mobile: +31 6 45408508 > >Telephone (work): +31 10 7033409 > >Fax +31 10 7044365 > >Website: http://www.martinrijlaarsdam.nl > > [[alternative HTML version deleted]]
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Dear Florian, Can I ask one more dummy question. When I add " col.title="black" " to the plotTracks parameter list, a black box appears around all title panels. Setting col.border.title="white" and/or lwd.border.title=0 does not help. I would prefer not to show any lines around the title panels. Thanks in advance for your help. Yours sincerely, Martin Rijlaarsdam -- M.A. (Martin) Rijlaarsdam MSc. MD Erasmus MC - University Medical Center Rotterdam Department of Pathology Room Be-432b Shipping adress: P.O. Box 2040, 3000 CA Rotterdam, The Netherlands Visiting adress: Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands Email: m.a.rijlaarsdam@gmail.com Mobile: +31 6 45408508 Telephone (work): +31 10 7033409 Fax +31 10 7044365 Website: http://www.martinrijlaarsdam.nl On Mon, May 12, 2014 at 1:54 PM, Hahne, Florian <florian.hahne@novartis.com>wrote: > Hi Martin, > You can control the rotation of the title text using the rotate.title > parameter. Please note that this will not automatically adjust the width > of the title panel, so you may want to decrease the font size, (cex.title) > or increase the title panel width (title.width), or maybe both. I will > have to re-work the while process of setting up the title panels for this > to work automatically. > With respect to the color bar: try the showColorBar and showSampleNames > parameters, they should do exactly what you ask for. > Florian > > > > On 01/05/14 11:33, "Martin Rijlaarsdam" <m.a.rijlaarsdam@gmail.com> wrote: > > >Dear Sirs, > > > >Thank you very much for Gviz! > > > >I have been using it for a while now but I have two issues that I cannot > >seem to figure out. Both are pretty trivial settings, so my apologies in > >advance. Please see the attached image as an example. > > > >1) I would like to rotate the text in the title panel for some of the > >tracks (HMM, ALL, DHP) so that the text is horizontal. > >2) I would like to remove the color bar and it's legend from the heatmap. > >Ik can remove the color gradient, but the legend (20,40,60,80) remains > >visible. I want to remove it because the current presentation suggests a > >relation between the tumor types presented. > > > >Thanks in advance for any suggestions that you might have. > > > >Kind regards, > >Martin > > > >-- > >M.A. (Martin) Rijlaarsdam MSc. MD > >Erasmus MC - University Medical Center Rotterdam > >Department of Pathology > >Room Be-432b > >Shipping adress: P.O. Box 2040, 3000 CA Rotterdam, The Netherlands > >Visiting adress: Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands > > > >Email: m.a.rijlaarsdam@gmail.com > >Mobile: +31 6 45408508 > >Telephone (work): +31 10 7033409 > >Fax +31 10 7044365 > >Website: http://www.martinrijlaarsdam.nl > > [[alternative HTML version deleted]]
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... and if I set col.title = "black" in specific track the same thing happens (black box around title panel) but now only for that specific track. Tnx! Martin -- M.A. (Martin) Rijlaarsdam MSc. MD Erasmus MC - University Medical Center Rotterdam Department of Pathology Room Be-432b Shipping adress: P.O. Box 2040, 3000 CA Rotterdam, The Netherlands Visiting adress: Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands Email: m.a.rijlaarsdam@gmail.com Mobile: +31 6 45408508 Telephone (work): +31 10 7033409 Fax +31 10 7044365 Website: http://www.martinrijlaarsdam.nl On Mon, May 12, 2014 at 5:25 PM, Martin Rijlaarsdam < m.a.rijlaarsdam@gmail.com> wrote: > Dear Florian, > > Can I ask one more dummy question. When I add " col.title="black" " to the > plotTracks parameter list, a black box appears around all title panels. > Setting col.border.title="white" and/or lwd.border.title=0 does not help. I > would prefer not to show any lines around the title panels. > > Thanks in advance for your help. > > Yours sincerely, > Martin Rijlaarsdam > > > -- > M.A. (Martin) Rijlaarsdam MSc. MD > Erasmus MC - University Medical Center Rotterdam > Department of Pathology > Room Be-432b > Shipping adress: P.O. Box 2040, 3000 CA Rotterdam, The Netherlands > Visiting