Making a video from an R loop

Iterative_R_images.r

#!/usr/bin/env Rscript

# Plotting surface plots via ggplot2/plotly
# Usage:
# $ Rscript CDmeltplot.R -i data.csv -o filename


############################################################
# General purpose heatmap plotting script for consistency. #
# This script can be slow as it was designed to be pretty  #
# bullet-proof when loading/installing necessary packages. #
#                                                          #
# By J. Healey                                             #
# Version 3
############################################################

# Load packages:
list.of.packages <- c("reshape2",
                      "plotly",
                      "argparse",
                      "ggplot2",
                      "RColorBrewer",
                      "tools",
                      "stringr",
                      "htmltools",
                      "magrittr",
                      "RSelenium")
new.packages <- list.of.packages[!(list.of.packages %in% installed.packages()[,"Package"])]
if(length(new.packages)) install.packages(new.packages)

suppressMessages(library("reshape2"))
suppressMessages(library("plotly"))
suppressMessages(library("argparse"))
suppressMessages(library("ggplot2"))
suppressMessages(library("RColorBrewer"))
suppressMessages(library("tools"))
suppressMessages(library("stringr"))
suppressMessages(library("htmltools"))
suppressMessages(library("magrittr"))
suppressMessages(library("RSelenium"))

parser <- ArgumentParser()

parser$add_argument('-i',
                    '--infile',
                    action='store',
                    required=TRUE,
                    help="Plain csv matrix file for plotting.")
parser$add_argument('-d',
                    '--device',
                    action='store',
                    default='svg',
                    choices=c('png','svg','jpeg','pdf','webp'),
                    help='Output image format/device. Default SVG.')
parser$add_argument('-o',
                    '--outfile',
                    action='store',
                    default='None',
                    help='Filename and path to save the image to. Defaults to the same as the infile with a new extension.')
parser$add_argument('-z',
                    '--zoom',
                    action='store',
                    default=2.5,
                    help='The zoom value of the camera, larger values move the camera away from the centre. Default 2.5')
parser$add_argument('-v',
                    '--vangle',
                    action='store',
                    default=0.4,
                    help='The vertical angle of the camera. Increased values will rotate the camera \'overhead\'. Default 0.4')
parser$add_argument('--movie',
                    action='store',
                    default='0.5:0.5:1',
                    help='Render multiple frames to create a video. Specify start:end:increment.')
parser$add_argument('--set_iter',
                    action='store',
                    default=0,
                    help='Set the iteration counter for the output images when rendering in multiple sessions. Keeps images numerically ordered to make video creation easier.')


args <-parser$parse_args()

# Prep variables for use
infile <- args$infile
outfile <- args$outfile
device <- args$device
movie <- args$movie
cam.zoom <- as.numeric(args$zoom)
ver.angle <- as.numeric(args$vangle)
set_iter <- as.numeric(args$set_iter)
browser <- args$browser
port <- as.numeric(args$port)
from <- as.numeric(strsplit(movie,":")[[1]][1])
to <- as.numeric(strsplit(movie,":")[[1]][2])
increment <- as.numeric(strsplit(movie,":")[[1]][3])

if (outfile == 'None'){
  outfile <- basename(file_path_sans_ext(infile))
}

cat("Starting RSelenium server", "\n")
RS_server <- rsDriver(verbose = FALSE)

# Read in and prepare data
df <- read.csv(infile, sep=",", check.names=FALSE, row.names = 1, header = TRUE)
matrix <- as.matrix(df)

scan <- as.numeric(rownames(df))
temp <- as.numeric(colnames(df))

matrix.list <- list(z = matrix,
                    x = temp,
                    y = scan)

font.pref <- list(size=18, family="Arial, sans-serif", color="black")
x.list <- list(title = "Temperature (˚C)",
               titlefont = font.pref,
               ticklen = 20,
               tickcolor = "white",
               zerolinecolor = "black",
               zerolinewidth = 2)
y.list <- list(title = "Wavelength (nm)",
               titlefont = font.pref,
               ticklen = 20,
               tickcolor = "white",
               zerolinecolor = "black",
               zerolinewidth = 2)
z.list <- list(title = "CD Intensity",
               titlefont = font.pref,
               ticklen = 20,
               tickcolor = "white",
               zerolinecolor = "black",
               zerolinewidth = 2)

iter = set_iter
for(i in seq(from, to, by=increment)){
  iter = iter + 1
  theta = i/100
  
  graph <- plot_ly(z =~matrix, x=temp, y=scan, type="surface",
                   colors= c('black','gray','green'),
                   colorbar = list(title="CD Intensity",
                                   yanchor="middle",
                                   len=1.5)) %>%
                   layout(scene=list(xaxis = x.list,
                                     yaxis = y.list,
                                     zaxis = z.list,
                                     camera = list(eye = list(x = cos((i/10))*cam.zoom,
                                                              y = sin((i/10))*cam.zoom,
                                                              z=ver.angle)
                                                  )
                                    )
                          )

  outfile_iter <- paste(outfile, ".", str_pad(iter, 4, pad ="0"), sep = "")
  outfile_iter_ext <- paste(outfile_iter, device, sep = ".")
  
# Render images:
export(p = graph, outfile_iter_ext, RS_server)

if (device == "pdf"){
    convert.installed <- system("convert --version", ignore.stdout = TRUE) == 0

    if (convert.installed == TRUE){
      cat("Calling ImageMagick to convert to formats other than PNG/JPEG", "\n")
      cat(sprintf('convert %s %s',
                  paste(outfile_iter, device, sep = "."),
                  paste(outfile_iter, "pdf", sep = ".")), "\n")
      system(sprintf('convert %s %s',
                     paste(outfile_iter, "png", sep = "."),
                     paste(outfile_iter, device, sep = ".")))
    } else {
      cat("Can't convert to that device. Make sure ImageMagick `convert` is in your PATH.", "\n")
    }
  }
  cat("Outfile:", outfile_iter_ext, '\n')


}


# Kill the webserver

RS_server[["server"]]$stop()