Suggestion for a small change to ChIPpeakAnno
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Julie Zhu ★ 4.3k
@julie-zhu-3596
Last seen 3 months ago
United States
Brad, Thanks for the suggestion ! We will look into it. Best regards, Julie > On Jul 2, 2014, at 5:55 PM, Brad Davis <bdavis@bcgsc.ca> wrote: > > Hello Dr. Zhu, > > I am working with your ChIPpeakAnno package for R and I find it very convenient, but I have a small suggestion to enhance it¡¯s functionality, at least from the perspective of automating data processing. At the moment your package creates the venn diagrams with a defined output filename ¡°Rplots.pdf¡±, but it would be very helpful if the user could specify that file name in the command and overwrite the default filename. I tried to do this by specifying filename= in the makeVennDiagram function, but it returns an error ¡°Error in venn.diagram(x = vennx, filename = NULL, cat.cex = 1, cat.col = "black", : > formal argument "filename" matched by multiple actual arguments¡±. > > Thanks, > Brad [[alternative HTML version deleted]]
ChIPpeakAnno ChIPpeakAnno • 685 views
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Ou, Jianhong ★ 1.2k
@ou-jianhong-4539
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Hi Brad, May I know what version of ChIPpeakAnno you are using? If you are using the released version 2.12.1, you can easily change the output filename by giving a filename for output, for example: Library(ChIPpeakAnno) peaks1 = RangedData(IRanges(start = c(967654, 2010897, 2496704), end = c(967754, 2010997, 2496804), names = c("Site1", "Site2", "Site3")), space = c("1", "2", "3"), strand=as.integer(1),feature=c("a","b","f")) peaks2 = RangedData(IRanges(start = c(967659, 2010898,2496700,3075866,3123260), end = c(967869, 2011108, 2496920, 3076166, 3123470), names = c("t1", "t2", "t3", "t4", "t5")), space = c("1", "2", "3", "1", "2"), strand = c(1, 1, -1,-1,1), feature=c("a","b","c","d","a")) pdf("path/to/AnyFileNameYouWant.pdf") makeVennDiagram(RangedDataList(peaks1,peaks2), NameOfPeaks=c("TF1", "TF2"), totalTest=100,scaled=F, euler.d=F) dev.off() And because we already defined the the filename arguments to NULL when calls venn.diagram, you can not define the filename by directly input the filename to makeVennDiagram. Why we do this is because it can output other formats of figure other than tiff. I am sorry this is not clear in the documentation file. We will improve the documentation later. Thank you. Yours Sincerely, Jianhong Ou LRB 670A Program in Gene Function and Expression 364 Plantation Street Worcester, MA 01605 From: <zhu>, "Lihua (Julie)" <julie.zhu@umassmed.edu<mailto:julie.zhu@umassmed.edu>> Date: Wednesday, July 2, 2014 8:10 PM To: Brad Davis <bdavis@bcgsc.ca<mailto:bdavis@bcgsc.ca>> Cc: Jianhong Ou <jianhong.ou@umassmed.edu<mailto:jianhong.ou@umassmed.edu>>, "<biocond uctor@stat.math.ethz.ch<mailto:bioconductor@stat.math.ethz.ch="">>" <bioc onductor@stat.math.ethz.ch<mailto:bioconductor@stat.math.ethz.ch="">> Subject: Re: Suggestion for a small change to ChIPpeakAnno Brad, Thanks for the suggestion ! We will look into it. Best regards, Julie On Jul 2, 2014, at 5:55 PM, Brad Davis <bdavis@bcgsc.ca<mailto:bdavis@bcgsc.ca>> wrote: Hello Dr. Zhu, I am working with your ChIPpeakAnno package for R and I find it very convenient, but I have a small suggestion to enhance it’s functionality, at least from the perspective of automating data processing. At the moment your package creates the venn diagrams with a defined output filename “Rplots.pdf”, but it would be very helpful if the user could specify that file name in the command and overwrite the default filename. I tried to do this by specifying filename= in the makeVennDiagram function, but it returns an error “Error in venn.diagram(x = vennx, filename = NULL, cat.cex = 1, cat.col = "black", : formal argument "filename" matched by multiple actual arguments”. Thanks, Brad [[alternative HTML version deleted]]
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Julie Zhu ★ 4.3k
@julie-zhu-3596
