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Mathelab / ALTRE

ALTered Regulatory Elements
http://mathelab.github.io/ALTRE/
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plotting function errors #47

Closed rfarouni closed 8 years ago

rfarouni commented 8 years ago

There are argument is of length zero errors at these lines: plottingfunctions.R #177 plottingfunctions.R #397 plottingfunctions.R#536

Warning: Error in if: argument is of length zero
Stack trace (innermost first):
    81: plotCombineAnnotatePeaks [/home/rick/Documents/repos/ALTRE/R/plottingfunctions.R#177]
    80: renderUI [/home/rick/R/x86_64-pc-linux-gnu-library/3.3/ALTRE/shinyApp/server.R#302]
    79: func
    78: origRenderFunc
    77: output$annotatebarplot
     2: shiny::runApp
     1: runShinyApp [/home/rick/Documents/repos/ALTRE/R/runshiny.R#10]
Found more than one class "connection" in cache; using the first, from namespace 'BiocGenerics'
Found more than one class "connection" in cache; using the first, from namespace 'BiocGenerics'
Found more than one class "connection" in cache; using the first, from namespace 'BiocGenerics'
Found more than one class "connection" in cache; using the first, from namespace 'BiocGenerics'
Warning: Error in if: argument is of length zero
Stack trace (innermost first):
    80: plotGetCounts [/home/rick/Documents/repos/ALTRE/R/plottingfunctions.R#397]
    79: func [/home/rick/R/x86_64-pc-linux-gnu-library/3.3/ALTRE/shinyApp/server.R#312]
    78: origRenderFunc
    77: output$densityplot
     2: shiny::runApp
     1: runShinyApp [/home/rick/Documents/repos/ALTRE/R/runshiny.R#10]

Warning: Error in if: argument is of length zero
Stack trace (innermost first):
    81: plotCountAnalysis [/home/rick/Documents/repos/ALTRE/R/plottingfunctions.R#536]
Mathelab commented 8 years ago

Why is this error only a problem with Shiny? What is palette set to in the Shiny Call? Ewy

From: Rick Farouni notifications@github.com<mailto:notifications@github.com> Reply-To: Mathelab/ALTRE reply@reply.github.com<mailto:reply@reply.github.com> Date: Wednesday, October 19, 2016 at 10:57 AM To: Mathelab/ALTRE ALTRE@noreply.github.com<mailto:ALTRE@noreply.github.com> Subject: [Mathelab/ALTRE] plotting function errors (#47)

There are errors at these lines: plottingfunctions.R #177 plottingfunctions.R #397

Warning: Error in if: argument is of length zero Stack trace (innermost first): 81: plotCombineAnnotatePeaks [/home/rick/Documents/repos/ALTRE/R/plottingfunctions.R#177] 80: renderUI [/home/rick/R/x86_64-pc-linux-gnu-library/3.3/ALTRE/shinyApp/server.R#302] 79: func 78: origRenderFunc 77: output$annotatebarplot 2: shiny::runApp 1: runShinyApp [/home/rick/Documents/repos/ALTRE/R/runshiny.R#10] Found more than one class "connection" in cache; using the first, from namespace 'BiocGenerics' Found more than one class "connection" in cache; using the first, from namespace 'BiocGenerics' Found more than one class "connection" in cache; using the first, from namespace 'BiocGenerics' Found more than one class "connection" in cache; using the first, from namespace 'BiocGenerics' Warning: Error in if: argument is of length zero Stack trace (innermost first): 80: plotGetCounts [/home/rick/Documents/repos/ALTRE/R/plottingfunctions.R#397] 79: func [/home/rick/R/x86_64-pc-linux-gnu-library/3.3/ALTRE/shinyApp/server.R#312] 78: origRenderFunc 77: output$densityplot 2: shiny::runApp 1: runShinyApp [/home/rick/Documents/repos/ALTRE/R/runshiny.R#10]

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osubmi784323 commented 8 years ago

I see what the problem is, I’ll fix. I’m not sure why it doesn’t show the error on the command line.

