flowCore - cloud() and lapply
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@steve-lauriault-3237
Last seen 7.9 years ago
I noticed the cloud function, and have tried to apply my flowFrame, but to no avail. Any hints on the annotation? The FCS file can be named MyData[1] or ?/Data/FMO.fcs?, and I would like to include FSC-H, SSC-H, and FL1-H into cloud(). FSC-H and SSC-H would be in linear, and FL1-H in log (10^0 to 10^4) scale. I think it would be cool to add a fourth colour-based dimension to a cloud plot. Let's say FL2-H is on scale[0,1]. Any relative fluorescence intensity of 0 would correspond to a yellow event, and a relative fluorescence intensity of 1 would correspond to red. 0.5 would be orange. Any value ascending from zero would become more-red and less-yellow. The light wavelength (colour) of the ?dot? wold be directly related to the fluorescence intensity of the corresponding event. The user would have the option to have the fourth dimension enabled or disabled (in the case of colours representing offspring gates, this function would complicate things). It would also be cool to ?cycle-through? FCS file visualizations within a 4-D cloud-based GUI. Is there a function or package like this currently available in R? These are just some thoughts. I hope you guys don't mind. Now back to figuring out how to use lapply to create a new flowSet out of separate directories located in "/Data" (HowTo-flowCore 2.2.1). Thanks, Stevan ? ? ?
GUI GUI • 919 views
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@nishant-gopalakrishnan-3253
Last seen 7.9 years ago
Hi Steve The cloud function from lattice takes a data frame as the argument and will not directly work with a flowFrame . You can use the exprs function to obtain a matrix from the flowFrame. Perhaps this example might help file.name <- system.file("extdata", "0877408774.B08", package = "flowCore") x <- read.FCSfile.name, transformation = FALSE) data<-data.frame(exprs(x), check.names=F) cloud(FSC-H~ SSC-H * FL1-H,data) Nishant Steve Lauriault wrote: > I noticed the cloud function, and have tried to apply my flowFrame, but to > no avail. Any hints on the annotation? The FCS file can be named MyData[1] > or ?/Data/FMO.fcs?, and I would like to include FSC-H, SSC-H, and FL1-H into > cloud(). FSC-H and SSC-H would be in linear, and FL1-H in log (10^0 to > 10^4) scale. > > I think it would be cool to add a fourth colour-based dimension to a cloud > plot. Let's say FL2-H is on scale[0,1]. Any relative fluorescence > intensity of 0 would correspond to a yellow event, and a relative > fluorescence intensity of 1 would correspond to red. 0.5 would be orange. > Any value ascending from zero would become more-red and less-yellow. The > light wavelength (colour) of the ?dot? wold be directly related to the > fluorescence intensity of the corresponding event. The user would have the > option to have the fourth dimension enabled or disabled (in the case of > colours representing offspring gates, this function would complicate > things). > > It would also be cool to ?cycle-through? FCS file visualizations within a > 4-D cloud-based GUI. Is there a function or package like this currently > available in R? > > These are just some thoughts. I hope you guys don't mind. Now back to > figuring out how to use lapply to create a new flowSet out of separate > directories located in "/Data" (HowTo-flowCore 2.2.1). > > Thanks, > > Stevan > > > > > > > > > -------------------------------------------------------------------- ---- > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Thank you Nishant, Not to be nit-picky, but is there a function that would allow one to rotate and/or zoom-in on the cube? If not, there is a plot developed in MatLab by Laszlo Balkay (sp?) that allows one to do this (rotate, zoom-in, etc) with 3-D FCS dataframes. Not sure how congruent the two languages are, or if this is any help at all, but I thought I'd relay the info. I thought it was a cool function, but it would be cooler if one could add colour to represent fluorescence intensity, offspring or subset populations in the 4th dimension. Regards, Steve --- Stevan Lauriault Founder, President and C.E.O. Lauritech Inc. steve at lauritech.com www.lauritech.com t/f: (416)283-4066 -----Original Message----- From: Nishant Gopalakrishnan [mailto:ngopalak@fhcrc.org] Sent: Wednesday, January 28, 2009 8:47 PM To: stevan at