adress: Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands > > Email: m.a.rijlaarsdam@gmail.com > Mobile: +31 6 45408508 > Telephone (work): +31 10 7033409 > Fax +31 10 7044365 > Website: http://www.martinrijlaarsdam.nl > > > On Mon, May 12, 2014 at 1:54 PM, Hahne, Florian < > florian.hahne@novartis.com> wrote: > >> Hi Martin, >> You can control the rotation of the title text using the rotate.title >> parameter. Please note that this will not automatically adjust the width >> of the title panel, so you may want to decrease the font size, (cex.title) >> or increase the title panel width (title.width), or maybe both. I will >> have to re-work the while process of setting up the title panels for this >> to work automatically. >> With respect to the color bar: try the showColorBar and showSampleNames >> parameters, they should do exactly what you ask for. >> Florian >> >> >> >> On 01/05/14 11:33, "Martin Rijlaarsdam" <m.a.rijlaarsdam@gmail.com> >> wrote: >> >> >Dear Sirs, >> > >> >Thank you very much for Gviz! >> > >> >I have been using it for a while now but I have two issues that I cannot >> >seem to figure out. Both are pretty trivial settings, so my apologies in >> >advance. Please see the attached image as an example. >> > >> >1) I would like to rotate the text in the title panel for some of the >> >tracks (HMM, ALL, DHP) so that the text is horizontal. >> >2) I would like to remove the color bar and it's legend from the heatmap. >> >Ik can remove the color gradient, but the legend (20,40,60,80) remains >> >visible. I want to remove it because the current presentation suggests a >> >relation between the tumor types presented. >> > >> >Thanks in advance for any suggestions that you might have. >> > >> >Kind regards, >> >Martin >> > >> >-- >> >M.A. (Martin) Rijlaarsdam MSc. MD >> >Erasmus MC - University Medical Center Rotterdam >> >Department of Pathology >> >Room Be-432b >> >Shipping adress: P.O. Box 2040, 3000 CA Rotterdam, The Netherlands >> >Visiting adress: Dr. Molewaterplein 50, 3015 GE Rotterdam, The >> Netherlands >> > >> >Email: m.a.rijlaarsdam@gmail.com >> >Mobile: +31 6 45408508 >> >Telephone (work): +31 10 7033409 >> >Fax +31 10 7044365 >> >Website: http://www.martinrijlaarsdam.nl >> >> > [[alternative HTML version deleted]]
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Hm, looks like the wrong parameter is being picked up for the title panel border. It should be col.border.title but obviously it takes col.title. I just fixed that, should become available with the 1.8.2 version of the package in the next couple of days. Florian From: Martin Rijlaarsdam <m.a.rijlaarsdam@gmail.com<mailto:m.a.rijlaarsdam@gmail.com>> Date: Monday 12 May 2014 17:29 To: Florian Hahne <florian.hahne@novartis.com<mailto:florian.hahne@novartis.com>> Cc: "bioconductor@r-project.org<mailto:bioconductor@r-project.org>" <bioconductor@r-project.org<mailto:bioconductor@r-project.org>> Subject: Re: [BioC] gviz data track (heatmap) and title panel questions ... and if I set col.title = "black" in specific track the same thing happens (black box around title panel) but now only for that specific track. Tnx! Martin -- M.A. (Martin) Rijlaarsdam MSc. MD Erasmus MC - University Medical Center Rotterdam Department of Pathology Room Be-432b Shipping adress: P.O. Box 2040, 3000 CA Rotterdam, The Netherlands Visiting adress: Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands Email: m.a.rijlaarsdam@gmail.com<mailto:m.a.rijlaarsdam@gmail.com> Mobile: +31 6 45408508 Telephone (work): +31 10 7033409 Fax +31 10 7044365 Website: http://www.martinrijlaarsdam.nl On Mon, May 12, 2014 at 5:25 PM, Martin Rijlaarsdam <m.a.rijlaarsdam@gmail.com<mailto:m.a.rijlaarsdam@gmail.com>> wrote: Dear Florian, Can I ask one more dummy question. When I add " col.title="black" " to the plotTracks parameter list, a black box appears around all title panels. Setting col.border.title="white" and/or lwd.border.title=0 does not help. I would prefer not to show any lines around the title panels. Thanks in advance for your help. Yours sincerely, Martin Rijlaarsdam -- M.A. (Martin) Rijlaarsdam MSc. MD Erasmus MC - University Medical Center Rotterdam Department of Pathology Room Be-432b Shipping adress: P.O. Box 2040, 3000 CA Rotterdam, The Netherlands Visiting