Phenoarch platform - Create a video of a trait in the plateform

I.Sanchez

septembre 04, 2020

Objective

Create a video of a given trait recorded in the phenoArch platform. This tutorial will use the imageGreenhouse() function and the animation R package.

https://cran.r-project.org/package=animation

SystemRequirements: ImageMagick (http://imagemagick.org) or GraphicsMagick (http://www.graphicsmagick.org) or LyX (http://www.lyx.org) for saveGIF(); (PDF)LaTeX for saveLatex(); SWF Tools (http://swftools.org) for saveSWF(); FFmpeg (http://ffmpeg.org) or avconv (https://libav.org/avconv.html) for saveVideo()

Code for creating a video

  # import a temporal dataframe from phisStatR package:
  data(plant1)

  str(plant1)
## 'data.frame':    47022 obs. of  14 variables:
##  $ Ref            : Factor w/ 1680 levels "manip1_10_10_WW",..: 131 131 131 131 131 131 131 131 131 131 ...
##  $ experimentAlias: Factor w/ 1 level "manip1": 1 1 1 1 1 1 1 1 1 1 ...
##  $ Day            : Factor w/ 42 levels "2013-02-01","2013-02-02",..: 3 4 5 6 7 9 9 10 11 12 ...
##  $ potAlias       : int  1 1 1 1 1 1 1 1 1 1 ...
##  $ scenario       : Factor w/ 2 levels "WD","WW": 2 2 2 2 2 2 2 2 2 2 ...
##  $ genotypeAlias  : Factor w/ 274 levels "11430_H","A310_H",..: 165 165 165 165 165 165 165 165 165 165 ...
##  $ repetition     : int  1 1 1 1 1 1 1 1 1 1 ...
##  $ Line           : int  1 1 1 1 1 1 1 1 1 1 ...
##  $ Position       : int  1 1 1 1 1 1 1 1 1 1 ...
##  $ thermalTime    : num  1.29 2.65 3.98 5.32 6.66 ...
##  $ plantHeight    : num  140 151 213 239 271 ...
##  $ leafArea       : num  0.018 0.019 0.0208 0.0222 0.0235 ...
##  $ biovolume      : num  0.253 0.62 1.201 1.68 3.396 ...
##  $ Repsce         : Factor w/ 15 levels "1_WD","1_WW",..: 2 2 2 2 2 2 2 2 2 2 ...
  head(plant1)
##             Ref experimentAlias        Day potAlias scenario genotypeAlias
## 1 manip1_1_1_WW          manip1 2013-02-04        1       WW      Lo1199_H
## 2 manip1_1_1_WW          manip1 2013-02-05        1       WW      Lo1199_H
## 3 manip1_1_1_WW          manip1 2013-02-06        1       WW      Lo1199_H
## 4 manip1_1_1_WW          manip1 2013-02-07        1       WW      Lo1199_H
## 5 manip1_1_1_WW          manip1 2013-02-08        1       WW      Lo1199_H
## 6 manip1_1_1_WW          manip1 2013-02-10        1       WW      Lo1199_H
##   repetition Line Position thermalTime plantHeight   leafArea biovolume Repsce
## 1          1    1        1    1.290456     140.300 0.01799736 0.2530896   1_WW
## 2          1    1        1    2.645803     151.225 0.01901210 0.6198236   1_WW
## 3          1    1        1    3.980055     213.325 0.02081664 1.2013394   1_WW
## 4          1    1        1    5.319284     239.200 0.02215532 1.6800266   1_WW
## 5          1    1        1    6.656157     270.825 0.02351661 3.3961557   1_WW
## 6          1    1        1    9.258258     358.225 0.02595851 5.9954879   1_WW
  # Number of Days in the dataframe (in the experiment)
  table(plant1[,"Day"])
## 
## 2013-02-01 2013-02-02 2013-02-04 2013-02-05 2013-02-06 2013-02-07 2013-02-08 
##        719        961        617       1843       1547       1573       1382 
## 2013-02-09 2013-02-10 2013-02-11 2013-02-12 2013-02-13 2013-02-14 2013-02-15 
##       1088       2425       2008       1590       1599       1812       1671 
## 2013-02-16 2013-02-17 2013-02-18 2013-02-19 2013-02-20 2013-02-21 2013-02-22 
##       1618       1681       1467       1529        866        744        824 
## 2013-02-23 2013-02-24 2013-02-25 2013-02-26 2013-02-27 2013-02-28 2013-03-01 
##        928        871        827        841        786        800        914 
## 2013-03-02 2013-03-03 2013-03-04 2013-03-05 2013-03-06 2013-03-07 2013-03-08 
##        819        873        800        987        843        871        531 
## 2013-03-09 2013-03-10 2013-03-11 2013-03-12 2013-03-13 2013-03-14 2013-03-15 
##       1154       1243       1568        979        583        120        120
  plant1<-arrange(plant1,Day)

The code below is not evaluated but just presented. Indeed, to create a video, R must save each temporal graphic in a repertory and then create the video using all the files. We just here show how to do this. Please try it with your own path and folder hierarchy.