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Brad, Thanks for the great suggestion! We could add two parameters: DrawPercentage (TRUE/FALSE, default FALSE) and overalapInBaseOrPeak (“peak”, “base”), default peak. If I understand you correctly, overlapBaseOrPeak selection only affects the venn diagram and p-value calculation. Correct? Do you have a small dataset and expected output for us to test the new feature? Thanks! Best regards, Julie On 7/8/14 1:14 PM, "Brad Davis" <bdavis@bcgsc.ca> wrote: Hello Jianhong and Julie, Absolutely, that’s great. I had two more suggestions for options for makeVennDiagram that would make it even more useful to me. The first would be to report the percentage (instead of the numbers) inside the venn diagrams? And second, it would be useful if instead of just reporting the total number of overlapping regions, if an option was available to report the total amount of overlap (in terms of the number of base pairs) instead of just the number of overlaps. That seems like it might be particularly relevant for some of the broad marks which can be called by some peak calling tools as a long series of short marks as opposed to a single long contiguous region? Thanks, Brad On 2014-07-08, 10:09 AM, "Zhu, Lihua (Julie)" <julie.zhu@umassmed.edu> wrote: Brad, Does the following code snippet meet your needs? Thanks! Best regards, Julie On 7/7/14 10:59 AM, "Umms" <jianhong.ou@umassmed.edu> wrote: Hi Brad, May I know what version of ChIPpeakAnno you are using? If you are using the released version 2.12.1, you can easily change the output filename by giving a filename for output, for example: Library(ChIPpeakAnno) peaks1 = RangedData(IRanges(start = c(967654, 2010897, 2496704), end = c(967754, 2010997, 2496804), names = c("Site1", "Site2", "Site3")), space = c("1", "2", "3"), strand=as.integer(1),feature=c("a","b","f")) peaks2 = RangedData(IRanges(start = c(967659, 2010898,2496700,3075866,3123260), end = c(967869, 2011108, 2496920, 3076166, 3123470), names = c("t1", "t2", "t3", "t4", "t5")), space = c("1", "2", "3", "1", "2"), strand = c(1, 1, -1,-1,1), feature=c("a","b","c","d","a")) pdf("path/to/AnyFileNameYouWant.pdf") makeVennDiagram(RangedDataList(peaks1,peaks2), NameOfPeaks=c("TF1", "TF2"), totalTest=100,scaled=F, euler.d=F) dev.off() And because we already defined the the filename arguments to NULL when calls venn.diagram, you can not define the filename by directly input the filename to makeVennDiagram. Why we do this is because it can output other formats of figure other than tiff. I am sorry this is not clear in the documentation file. We will improve the documentation later. Thank you. Yours Sincerely, Jianhong Ou LRB 670A Program in Gene Function and Expression 364 Plantation Street Worcester, MA 01605 From: <zhu>, "Lihua (Julie)" <julie.zhu@umassmed.edu> Date: Wednesday, July 2, 2014 8:10 PM To: Brad Davis <bdavis@bcgsc.ca> Cc: Jianhong Ou <jianhong.ou@umassmed.edu>, "<bioconductor@stat.math.ethz.ch>" <bioconductor@stat.math.ethz.ch> Subject: Re: Suggestion for a small change to ChIPpeakAnno Brad, Thanks for the suggestion ! We will look into it. Best regards, Julie On Jul 2, 2014, at 5:55 PM, Brad Davis <bdavis@bcgsc.ca> wrote: Suggestion for a small change to ChIPpeakAnno Hello Dr. Zhu, I am working with your ChIPpeakAnno package for R and I find it very convenient, but I have a small suggestion to enhance it’s functionality, at least from the perspective of automating data processing. At the moment your package creates the venn diagrams with a defined output filename “Rplots.pdf”, but it would be very helpful if the user could specify that file name in the command and overwrite the default filename. I tried to do this by specifying filename= in the makeVennDiagram function, but it returns an error “Error in venn.diagram(x = vennx, filename = NULL, cat.cex = 1, cat.col = "black", : formal argument "filename" matched by multiple actual arguments”. Thanks, Brad [[alternative HTML version deleted]]
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Brad, Thinking it over, I think it would be impossible to draw percentage for the overlap part since it will be different for different input peak sets unless all input peak lists have exactly the same number of peaks or bases. Please let us know if I misunderstood you. Thanks! Best regards, Julie On 7/8/14 1:33 PM, "Lihua Julie Zhu" <julie.zhu@umassmed.edu> wrote: Brad, Thanks for the great suggestion! We could add two parameters: DrawPercentage (TRUE/FALSE, default FALSE) and overalapInBaseOrPeak (“peak”, “base”), default peak. If I understand you correctly, overlapBaseOrPeak selection only affects the venn diagram and p-value calculation. Correct? Do you have a small dataset and expected output for us to test the new feature? Thanks! Best regards, Julie On 7/8/14 1:14 PM, "Brad Davis" <bdavis@bcgsc.ca> wrote: Hello Jianhong and Julie, Absolutely, that’s great. I had two more suggestions for options for makeVennDiagram that would make it even more useful to me. The first would be to report the percentage (instead of the numbers) inside the venn