adress: Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands Email: m.a.rijlaarsdam@gmail.com<mailto:m.a.rijlaarsdam@gmail.com> Mobile: +31 6 45408508<tel:%2b31%206%2045408508> Telephone (work): +31 10 7033409<tel:%2b31%2010%207033409> Fax +31 10 7044365<tel:%2b31%2010%207044365> Website: http://www.martinrijlaarsdam.nl On Mon, May 12, 2014 at 1:54 PM, Hahne, Florian <florian.hahne@novartis.com<mailto:florian.hahne@novartis.com>> wrote: Hi Martin, You can control the rotation of the title text using the rotate.title parameter. Please note that this will not automatically adjust the width of the title panel, so you may want to decrease the font size, (cex.title) or increase the title panel width (title.width), or maybe both. I will have to re-work the while process of setting up the title panels for this to work automatically. With respect to the color bar: try the showColorBar and showSampleNames parameters, they should do exactly what you ask for. Florian On 01/05/14 11:33, "Martin Rijlaarsdam" <m.a.rijlaarsdam@gmail.com<mailto:m.a.rijlaarsdam@gmail.com>> wrote: >Dear Sirs, > >Thank you very much for Gviz! > >I have been using it for a while now but I have two issues that I cannot >seem to figure out. Both are pretty trivial settings, so my apologies in >advance. Please see the attached image as an example. > >1) I would like to rotate the text in the title panel for some of the >tracks (HMM, ALL, DHP) so that the text is horizontal. >2) I would like to remove the color bar and it's legend from the heatmap. >Ik can remove the color gradient, but the legend (20,40,60,80) remains >visible. I want to remove it because the current presentation suggests a >relation between the tumor types presented. > >Thanks in advance for any suggestions that you might have. > >Kind regards, >Martin > >-- >M.A. (Martin) Rijlaarsdam MSc. MD >Erasmus MC - University Medical Center Rotterdam >Department of Pathology >Room Be-432b >Shipping adress: P.O. Box 2040, 3000 CA Rotterdam, The Netherlands >Visiting adress: Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands > >Email: m.a.rijlaarsdam@gmail.com<mailto:m.a.rijlaarsdam@gmail.com> >Mobile: +31 6 45408508<tel:%2b31%206%2045408508> >Telephone (work): +31 10 7033409<tel:%2b31%2010%207033409> >Fax +31 10 7044365<tel:%2b31%2010%207044365> >Website: http://www.martinrijlaarsdam.nl [[alternative HTML version deleted]]
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Dear Florian, Thank you. Will you also implement this (small) bugfix in the release branch? Best, Martin -- M.A. (Martin) Rijlaarsdam MSc. MD Erasmus MC - University Medical Center Rotterdam Department of Pathology Room Be-432b Shipping adress: P.O. Box 2040, 3000 CA Rotterdam, The Netherlands Visiting adress: Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands Email: m.a.rijlaarsdam@gmail.com Mobile: +31 6 45408508 Telephone (work): +31 10 7033409 Fax +31 10 7044365 Website: http://www.martinrijlaarsdam.nl On Tue, May 13, 2014 at 9:04 AM, Hahne, Florian <florian.hahne@novartis.com>wrote: > Hm, looks like the wrong parameter is being picked up for the title > panel border. It should be col.border.title but obviously it takes > col.title. I just fixed that, should become available with the 1.8.2 > version of the package in the next couple of days. > Florian > > From: Martin Rijlaarsdam <m.a.rijlaarsdam@gmail.com> > Date: Monday 12 May 2014 17:29 > To: Florian Hahne <florian.hahne@novartis.com> > Cc: "bioconductor@r-project.org" <bioconductor@r-project.org> > Subject: Re: [BioC] gviz data track (heatmap) and title panel questions > > ... and if I set col.title = "black" in specific track the same thing > happens (black box around title panel) but now only for that specific > track. > > Tnx! > Martin > > > -- > M.A. (Martin) Rijlaarsdam MSc. MD > Erasmus MC - University Medical Center Rotterdam > Department of Pathology > Room Be-432b > Shipping adress: P.O. Box 2040, 3000 CA Rotterdam, The Netherlands > Visiting adress: Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands > > Email: m.a.rijlaarsdam@gmail.com > Mobile: +31 6 45408508 > Telephone (work): +31 10 7033409 > Fax +31 10 7044365 > Website: http://www.martinrijlaarsdam.nl > > > On Mon, May 12, 2014 at 5:25 PM, Martin Rijlaarsdam < > m.a.rijlaarsdam@gmail.com> wrote: > >> Dear Florian, >> >> Can I ask