Liz

From: Mathelab notifications@github.com<mailto:notifications@github.com> Reply-To: Mathelab/ALTRE reply@reply.github.com<mailto:reply@reply.github.com> Date: Wed, 19 Oct 2016 11:14:00 -0400 To: Mathelab/ALTRE ALTRE@noreply.github.com<mailto:ALTRE@noreply.github.com> Cc: Elizabeth Baskin elizabeth.baskin@osumc.edu<mailto:elizabeth.baskin@osumc.edu>, Assign assign@noreply.github.com<mailto:assign@noreply.github.com> Subject: Re: [Mathelab/ALTRE] plotting function errors (#47)

Why is this error only a problem with Shiny? What is palette set to in the Shiny Call? Ewy

From: Rick Farouni notifications@github.com<mailto:notifications@github.commailto:notifications@github.com> Reply-To: Mathelab/ALTRE reply@reply.github.com<mailto:reply@reply.github.commailto:reply@reply.github.com> Date: Wednesday, October 19, 2016 at 10:57 AM To: Mathelab/ALTRE ALTRE@noreply.github.com<mailto:ALTRE@noreply.github.commailto:ALTRE@noreply.github.com> Subject: [Mathelab/ALTRE] plotting function errors (#47)

There are errors at these lines: plottingfunctions.R #177 plottingfunctions.R #397

Warning: Error in if: argument is of length zero Stack trace (innermost first): 81: plotCombineAnnotatePeaks [/home/rick/Documents/repos/ALTRE/R/plottingfunctions.R#177] 80: renderUI [/home/rick/R/x86_64-pc-linux-gnu-library/3.3/ALTRE/shinyApp/server.R#302] 79: func 78: origRenderFunc 77: output$annotatebarplot 2: shiny::runApp 1: runShinyApp [/home/rick/Documents/repos/ALTRE/R/runshiny.R#10] Found more than one class "connection" in cache; using the first, from namespace 'BiocGenerics' Found more than one class "connection" in cache; using the first, from namespace 'BiocGenerics' Found more than one class "connection" in cache; using the first, from namespace 'BiocGenerics' Found more than one class "connection" in cache; using the first, from namespace 'BiocGenerics' Warning: Error in if: argument is of length zero Stack trace (innermost first): 80: plotGetCounts [/home/rick/Documents/repos/ALTRE/R/plottingfunctions.R#397] 79: func [/home/rick/R/x86_64-pc-linux-gnu-library/3.3/ALTRE/shinyApp/server.R#312] 78: origRenderFunc 77: output$densityplot 2: shiny::runApp 1: runShinyApp [/home/rick/Documents/repos/ALTRE/R/runshiny.R#10]

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Mathelab commented 8 years ago

What is the problem? Ewy

From: baskineliz notifications@github.com<mailto:notifications@github.com> Reply-To: Mathelab/ALTRE reply@reply.github.com<mailto:reply@reply.github.com> Date: Wednesday, October 19, 2016 at 11:17 AM To: Mathelab/ALTRE ALTRE@noreply.github.com<mailto:ALTRE@noreply.github.com> Cc: Ewy Mathe Ewy.Mathe@osumc.edu<mailto:Ewy.Mathe@osumc.edu>, Assign assign@noreply.github.com<mailto:assign@noreply.github.com> Subject: Re: [Mathelab/ALTRE] plotting function errors (#47)

I see what the problem is, I’ll fix. I’m not sure why it doesn’t show the error on the command line.

Liz

From: Mathelab notifications@github.com<mailto:notifications@github.commailto:notifications@github.com> Reply-To: Mathelab/ALTRE reply@reply.github.com<mailto:reply@reply.github.commailto:reply@reply.github.com> Date: Wed, 19 Oct 2016 11:14:00 -0400 To: Mathelab/ALTRE ALTRE@noreply.github.com<mailto:ALTRE@noreply.github.commailto:ALTRE@noreply.github.com> Cc: Elizabeth Baskin elizabeth.baskin@osumc.edu<mailto:elizabeth.baskin@osumc.edumailto:elizabeth.baskin@osumc.edu>, Assign assign@noreply.github.com<mailto:assign@noreply.github.commailto:assign@noreply.github.com> Subject: Re: [Mathelab/ALTRE] plotting function errors (#47)

Why is this error only a problem with Shiny? What is palette set to in the Shiny Call? Ewy

From: Rick Farouni notifications@github.com<mailto:notifications@github.commailto:notifications@github.commailto:notifications@github.com> Reply-To: Mathelab/ALTRE reply@reply.github.com<mailto:reply@reply.github.commailto:reply@reply.github.commailto:reply@reply.github.com> Date: Wednesday, October 19, 2016 at 10:57 AM To: Mathelab/ALTRE ALTRE@noreply.github.com<mailto:ALTRE@noreply.github.commailto:ALTRE@noreply.github.commailto:ALTRE@noreply.github.com> Subject: [Mathelab/ALTRE] plotting function errors (#47)

