csv files from acrophase plot in the Oscillation analysis cannot be downloaded

[devang-mehta]

Hi, first of all thank you so much for creating this app! It's a rea lifesaver.

I found a bug where when I click the CSV download button in the Acrophase tab under the Method Comparison window it fails to dowmload and gives the following error in by download bar. .This has happened with both your instance of the shiny app and a local instance, and with your simulated data and my own data.

"dlOverlaps.txt - Failed -Server problem"

I'm basically trying to reproduce the rose plot of the acrophases that you display. I wanted to make it a litte nicer with my own theme so I was hoping I could download the binned and filtered data to then just quickly plot it myself, hence I need this csv.

I also tried creating the histogram myself but couldn't get it to work, I always end up with missing values in the 0 period bins...

[matthewcarlucci]

Hello, thanks for identifying the bug! I have reproduced this issue with the latest version and this sounds easy enough to fix, but I do not think it will help much for your task (it does not produce the CSV you are looking for).

On Customizing Rose Plots

I'm basically trying to reproduce the rose plot of the acrophases that you display. I wanted to make it a litte nicer with my own theme so I was hoping I could download the binned and filtered data to then just quickly plot it myself, hence I need this csv.

It sounds like you were able to obtain the raw CSV of results and it is just that the rose diagram is difficult to reproduce and customize. The filtered CSV you have in mind is a good suggestion for the future (a download beside the rose plots maybe), but I am not sure when this would be added.

Do you have some familiarity with R + ggplot? If you do, then you may benefit from taking a look at the code that was used to produce these plots from the list of acrophases. The plot object output by this function can also be directly modified to some degree with additional ggplot elements.

[devang-mehta]

Hi Matthew, Thanks for getting back to me so quickly! I did eventually manage to get the plot working after borrowing code from your github. But I'm not sure I still understand what the code is doing, haha. Would you mind just explaining how the data is adjusted to make that plot? Best wishes, Devang *--------------------------------* *Dr. Devang Mehta* *Post-Doctoral Fellow* Plant Genomics Laboratory *University of Alberta* www.uhriglab.com ***@***.*** www.devang.bio

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On Fri, Aug 20, 2021 at 9:05 AM Matthew Carlucci ***@***.***> wrote: Hello, thanks for identifying the bug! I have reproduced this issue with the latest version and this sounds easy enough to fix, but I do not think it will help much for your task (it does not produce the CSV you are looking for). On Customizing Rose Plots I'm basically trying to reproduce the rose plot of the acrophases that you display. I wanted to make it a litte nicer with my own theme so I was hoping I could download the binned and filtered data to then just quickly plot it myself, hence I need this csv. It sounds like you were able to obtain the raw CSV of results and it is just that the rose diagram is difficult to reproduce and customize. The filtered CSV you have in mind is a good suggestion for the future (a download beside the rose plots maybe), but I am not sure when this would be added. Do you have some familiarity with R + ggplot? If you do, then you may benefit from taking a look at the code <https://github.com/matthewcarlucci/DiscoRhythm/blob/3b660f1350db1da2c62c2e89e82246df4cb961ca/inst/app/code/server/plots.R#L354-L448> that was used to produce these plots from the list of acrophases. The plot object output by this function can also be directly modified to some degree with additional ggplot elements. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#6 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AHBVATETVMS2EMO4MMF7HYDT5ZVKBANCNFSM5CPMVD5Q> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&utm_campaign=notification-email> .

[matthewcarlucci]

Hi Devang,

The code is only performing custom binning and grid/labels for aesthetic reasons (no data was "adjusted") so I would suggest not to worry about understanding the code. At the end of the day, the rose plot is still a simple histogram and you can obtain a very basic version of this circular format easily directly with ggplot which should roughly reproduce the figure:

library(ggplot2)
# vec is a numeric vector of acrophase estimates
vec=runif(200)*24
ggplot(data.frame(acrophase=vec)) +
    geom_histogram( aes(x = acrophase)) +
    scale_x_continuous(limits = c(0, 24), breaks = seq(0, 24, length.out = 5)) +
    coord_polar()

I will leave this issue open just until I fix the original CSV download bug.

[matthewcarlucci]

Noting that this bug appears for both the overlap and acrophase tabs of "Method Comparison".