one more dummy question. When I add " col.title="black" " to >> the plotTracks parameter list, a black box appears around all title panels. >> Setting col.border.title="white" and/or lwd.border.title=0 does not help. I >> would prefer not to show any lines around the title panels. >> >> Thanks in advance for your help. >> >> Yours sincerely, >> Martin Rijlaarsdam >> >> >> -- >> M.A. (Martin) Rijlaarsdam MSc. MD >> Erasmus MC - University Medical Center Rotterdam >> Department of Pathology >> Room Be-432b >> Shipping adress: P.O. Box 2040, 3000 CA Rotterdam, The Netherlands >> Visiting adress: Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands >> >> Email: m.a.rijlaarsdam@gmail.com >> Mobile: +31 6 45408508 >> Telephone (work): +31 10 7033409 >> Fax +31 10 7044365 >> Website: http://www.martinrijlaarsdam.nl >> >> >> On Mon, May 12, 2014 at 1:54 PM, Hahne, Florian < >> florian.hahne@novartis.com> wrote: >> >>> Hi Martin, >>> You can control the rotation of the title text using the rotate.title >>> parameter. Please note that this will not automatically adjust the width >>> of the title panel, so you may want to decrease the font size, >>> (cex.title) >>> or increase the title panel width (title.width), or maybe both. I will >>> have to re-work the while process of setting up the title panels for this >>> to work automatically. >>> With respect to the color bar: try the showColorBar and showSampleNames >>> parameters, they should do exactly what you ask for. >>> Florian >>> >>> >>> >>> On 01/05/14 11:33, "Martin Rijlaarsdam" <m.a.rijlaarsdam@gmail.com> >>> wrote: >>> >>> >Dear Sirs, >>> > >>> >Thank you very much for Gviz! >>> > >>> >I have been using it for a while now but I have two issues that I cannot >>> >seem to figure out. Both are pretty trivial settings, so my apologies >>> in >>> >advance. Please see the attached image as an example. >>> > >>> >1) I would like to rotate the text in the title panel for some of the >>> >tracks (HMM, ALL, DHP) so that the text is horizontal. >>> >2) I would like to remove the color bar and it's legend from the >>> heatmap. >>> >Ik can remove the color gradient, but the legend (20,40,60,80) remains >>> >visible. I want to remove it because the current presentation suggests a >>> >relation between the tumor types presented. >>> > >>> >Thanks in advance for any suggestions that you might have. >>> > >>> >Kind regards, >>> >Martin >>> > >>> >-- >>> >M.A. (Martin) Rijlaarsdam MSc. MD >>> >Erasmus MC - University Medical Center Rotterdam >>> >Department of Pathology >>> >Room Be-432b >>> >Shipping adress: P.O. Box 2040, 3000 CA Rotterdam, The Netherlands >>> >Visiting adress: Dr. Molewaterplein 50, 3015 GE Rotterdam, The >>> Netherlands >>> > >>> >Email: m.a.rijlaarsdam@gmail.com >>> >Mobile: +31 6 45408508 >>> >Telephone (work): +31 10 7033409 >>> >Fax +31 10 7044365 >>> >Website: http://www.martinrijlaarsdam.nl >>> >>> >> > [[alternative HTML version deleted]]
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1.8.2. is the release branch. Changes are committed now. Florian From: Martin Rijlaarsdam <m.a.rijlaarsdam@gmail.com<mailto:m.a.rijlaarsdam@gmail.com>> Date: Tuesday 13 May 2014 09:06 To: Florian Hahne <florian.hahne@novartis.com<mailto:florian.hahne@novartis.com>> Cc: "bioconductor@r-project.org<mailto:bioconductor@r-project.org>" <bioconductor@r-project.org<mailto:bioconductor@r-project.org>> Subject: Re: [BioC] gviz data track (heatmap) and title panel questions Dear Florian, Thank you. Will you also implement this (small) bugfix in the release branch? Best, Martin -- M.A. (Martin) Rijlaarsdam MSc. MD Erasmus MC - University Medical Center Rotterdam Department of Pathology Room Be-432b Shipping adress: P.O. Box 2040, 3000 CA Rotterdam, The Netherlands Visiting adress: Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands Email: m.a.rijlaarsdam@gmail.com<mailto:m.a.rijlaarsdam@gmail.com> Mobile: +31 6 45408508 Telephone (work): +31 10 7033409 Fax +31 10 7044365 Website: http://www.martinrijlaarsdam.nl On Tue, May 13, 2014 at 9:04 AM, Hahne, Florian <florian.hahne@novartis.com<mailto:florian.hahne@novartis.com>> wrote: Hm, looks like the wrong parameter is being picked up for the title panel border. It should be col.border.title but obviously it takes col.title. I just fixed that, should