R/dygraphPAM.R

In KiranLDA/PAMLr: Suite Of Functions For Manipulating Pressure, Activity, Magnetism, Temperature And Light Data In R

#' Plot PAM data with dygraphs
#'
#' @description This opens a java dygraph application which allows the user to zoom in and out. In Rstudio it will open in the viewer pane and in base R in an html readers. Note that this can be a bit slow
#'
#' @param dta PAM data to be plotted
#' @param from date that plotting starts
#' @param to date that plotting ends
#' @param toPLOT names of the variables to plot. For now this includes `light`, `pressure`, `acceleration` and `temperature`
#'
#' @return a plot of all the measurements
#'
#' @references Vanderkam, D., Allaire, J., Owen, J., Gromer, D., Shevtsov, P. and Thieurmel, B., dygraphs: Interface to Dygraphs Interactive Time Series Charting Library, 2015. URL http://CRAN. R-project. org/package= dygraphs. R package version 0.4, 5, p.7.
#'
#' @examples
#' ##load dummy data
#' #data(hoopoe)
#' #PAM_data=hoopoe
#'
#' ## This bit is for Rstudio users to prevent html from opening in Viewer pane and crashing
#' ## It opens in web browser instead
#' #backup_options <- options()
#' #options(viewer=NULL)
#'
#' ## Plot interactive graphics
#' #dygraphPAM(dta = PAM_data)
#'
#' ## restore Rstudio settings from before plot
#' #options(backup_options)
#'
#'
#' @importFrom dygraphs dygraph dyRangeSelector dyHighlight dyLegend dyOptions dyShading "%>%"
#' @importFrom htmltools browsable tagList
#' @importFrom xts xts
#' @export
dygraphPAM <- function(dta,
                       from = dta$light$date[1],
                       to = dta$light$date[length(dta$light$date)],
                       toPLOT = names(dta)) {
  print("Error: This function is deprecated, use plot_interactive_timeseries, or install v.1.0 of PAMLr by running devtools::install_github('KiranLDA/PAMLr', ref = 'v.1.0')")

  # # backup_options <- options()
  # len = ifelse( ("id" %in% toPLOT) , length(names(dta))-1, length(names(dta)))
  #
  # dy_graph = list()
  #
  # if ("light" %in% toPLOT ){
  #   dy_graph$light = dygraph(xts(x = dta$light$obs, order.by = dta$light$date),
  #                            xlab = "Time",
  #                            ylab = "Light",
  #                            group = dta$light$date, #This is useful for synchronosing multiple graphs
  #                            main="Light as a function of time") %>%
  #     dyRangeSelector(dateWindow = c(from, to)) %>%
  #     dyHighlight(highlightSeriesOpts = list(strokeWidth = 2)) %>%
  #     dyLegend(hideOnMouseOut = TRUE, width = 600) %>%
  #     dyOptions(colors ="#66C2A5")
  # }
  # if ("temperature" %in% toPLOT ){
  #   dy_graph$temperature = dygraph(xts(x = dta$temperature$obs, order.by = dta$temperature$date),
  #                                  xlab = "Time",
  #                                  ylab = "Temperature (C)",
  #                                  group = dta$light$date,#dta$temperature$date, #This is useful for synchronosing multiple graphs
  #                                  main="Temperature as a function of time") %>%
  #     dyRangeSelector(dateWindow = c(from, to)) %>%
  #     dyHighlight(highlightSeriesOpts = list(strokeWidth = 2)) %>%
  #     dyLegend(hideOnMouseOut = TRUE, width = 600) %>%
  #     dyOptions(colors ="#A6D854")
  # }
  # if ("pressure" %in% toPLOT ){
  #   dy_graph$pressure = dygraph(xts(x = dta$pressure$obs, order.by = dta$pressure$date),
  #                            xlab = "Time",
  #                            ylab = "Pressure (hPa)",
  #                            group = dta$light$date,#dta$pressure$date, #This is useful for synchronosing multiple graphs
  #                            main="Pressure as a function of time") %>%
  #     dyRangeSelector(dateWindow = c(from, to)) %>%
  #     dyHighlight(highlightSeriesOpts = list(strokeWidth = 2)) %>%
  #     dyLegend(hideOnMouseOut = TRUE, width = 600) %>%
  #     dyOptions(colors ="#FC8D62")
  # }
  # if ("acceleration" %in% toPLOT ){
  #   dy_graph$activity = dygraph(xts(x = dta$acceleration$act, order.by = dta$acceleration$date),
  #                               xlab = "Time",
  #                               ylab = "Activity",
  #                               group = dta$light$date,#dta$acceleration$date, #This is useful for synchronosing multiple graphs
  #                               main="Activity as a function of time") %>%
  #     dyRangeSelector(dateWindow = c(from, to)) %>%
  #     dyHighlight(highlightSeriesOpts = list(strokeWidth = 2)) %>%
  #     dyLegend(hideOnMouseOut = TRUE, width = 600) %>%
  #     dyOptions(colors ="#8DA0CB")
  #   dy_graph$pitch = dygraph(xts(x = dta$acceleration$pit, order.by = dta$acceleration$date),
  #                                   xlab = "Time",
  #                                   ylab = "Pitch",
  #                                   group = dta$light$date,#dta$acceleration$date, #This is useful for synchronosing multiple graphs
  #                                   main="Pitch as a function of time") %>%
  #     dyRangeSelector(dateWindow = c(from, to)) %>%
  #     dyHighlight(highlightSeriesOpts = list(strokeWidth = 2)) %>%
  #     dyLegend(hideOnMouseOut = TRUE, width = 600) %>%
  #     dyOptions(colors ="#E78AC3")
  # }
  # if ("magnetic" %in% toPLOT ){
  #   dy_graph$magneticg = dygraph(xts(x = dta$magnetic[,c(2,3,4)], order.by = dta$magnetic$date),
  #                                  xlab = "Time",
  #                                  ylab = "Magnetic gX, gY,and gZ",
  #                                  group = dta$light$date,#dta$temperature$date, #This is useful for synchronosing multiple graphs
  #                                  main="Mgnetism g as a function of time") %>%
  #     dyRangeSelector(dateWindow = c(from, to)) %>%
  #     dyHighlight(highlightSeriesOpts = list(strokeWidth = 2)) %>%
  #     dyLegend(hideOnMouseOut = TRUE, width = 600) %>%
  #     dyOptions(colors = c("#8DA0CB","#A6D854","#FC8D62"))
  #   dy_graph$magneticm = dygraph(xts(x = dta$magnetic[,c(5,6,7)], order.by = dta$magnetic$date),
  #                                  xlab = "Time",
  #                                  ylab = "Magnetic mX, mY,and mZ",
  #                                  group = dta$light$date,#dta$temperature$date, #This is useful for synchronosing multiple graphs
  #                                  main="Magnetism m as a function of time") %>%
  #     dyRangeSelector(dateWindow = c(from, to)) %>%
  #     dyHighlight(highlightSeriesOpts = list(strokeWidth = 2)) %>%
  #     dyLegend(hideOnMouseOut = TRUE, width = 600) %>%
  #     dyOptions(colors = c("#8DA0CB","#A6D854","#FC8D62"))
  # }
  #
  #
  # # options(viewer=NULL)
  # browsable(tagList(dy_graph))
  # # options(backup_options)
}