There are errors at these lines: plottingfunctions.R #177 plottingfunctions.R #397

Warning: Error in if: argument is of length zero Stack trace (innermost first): 81: plotCombineAnnotatePeaks [/home/rick/Documents/repos/ALTRE/R/plottingfunctions.R#177] 80: renderUI [/home/rick/R/x86_64-pc-linux-gnu-library/3.3/ALTRE/shinyApp/server.R#302] 79: func 78: origRenderFunc 77: output$annotatebarplot 2: shiny::runApp 1: runShinyApp [/home/rick/Documents/repos/ALTRE/R/runshiny.R#10] Found more than one class "connection" in cache; using the first, from namespace 'BiocGenerics' Found more than one class "connection" in cache; using the first, from namespace 'BiocGenerics' Found more than one class "connection" in cache; using the first, from namespace 'BiocGenerics' Found more than one class "connection" in cache; using the first, from namespace 'BiocGenerics' Warning: Error in if: argument is of length zero Stack trace (innermost first): 80: plotGetCounts [/home/rick/Documents/repos/ALTRE/R/plottingfunctions.R#397] 79: func [/home/rick/R/x86_64-pc-linux-gnu-library/3.3/ALTRE/shinyApp/server.R#312] 78: origRenderFunc 77: output$densityplot 2: shiny::runApp 1: runShinyApp [/home/rick/Documents/repos/ALTRE/R/runshiny.R#10]

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osubmi784323 commented 8 years ago

Right now the function checks to see if a palette was specified or if the user wishes to manually enter their own palette argument. If palette is length 1 it assumes an R color brewer palette was entered. If it is of length four it assumes colors have been entered. I though this was the problem — that Rshiny doesn’t like how the argument length has to be checked, but I used the viewer argument to prevent this argument from being checked in Rshiny (it could be ok to use palettes exclusively there…) and the error changed to being about Rcolorbrewer:

Warning: Error in if: argument is of length zero Stack trace (innermost first): 82: RColorBrewer::brewer.pal 81: plotCountAnalysis 80: renderUI [/Users/bask05/Library/R/3.3/library/ALTRE/shinyApp/server.R#322] 79: func 78: origRenderFunc 77: output$volcano 2: shiny::runApp 1: runShinyApp

Is this new? Haven’t we been using Rcolorbrewer for a while now? I’m not sure how to address the error. Probably it is something to do with with how the palette input is input$palette4?

From: Mathelab notifications@github.com<mailto:notifications@github.com> Reply-To: Mathelab/ALTRE reply@reply.github.com<mailto:reply@reply.github.com> Date: Wed, 19 Oct 2016 11:19:28 -0400 To: Mathelab/ALTRE ALTRE@noreply.github.com<mailto:ALTRE@noreply.github.com> Cc: Elizabeth Baskin elizabeth.baskin@osumc.edu<mailto:elizabeth.baskin@osumc.edu>, Assign assign@noreply.github.com<mailto:assign@noreply.github.com> Subject: Re: [Mathelab/ALTRE] plotting function errors (#47)

What is the problem? Ewy

From: baskineliz notifications@github.com<mailto:notifications@github.commailto:notifications@github.com> Reply-To: Mathelab/ALTRE reply@reply.github.com<mailto:reply@reply.github.commailto:reply@reply.github.com> Date: Wednesday, October 19, 2016 at 11:17 AM To: Mathelab/ALTRE ALTRE@noreply.github.com<mailto:ALTRE@noreply.github.commailto:ALTRE@noreply.github.com> Cc: Ewy Mathe Ewy.Mathe@osumc.edu<mailto:Ewy.Mathe@osumc.edumailto:Ewy.Mathe@osumc.edu>, Assign assign@noreply.github.com<mailto:assign@noreply.github.commailto:assign@noreply.github.com> Subject: Re: [Mathelab/ALTRE] plotting function errors (#47)

I see what the problem is, I’ll fix. I’m not sure why it doesn’t show the error on the command line.