diagrams? And second, it would be useful if instead of just reporting the total number of overlapping regions, if an option was available to report the total amount of overlap (in terms of the number of base pairs) instead of just the number of overlaps. That seems like it might be particularly relevant for some of the broad marks which can be called by some peak calling tools as a long series of short marks as opposed to a single long contiguous region? Thanks, Brad On 2014-07-08, 10:09 AM, "Zhu, Lihua (Julie)" <julie.zhu@umassmed.edu> wrote: Brad, Does the following code snippet meet your needs? Thanks! Best regards, Julie On 7/7/14 10:59 AM, "Umms" <jianhong.ou@umassmed.edu> wrote: Hi Brad, May I know what version of ChIPpeakAnno you are using? If you are using the released version 2.12.1, you can easily change the output filename by giving a filename for output, for example: Library(ChIPpeakAnno) peaks1 = RangedData(IRanges(start = c(967654, 2010897, 2496704), end = c(967754, 2010997, 2496804), names = c("Site1", "Site2", "Site3")), space = c("1", "2", "3"), strand=as.integer(1),feature=c("a","b","f")) peaks2 = RangedData(IRanges(start = c(967659, 2010898,2496700,3075866,3123260), end = c(967869, 2011108, 2496920, 3076166, 3123470), names = c("t1", "t2", "t3", "t4", "t5")), space = c("1", "2", "3", "1", "2"), strand = c(1, 1, -1,-1,1), feature=c("a","b","c","d","a")) pdf("path/to/AnyFileNameYouWant.pdf") makeVennDiagram(RangedDataList(peaks1,peaks2), NameOfPeaks=c("TF1", "TF2"), totalTest=100,scaled=F, euler.d=F) dev.off() And because we already defined the the filename arguments to NULL when calls venn.diagram, you can not define the filename by directly input the filename to makeVennDiagram. Why we do this is because it can output other formats of figure other than tiff. I am sorry this is not clear in the documentation file. We will improve the documentation later. Thank you. Yours Sincerely, Jianhong Ou LRB 670A Program in Gene Function and Expression 364 Plantation Street Worcester, MA 01605 From: <zhu>, "Lihua (Julie)" <julie.zhu@umassmed.edu> Date: Wednesday, July 2, 2014 8:10 PM To: Brad Davis <bdavis@bcgsc.ca> Cc: Jianhong Ou <jianhong.ou@umassmed.edu>, "<bioconductor@stat.math.ethz.ch>" <bioconductor@stat.math.ethz.ch> Subject: Re: Suggestion for a small change to ChIPpeakAnno Brad, Thanks for the suggestion ! We will look into it. Best regards, Julie On Jul 2, 2014, at 5:55 PM, Brad Davis <bdavis@bcgsc.ca> wrote: Suggestion for a small change to ChIPpeakAnno Hello Dr. Zhu, I am working with your ChIPpeakAnno package for R and I find it very convenient, but I have a small suggestion to enhance it’s functionality, at least from the perspective of automating data processing. At the moment your package creates the venn diagrams with a defined output filename “Rplots.pdf”, but it would be very helpful if the user could specify that file name in the command and overwrite the default filename. I tried to do this by specifying filename= in the makeVennDiagram function, but it returns an error “Error in venn.diagram(x = vennx, filename = NULL, cat.cex = 1, cat.col = "black", : formal argument "filename" matched by multiple actual arguments”. Thanks, Brad [[alternative HTML version deleted]]
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Julie Zhu ★ 4.3k
@julie-zhu-3596
Last seen 3 months ago
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Brad, Thanks for the clarification! Do you mean |30-100|/100 in your example? BTW, do you have a small dataset and expected output for us to test the new feature? Thanks! FYI, Jianhong has a lot in his plate now. So it might take some time to get this implemented. Best regards, Julie On 7/8/14 1:47 PM, "Brad Davis" <bdavis@bcgsc.ca> wrote: Hi Julie, The way I would calculate the percentage is for each intersection I would divide the number of elements identified in that intersection by the total number of elements contained in each of the included sets. So if set 1 had 100 elements, and set 2 had 50 elements, and the intersection has 30 elements, then the percentage of the intersection would be 30/(100+50), while the percentage for set 1 would be |50-100|/100 and set 2 would be |50-30|/50, that way the percentages would represent the fraction of the elements contained in that set that potentially could be found in that set that are found in that set. Alternately one could calculate the percentages as the number of elements found in that set divided by the total number of (unique) elements found in all sets, in which case the percentage represents the