become available with the 1.8.2 version of the package in the next couple of days. Florian From: Martin Rijlaarsdam <m.a.rijlaarsdam@gmail.com<mailto:m.a.rijlaarsdam@gmail.com>> Date: Monday 12 May 2014 17:29 To: Florian Hahne <florian.hahne@novartis.com<mailto:florian.hahne@novartis.com>> Cc: "bioconductor@r-project.org<mailto:bioconductor@r-project.org>" <bioconductor@r-project.org<mailto:bioconductor@r-project.org>> Subject: Re: [BioC] gviz data track (heatmap) and title panel questions ... and if I set col.title = "black" in specific track the same thing happens (black box around title panel) but now only for that specific track. Tnx! Martin -- M.A. (Martin) Rijlaarsdam MSc. MD Erasmus MC - University Medical Center Rotterdam Department of Pathology Room Be-432b Shipping adress: P.O. Box 2040, 3000 CA Rotterdam, The Netherlands Visiting adress: Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands Email: m.a.rijlaarsdam@gmail.com<mailto:m.a.rijlaarsdam@gmail.com> Mobile: +31 6 45408508<tel:%2b31%206%2045408508> Telephone (work): +31 10 7033409<tel:%2b31%2010%207033409> Fax +31 10 7044365<tel:%2b31%2010%207044365> Website: http://www.martinrijlaarsdam.nl On Mon, May 12, 2014 at 5:25 PM, Martin Rijlaarsdam <m.a.rijlaarsdam@gmail.com<mailto:m.a.rijlaarsdam@gmail.com>> wrote: Dear Florian, Can I ask one more dummy question. When I add " col.title="black" " to the plotTracks parameter list, a black box appears around all title panels. Setting col.border.title="white" and/or lwd.border.title=0 does not help. I would prefer not to show any lines around the title panels. Thanks in advance for your help. Yours sincerely, Martin Rijlaarsdam -- M.A. (Martin) Rijlaarsdam MSc. MD Erasmus MC - University Medical Center Rotterdam Department of Pathology Room Be-432b Shipping adress: P.O. Box 2040, 3000 CA Rotterdam, The Netherlands Visiting adress: Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands Email: m.a.rijlaarsdam@gmail.com<mailto:m.a.rijlaarsdam@gmail.com> Mobile: +31 6 45408508<tel:%2b31%206%2045408508> Telephone (work): +31 10 7033409<tel:%2b31%2010%207033409> Fax +31 10 7044365<tel:%2b31%2010%207044365> Website: http://www.martinrijlaarsdam.nl On Mon, May 12, 2014 at 1:54 PM, Hahne, Florian <florian.hahne@novartis.com<mailto:florian.hahne@novartis.com>> wrote: Hi Martin, You can control the rotation of the title text using the rotate.title parameter. Please note that this will not automatically adjust the width of the title panel, so you may want to decrease the font size, (cex.title) or increase the title panel width (title.width), or maybe both. I will have to re-work the while process of setting up the title panels for this to work automatically. With respect to the color bar: try the showColorBar and showSampleNames parameters, they should do exactly what you ask for. Florian On 01/05/14 11:33, "Martin Rijlaarsdam" <m.a.rijlaarsdam@gmail.com<mailto:m.a.rijlaarsdam@gmail.com>> wrote: >Dear Sirs, > >Thank you very much for Gviz! > >I have been using it for a while now but I have two issues that I cannot >seem to figure out. Both are pretty trivial settings, so my apologies in >advance. Please see the attached image as an example. > >1) I would like to rotate the text in the title panel for some of the >tracks (HMM, ALL, DHP) so that the text is horizontal. >2) I would like to remove the color bar and it's legend from the heatmap. >Ik can remove the color gradient, but the legend (20,40,60,80) remains >visible. I want to remove it because the current presentation suggests a >relation between the tumor types presented. > >Thanks in advance for any suggestions that you might have. > >Kind regards, >Martin > >-- >M.A. (Martin) Rijlaarsdam MSc. MD >Erasmus MC - University Medical Center Rotterdam >Department of Pathology >Room Be-432b >Shipping adress: P.O. Box 2040, 3000 CA Rotterdam, The Netherlands >Visiting adress: Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands > >Email: m.a.rijlaarsdam@gmail.com<mailto:m.a.rijlaarsdam@gmail.com> >Mobile: +31 6 45408508<tel:%2b31%206%2045408508> >Telephone (work): +31 10 7033409<tel:%2b31%2010%207033409> >Fax +31 10 7044365<tel:%2b31%2010%207044365> >Website: http://www.martinrijlaarsdam.nl [[alternative HTML version deleted]]
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