Liz

From: Mathelab notifications@github.com<mailto:notifications@github.commailto:notifications@github.commailto:notifications@github.com> Reply-To: Mathelab/ALTRE reply@reply.github.com<mailto:reply@reply.github.commailto:reply@reply.github.commailto:reply@reply.github.com> Date: Wed, 19 Oct 2016 11:14:00 -0400 To: Mathelab/ALTRE ALTRE@noreply.github.com<mailto:ALTRE@noreply.github.commailto:ALTRE@noreply.github.commailto:ALTRE@noreply.github.com> Cc: Elizabeth Baskin elizabeth.baskin@osumc.edu<mailto:elizabeth.baskin@osumc.edumailto:elizabeth.baskin@osumc.edumailto:elizabeth.baskin@osumc.edu>, Assign assign@noreply.github.com<mailto:assign@noreply.github.commailto:assign@noreply.github.commailto:assign@noreply.github.com> Subject: Re: [Mathelab/ALTRE] plotting function errors (#47)

Why is this error only a problem with Shiny? What is palette set to in the Shiny Call? Ewy

From: Rick Farouni notifications@github.com<mailto:notifications@github.commailto:notifications@github.commailto:notifications@github.commailto:notifications@github.com> Reply-To: Mathelab/ALTRE reply@reply.github.com<mailto:reply@reply.github.commailto:reply@reply.github.commailto:reply@reply.github.commailto:reply@reply.github.com> Date: Wednesday, October 19, 2016 at 10:57 AM To: Mathelab/ALTRE ALTRE@noreply.github.com<mailto:ALTRE@noreply.github.commailto:ALTRE@noreply.github.commailto:ALTRE@noreply.github.commailto:ALTRE@noreply.github.com> Subject: [Mathelab/ALTRE] plotting function errors (#47)

There are errors at these lines: plottingfunctions.R #177 plottingfunctions.R #397

Warning: Error in if: argument is of length zero Stack trace (innermost first): 81: plotCombineAnnotatePeaks [/home/rick/Documents/repos/ALTRE/R/plottingfunctions.R#177] 80: renderUI [/home/rick/R/x86_64-pc-linux-gnu-library/3.3/ALTRE/shinyApp/server.R#302] 79: func 78: origRenderFunc 77: output$annotatebarplot 2: shiny::runApp 1: runShinyApp [/home/rick/Documents/repos/ALTRE/R/runshiny.R#10] Found more than one class "connection" in cache; using the first, from namespace 'BiocGenerics' Found more than one class "connection" in cache; using the first, from namespace 'BiocGenerics' Found more than one class "connection" in cache; using the first, from namespace 'BiocGenerics' Found more than one class "connection" in cache; using the first, from namespace 'BiocGenerics' Warning: Error in if: argument is of length zero Stack trace (innermost first): 80: plotGetCounts [/home/rick/Documents/repos/ALTRE/R/plottingfunctions.R#397] 79: func [/home/rick/R/x86_64-pc-linux-gnu-library/3.3/ALTRE/shinyApp/server.R#312] 78: origRenderFunc 77: output$densityplot 2: shiny::runApp 1: runShinyApp [/home/rick/Documents/repos/ALTRE/R/runshiny.R#10]

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rfarouni commented 8 years ago

Shiny side needs to have a default value in the argument, so there is nothing to be done there. At any rate, why do we want users to enter hex colors? The previous solution that worked was this.

plotConsensusPeaks <- function(...., palette = NULL) {
  if ( !is.null(palette) ) {
    cols <- RColorBrewer::brewer.pal(3, palette)
  } else {
    cols <- RColorBrewer::brewer.pal(3, "Set1")
  }
osubmi784323 commented 8 years ago

Ewy wanted the ambiguous points on the volcano plot to be grey in the vignette. To be able to have that level of control, you need to be able to enter colors.

From: Rick Farouni notifications@github.com<mailto:notifications@github.com> Reply-To: Mathelab/ALTRE reply@reply.github.com<mailto:reply@reply.github.com> Date: Wed, 19 Oct 2016 14:01:03 -0400 To: Mathelab/ALTRE ALTRE@noreply.github.com<mailto:ALTRE@noreply.github.com> Cc: Elizabeth Baskin elizabeth.baskin@osumc.edu<mailto:elizabeth.baskin@osumc.edu>, Assign assign@noreply.github.com<mailto:assign@noreply.github.com> Subject: Re: [Mathelab/ALTRE] plotting function errors (#47)

Shiny side needs to have a default value in the argument, so there is nothing to be done there. At any rate, why do we want users to enter hex colors? The previous solution that worked was this.

plotConsensusPeaks <- function(...., palette = NULL) { if ( !is.null(palette) ) { cols <- RColorBrewer::brewer.pal(3, palette) } else { cols <- RColorBrewer::brewer.pal(3, "Set1") }

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rfarouni commented 8 years ago

Right won't make a difference since we always have a character vector

str(RColorBrewer::brewer.pal(3, "Set1"))
 chr [1:3] "#E41A1C" "#377EB8" "#4DAF4A"

The shiny function sends the default palette but I think also a NULL if the object is not yet available. You probably just need to handle this exception by adding !is.null(palette)

Mathelab commented 8 years ago

I think the error does come from the Shiny server side, that somehow the input is not set appropriately by default (even though it looks to be).