  • Using the saveVideo() function, we need to do a for loop on the vector of days of the experiment
  • For each day, the imageGreenhouse() function is used to create a heatmap of the biovolume in the greenhouse with the typeI parameter set to “video”.
  • each graphic is saved as a png file (ani.options)
  • the video is created in the /output/ directory of our project (video.name line) as a GIF video. you can change the path…
  • you can set other options to ffmepg (other.opts)
  • To incorporate the GIF in a Rmarkdown file, you have just to call the video in the chunk.
    #----------------------------------------------------
    #heat map biovolume per Day and creation of a gif video
    #----------------------------------------------------
    vecDay<-na.omit(unique(plant1[,"Day"]))

    videoFileName<-"biovolume"

    saveVideo({
      for (tmpday in 1:length(vecDay)){
        imageGreenhouse(datain=filter(plant1,Day==vecDay[tmpday]),trait="biovolume",typeD=1,typeT=1,ylim=NULL,
                        xcol="Line",ycol="Position",numrow=28,numcol=60,
                        typeI="video")
      }
      ani.options(interval = 1,ani.dev="png",ani.height=480)
      },
      video.name = paste0(thepath,"/output/",videoFileName,".gif"),
      other.opts = paste0("-y -r ",length(vecDay)+2," -i Rplot%d.png -dframes ",
                          length(vecDay)+2," -r ",length(vecDay)+2)
    )

  # Call the video in a Rmarkdown file
  #![](/my-path-to-project/output/humidity.gif)

Session info

## R version 4.0.2 (2020-06-22)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 18363)
## 
## Matrix products: default
## 
## locale:
## [1] LC_COLLATE=French_France.1252  LC_CTYPE=French_France.1252   
## [3] LC_MONETARY=French_France.1252 LC_NUMERIC=C                  
## [5] LC_TIME=French_France.1252    
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] animation_2.6        openSilexStatR_1.1.0 dplyr_1.0.2         
## [4] tidyr_1.1.2         
## 
## loaded via a namespace (and not attached):
##  [1] splines_4.0.2      dotCall64_1.0-0    gtools_3.8.2       assertthat_0.2.1  
##  [5] expm_0.999-5       CARBayesdata_2.2   sp_1.4-2           stats4_4.0.2      
##  [9] yaml_2.2.1         LearnBayes_2.15.1  truncdist_1.0-2    pillar_1.4.6      
## [13] backports_1.1.9    lattice_0.20-41    glue_1.4.2         digest_0.6.25     
## [17] RColorBrewer_1.1-2 colorspace_1.4-1   plyr_1.8.6         htmltools_0.5.0   
## [21] Matrix_1.2-18      pkgconfig_2.0.3    raster_3.3-13      CARBayesST_3.1    
## [25] gmodels_2.18.1     purrr_0.3.4        scales_1.1.1       gdata_2.18.0      
## [29] tibble_3.0.3       generics_0.0.2     ggplot2_3.3.2      ellipsis_0.3.1    
## [33] magrittr_1.5       crayon_1.3.4       deldir_0.1-28      memoise_1.1.0     
## [37] evaluate_0.14      GGally_2.0.0       fs_1.4.2           nlme_3.1-148      
## [41] MASS_7.3-51.6      foreign_0.8-80     truncnorm_1.0-8    class_7.3-17      
## [45] data.table_1.13.0  tools_4.0.2        shapefiles_0.7     lifecycle_0.2.0   
## [49] matrixStats_0.56.0 stringr_1.4.0      munsell_0.5.0      compiler_4.0.2    
## [53] pkgdown_1.5.1      e1071_1.7-3        evd_2.3-3          rlang_0.4.7       
## [57] classInt_0.4-3     units_0.6-7        grid_4.0.2         rstudioapi_0.11   
## [61] htmlwidgets_1.5.1  spam_2.5-1         crosstalk_1.1.0.1  rmarkdown_2.3     
## [65] SpATS_1.0-11       boot_1.3-25        testthat_2.3.2     gtable_0.3.0      
## [69] codetools_0.2-16   reshape_0.8.8      DBI_1.1.0          R6_2.4.1          
## [73] lubridate_1.7.9    gridExtra_2.3      knitr_1.29         rgdal_1.5-16      
## [77] rprojroot_1.3-2    spdep_1.1-5        KernSmooth_2.23-17 desc_1.2.0        
## [81] matrixcalc_1.0-3   stringi_1.4.6      Rcpp_1.0.5         vctrs_0.3.4       
## [85] sf_0.9-5           leaflet_2.0.3      spData_0.3.8       tidyselect_1.1.0  
## [89] xfun_0.16          coda_0.19-3

References

  1. R Development Core Team (2015). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org.
  2. Yihui Xie (2013). animation: An R Package for Creating Animations and Demonstrating Statistical Methods. Journal of Statistical Software, 53(1), 1-27. URL http://www.jstatsoft.org/v53/i01/.