lauriault.com Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] flowCore - cloud() and lapply Hi Steve The cloud function from lattice takes a data frame as the argument and will not directly work with a flowFrame . You can use the exprs function to obtain a matrix from the flowFrame. Perhaps this example might help file.name <- system.file("extdata", "0877408774.B08", package = "flowCore") x <- read.FCSfile.name, transformation = FALSE) data<-data.frame(exprs(x), check.names=F) cloud(FSC-H~ SSC-H * FL1-H,data) Nishant Steve Lauriault wrote: > I noticed the cloud function, and have tried to apply my flowFrame, but to > no avail. Any hints on the annotation? The FCS file can be named MyData[1] > or "/Data/FMO.fcs", and I would like to include FSC-H, SSC-H, and FL1-H into > cloud(). FSC-H and SSC-H would be in linear, and FL1-H in log (10^0 to > 10^4) scale. > > I think it would be cool to add a fourth colour-based dimension to a cloud > plot. Let's say FL2-H is on scale[0,1]. Any relative fluorescence > intensity of 0 would correspond to a yellow event, and a relative > fluorescence intensity of 1 would correspond to red. 0.5 would be orange. > Any value ascending from zero would become more-red and less-yellow. The > light wavelength (colour) of the "dot" wold be directly related to the > fluorescence intensity of the corresponding event. The user would have the > option to have the fourth dimension enabled or disabled (in the case of > colours representing offspring gates, this function would complicate > things). > > It would also be cool to "cycle-through" FCS file visualizations within a > 4-D cloud-based GUI. Is there a function or package like this currently > available in R? > > These are just some thoughts. I hope you guys don't mind. Now back to > figuring out how to use lapply to create a new flowSet out of separate > directories located in "/Data" (HowTo-flowCore 2.2.1). > > Thanks, > > Stevan > > > > > > > > > -------------------------------------------------------------------- ---- > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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On 1/29/09, Steve Lauriault <stevan at="" lauriault.com=""> wrote: > Thank you Nishant, > > Not to be nit-picky, but is there a function that would allow one to rotate > and/or zoom-in on the cube? If not, there is a plot developed in MatLab by > Laszlo Balkay (sp?) that allows one to do this (rotate, zoom-in, etc) with > 3-D FCS dataframes. Not sure how congruent the two languages are, or if > this is any help at all, but I thought I'd relay the info. I thought it was > a cool function, but it would be cooler if one could add colour to represent > fluorescence intensity, offspring or subset populations in the 4th > dimension. The rgl package should be able to do all this fairly easily. There is no convenience API predefined to allow this with flowFrames, but as Nishant said, there is only one extra step needed: 1. extract the expressions from a flowFrame as a data frame or matrix 2. use the standard rgl API There are many examples accompanying rgl that should get you started. -Deepayan
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> rgl.init() Error in rgl.init() : Assertion failure: gpWin32GUIFactory == NULL File: win32lib.cpp Line: 39 Please report to rgl maintainer. Not sure who the rgl maintainer is, but this is me reporting. Steve -----Original Message----- From: Deepayan Sarkar [mailto:deepayan.sarkar@gmail.com] Sent: Thursday, January 29, 2009 12:32 PM To: stevan at lauriault.com Cc: Nishant Gopalakrishnan; bioconductor at stat.math.ethz.ch Subject: Re: [BioC] flowCore - cloud() On 1/29/09, Steve Lauriault <stevan at="" lauriault.com=""> wrote: > Thank you Nishant, > > Not to be nit-picky, but is there a function that would allow one to rotate > and/or zoom-in on the cube? If not, there is a plot developed in MatLab by > Laszlo Balkay (sp?) that allows one to do this (rotate, zoom-in, etc) with > 3-D FCS dataframes. Not sure how congruent the two languages are, or if > this is any help at all, but I thought I'd relay the info. I thought it was > a cool function, but it would be cooler if one could add colour to represent > fluorescence intensity, offspring or subset populations in the 4th > dimension. The rgl package should be able to do all this fairly easily. There is no convenience API predefined to allow this with flowFrames, but as Nishant said, there is only one extra step needed: 1. extract the expressions from a flowFrame as a data frame or matrix 2. use the standard rgl API There are many examples accompanying rgl that should get you started. -Deepayan