How about trying out something like this?

if (hex color) { ….. } else if (allowable brewer.pal palette){ cols <- RColorBrewer::brewer.pal(3, palette) } else {cols <- RColorBrewer::brewer.pal(3, "Set1")t}

From: baskineliz notifications@github.com<mailto:notifications@github.com> Reply-To: Mathelab/ALTRE reply@reply.github.com<mailto:reply@reply.github.com> Date: Wednesday, October 19, 2016 at 2:04 PM To: Mathelab/ALTRE ALTRE@noreply.github.com<mailto:ALTRE@noreply.github.com> Cc: Ewy Mathe Ewy.Mathe@osumc.edu<mailto:Ewy.Mathe@osumc.edu>, Assign assign@noreply.github.com<mailto:assign@noreply.github.com> Subject: Re: [Mathelab/ALTRE] plotting function errors (#47)

Ewy wanted the ambiguous points on the volcano plot to be grey in the vignette. To be able to have that level of control, you need to be able to enter colors.

From: Rick Farouni notifications@github.com<mailto:notifications@github.commailto:notifications@github.com> Reply-To: Mathelab/ALTRE reply@reply.github.com<mailto:reply@reply.github.commailto:reply@reply.github.com> Date: Wed, 19 Oct 2016 14:01:03 -0400 To: Mathelab/ALTRE ALTRE@noreply.github.com<mailto:ALTRE@noreply.github.commailto:ALTRE@noreply.github.com> Cc: Elizabeth Baskin elizabeth.baskin@osumc.edu<mailto:elizabeth.baskin@osumc.edumailto:elizabeth.baskin@osumc.edu>, Assign assign@noreply.github.com<mailto:assign@noreply.github.commailto:assign@noreply.github.com> Subject: Re: [Mathelab/ALTRE] plotting function errors (#47)

Shiny side needs to have a default value in the argument, so there is nothing to be done there. At any rate, why do we want users to enter hex colors? The previous solution that worked was this.

plotConsensusPeaks <- function(...., palette = NULL) { if ( !is.null(palette) ) { cols <- RColorBrewer::brewer.pal(3, palette) } else { cols <- RColorBrewer::brewer.pal(3, "Set1") }

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rfarouni commented 8 years ago

In Shiny the function is called repeatedly not just once. Anytime there is an event or update on the screen, the function gets called. The first event is when the webpage first loads.There the object returned can be a NULL, but I haven't tested

Mathelab commented 8 years ago

Ok Rick. I thought that the function would not be called unless the getcountsObj() was returned as non-null (with the req() function).

So yes, checking for null should do the trick…

Ewy

From: Rick Farouni notifications@github.com<mailto:notifications@github.com> Reply-To: Mathelab/ALTRE reply@reply.github.com<mailto:reply@reply.github.com> Date: Wednesday, October 19, 2016 at 2:56 PM To: Mathelab/ALTRE ALTRE@noreply.github.com<mailto:ALTRE@noreply.github.com> Cc: Ewy Mathe Ewy.Mathe@osumc.edu<mailto:Ewy.Mathe@osumc.edu>, Assign assign@noreply.github.com<mailto:assign@noreply.github.com> Subject: Re: [Mathelab/ALTRE] plotting function errors (#47)

In Shiny the function is called repeatedly not just once. Anytime there is an event or update on the screen, the function gets called. The first event is when the webpage first loads.There the object returned can be a NULL, but I haven't tested

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osubmi784323 commented 8 years ago

Thanks, it worked, I pushed.

Mathelab commented 8 years ago

OK thanks! will check it out soon and planning to resubmit by the end of the weekend…

Ewy

From: baskineliz notifications@github.com<mailto:notifications@github.com> Reply-To: Mathelab/ALTRE reply@reply.github.com<mailto:reply@reply.github.com> Date: Thursday, October 20, 2016 at 9:28 AM To: Mathelab/ALTRE ALTRE@noreply.github.com<mailto:ALTRE@noreply.github.com> Cc: Ewy Mathe Ewy.Mathe@osumc.edu<mailto:Ewy.Mathe@osumc.edu>, Assign assign@noreply.github.com<mailto:assign@noreply.github.com> Subject: Re: [Mathelab/ALTRE] plotting function errors (#47)

Thanks, it worked, I pushed.

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