fraction of elements that are unique to that particular set. Both would be useful, actually, but just for illustrating different things. Brad On 2014-07-08, 10:40 AM, "Zhu, Lihua (Julie)" <julie.zhu@umassmed.edu> wrote: Brad, Thinking it over, I think it would be impossible to draw percentage for the overlap part since it will be different for different input peak sets unless all input peak lists have exactly the same number of peaks or bases. Please let us know if I misunderstood you. Thanks! Best regards, Julie On 7/8/14 1:33 PM, "Lihua Julie Zhu" <julie.zhu@umassmed.edu> wrote: Brad, Thanks for the great suggestion! We could add two parameters: DrawPercentage (TRUE/FALSE, default FALSE) and overalapInBaseOrPeak (“peak”, “base”), default peak. If I understand you correctly, overlapBaseOrPeak selection only affects the venn diagram and p-value calculation. Correct? Do you have a small dataset and expected output for us to test the new feature? Thanks! Best regards, Julie On 7/8/14 1:14 PM, "Brad Davis" <bdavis@bcgsc.ca> wrote: Hello Jianhong and Julie, Absolutely, that’s great. I had two more suggestions for options for makeVennDiagram that would make it even more useful to me. The first would be to report the percentage (instead of the numbers) inside the venn diagrams? And second, it would be useful if instead of just reporting the total number of overlapping regions, if an option was available to report the total amount of overlap (in terms of the number of base pairs) instead of just the number of overlaps. That seems like it might be particularly relevant for some of the broad marks which can be called by some peak calling tools as a long series of short marks as opposed to a single long contiguous region? Thanks, Brad On 2014-07-08, 10:09 AM, "Zhu, Lihua (Julie)" <julie.zhu@umassmed.edu> wrote: Brad, Does the following code snippet meet your needs? Thanks! Best regards, Julie On 7/7/14 10:59 AM, "Umms" <jianhong.ou@umassmed.edu> wrote: Hi Brad, May I know what version of ChIPpeakAnno you are using? If you are using the released version 2.12.1, you can easily change the output filename by giving a filename for output, for example: Library(ChIPpeakAnno) peaks1 = RangedData(IRanges(start = c(967654, 2010897, 2496704), end = c(967754, 2010997, 2496804), names = c("Site1", "Site2", "Site3")), space = c("1", "2", "3"), strand=as.integer(1),feature=c("a","b","f")) peaks2 = RangedData(IRanges(start = c(967659, 2010898,2496700,3075866,3123260), end = c(967869, 2011108, 2496920, 3076166, 3123470), names = c("t1", "t2", "t3", "t4", "t5")), space = c("1", "2", "3", "1", "2"), strand = c(1, 1, -1,-1,1), feature=c("a","b","c","d","a")) pdf("path/to/AnyFileNameYouWant.pdf") makeVennDiagram(RangedDataList(peaks1,peaks2), NameOfPeaks=c("TF1", "TF2"), totalTest=100,scaled=F, euler.d=F) dev.off() And because we already defined the the filename arguments to NULL when calls venn.diagram, you can not define the filename by directly input the filename to makeVennDiagram. Why we do this is because it can output other formats of figure other than tiff. I am sorry this is not clear in the documentation file. We will improve the documentation later. Thank you. Yours Sincerely, Jianhong Ou LRB 670A Program in Gene Function and Expression 364 Plantation Street Worcester, MA 01605 From: <zhu>, "Lihua (Julie)" <julie.zhu@umassmed.edu> Date: Wednesday, July 2, 2014 8:10 PM To: Brad Davis <bdavis@bcgsc.ca> Cc: Jianhong Ou <jianhong.ou@umassmed.edu>, "<bioconductor@stat.math.ethz.ch>" <bioconductor@stat.math.ethz.ch> Subject: Re: Suggestion for a small change to ChIPpeakAnno Brad, Thanks for the suggestion ! We will look into it. Best regards, Julie On Jul 2, 2014, at 5:55 PM, Brad Davis <bdavis@bcgsc.ca> wrote: Suggestion for a small change to ChIPpeakAnno Hello Dr. Zhu, I am working with your ChIPpeakAnno package for R and I find it very convenient, but I have a small suggestion to enhance it’s functionality, at least from the perspective of automating data processing. At the moment your package creates the venn diagrams with a defined output filename “Rplots.pdf”, but it would be very helpful if the user could specify that file name in the command and overwrite the default filename. I tried to do this by specifying filename= in the makeVennDiagram function, but it returns an error “Error in venn.diagram(x = vennx, filename = NULL, cat.cex = 1, cat.col = "black", : formal argument "filename" matched by multiple actual arguments”. Thanks, Brad [[alternative HTML version deleted]]
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