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You do a R> packageDescription("rgl") to find a relevant email. The maintainer should always be cc'ed when you report bugs. When you report bugs always include sessionInfo() and additional helpful information (in this case I am sure they want to know the version of Windows). In this case rgl is a CRAN package, not a Bioconductor one, so you might get more help by reporting this on the r-help email list. Finally, always search the archives for posts on similar problems. Kasper On Jan 29, 2009, at 11:47 , Steve Lauriault wrote: >> rgl.init() > > Error in rgl.init() : Assertion failure: gpWin32GUIFactory == NULL > File: win32lib.cpp > Line: 39 > Please report to rgl maintainer. > > Not sure who the rgl maintainer is, but this is me reporting. > > Steve > > > > > > -----Original Message----- > From: Deepayan Sarkar [mailto:deepayan.sarkar at gmail.com] > Sent: Thursday, January 29, 2009 12:32 PM > To: stevan at lauriault.com > Cc: Nishant Gopalakrishnan; bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] flowCore - cloud() > > On 1/29/09, Steve Lauriault <stevan at="" lauriault.com=""> wrote: >> Thank you Nishant, >> >> Not to be nit-picky, but is there a function that would allow one to > rotate >> and/or zoom-in on the cube? If not, there is a plot developed in >> MatLab > by >> Laszlo Balkay (sp?) that allows one to do this (rotate, zoom-in, etc) > with >> 3-D FCS dataframes. Not sure how congruent the two languages are, >> or if >> this is any help at all, but I thought I'd relay the info. I >> thought it > was >> a cool function, but it would be cooler if one could add colour to > represent >> fluorescence intensity, offspring or subset populations in the 4th >> dimension. > > The rgl package should be able to do all this fairly easily. There is > no convenience API predefined to allow this with flowFrames, but as > Nishant said, there is only one extra step needed: > > 1. extract the expressions from a flowFrame as a data frame or matrix > > 2. use the standard rgl API > > There are many examples accompanying rgl that should get you started. > > -Deepayan > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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On Thu, Jan 29, 2009 at 2:47 PM, Steve Lauriault <stevan@lauriault.com>wrote: > > rgl.init() > > Error in rgl.init() : Assertion failure: gpWin32GUIFactory == NULL > File: win32lib.cpp > Line: 39 > Please report to rgl maintainer. > > Not sure who the rgl maintainer is, but this is me reporting. > Hi, Steve. Unfortunately, rgl is not a bioconductor package, so reporting here is not likely to help much. If you utilize the R help system and do: help(package=rgl) the maintainer's email is listed. My guess is that that person will need at least the output of sessionInfo() to begin to diagnose the problem. Sean > > -----Original Message----- > From: Deepayan Sarkar [mailto:deepayan.sarkar@gmail.com] > Sent: Thursday, January 29, 2009 12:32 PM > To: stevan@lauriault.com > Cc: Nishant Gopalakrishnan; bioconductor@stat.math.ethz.ch > Subject: Re: [BioC] flowCore - cloud() > > On 1/29/09, Steve Lauriault <stevan@lauriault.com> wrote: > > Thank you Nishant, > > > > Not to be nit-picky, but is there a function that would allow one to > rotate > > and/or zoom-in on the cube? If not, there is a plot developed in MatLab > by > > Laszlo Balkay (sp?) that allows one to do this (rotate, zoom-in, etc) > with > > 3-D FCS dataframes. Not sure how congruent the two languages are, or if > > this is any help at all, but I thought I'd relay the info. I thought it > was > > a cool function, but it would be cooler if one could add colour to > represent > > fluorescence intensity, offspring or subset populations in the 4th > > dimension. > > The rgl package should be able to do all this fairly easily. There is > no convenience API predefined to allow this with flowFrames, but as > Nishant said, there is only one extra step needed: > > 1. extract the expressions from a flowFrame as a data frame or matrix > > 2. use the standard rgl API > > There are many examples accompanying rgl that should get you started. > > -Deepayan > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]