R/plot_images.R
In kateharborne/SimSpin: SimSpin - A package for the kinematic analysis of galaxy simulations
Defines functions
.image_nan
plot_voronoi
plot_OH
plot_SFR
plot_particles
plot_metallicity
plot_age
plot_h4
plot_h3
plot_dispersion
plot_velocity
plot_mass
plot_flux
Documented in
plot_age
plot_dispersion
plot_flux
plot_h3
plot_h4
plot_mass
plot_metallicity
plot_OH
plot_particles
plot_SFR
plot_velocity
plot_voronoi
# Author: Kate Harborne
# Date: 25/10/2023
# Title: plot_images - a suite of function for plotting pretty images
#' Plotting pretty flux images
#'
#' A function to produce a plot of the flux image produced by
#' \code{build_datacube()} with associated colour bar and labels.
#'
#' @param flux_image Numeric array containing the flux image
#' @param fig Numeric array of length 4 describing the boundary of the image
#' @param new Boolean. Should the image be added to the existing plot? Default
#' is FALSE.
#' @param units String describing the units of the values contained
#' in the image.
#' @param main Image title, default "".
#' @param radii list - containing a, b, and ang (if wishing to plot half-mass
#' radii ellipse).
#' @param na.color String. Colour given to NA values in the image.
#' @param zlim Numeric array of length 2. Describing the numeric range of
#' colours in the image. Default is NA, in which the range will be described by
#' the minimum and maximum values in the image.
#' @param legend Boolean to determine if the colour bar axis should be printed
#' at the bottom of the image. Default is T.
#' @param titleshift Numeric. Describes the distance between the colour bar and
#' the units. Default is -4.
#' @param labN Numeric. Describes the minimum number of numeric labels added to
#' the colour bar. Default is 5.
#' @param radii_col String. Describing the colour of the ellipse drawn if
#' \code{radii} list is specified. Default is "red".
#' @param ... Further variables passed to magimage. See
#' \code{\link[magicaxis]{magimage}} for further details.
#' @return Returns an image to the plotting window of the input
#' \code{build_datacube} image.
#' @examples
#' ss_pd_gadget = system.file("extdata", "SimSpin_example_Gadget",
#' package = "SimSpin")
#' ss_gadget = make_simspin_file(ss_pd_gadget, write_to_file = FALSE)
#' cube = build_datacube(simspin_file = ss_gadget,
#' telescope = telescope(type="SAMI"),
#' observing_strategy = observing_strategy(),
#' method = "velocity")
#' plot_flux(cube$observed_images$flux_image)
plot_flux <- function(flux_image, fig = c(0,1,0,1), new=F,
units = expression("Flux, CGS"), main="",
radii = NA, na.color = "white", zlim = NA, legend = T,
titleshift = -4, labN=5, radii_col="red", ...){
Flux = flux_image
im_dim = dim(Flux)/2
flux_val = c(min(Flux, na.rm = T), max(Flux, na.rm = T))
if (all(flux_val == 0)){
stop("Image contains only '0'. No image can be produced in this case. \n
Please check your build_datacube function and try again.")
}
flux_map_cols = cmocean::cmocean("thermal", version = "2.0", start = .1, end=1)(50)
par(pty="s", fig=fig, xpd=FALSE, ps=12, cex=1, new=new); options(scipen = 1)
.image_nan(z = Flux, zlim = if(is.na(zlim[1])){flux_val}else{zlim}, col = flux_map_cols, na.color = na.color, xaxt="n",
yaxt="n", ann=FALSE, magmap=FALSE, family="mono", font=1, main = main, ...)
if (!is.na(radii[1])){
plotrix::draw.ellipse(im_dim[1], im_dim[2], radii$a, radii$b, radii$ang, border = radii_col, density = NULL, lwd=2)
}
if (legend){
.magcolbar(position = "bottom", range = if(is.na(zlim[1])){flux_val}else{zlim}, scale = c(1, 1/20),
col = flux_map_cols, orient = "h", inset = -1/20, labN=labN, title = units,
titleshift = titleshift)
}
}
#' Plotting pretty mass images
#'
#' A function to produce a plot of the mass image produced by
#' \code{build_datacube()} with associated colour bar and labels.
#'
#' @param mass_image Numeric array containing the mass image
#' @param fig Numeric array of length 4 describing the boundary of the image
#' @param new Boolean. Should the image be added to the existing plot? Default
#' is FALSE.
#' @param units String describing the units of the values contained
#' in the image.
#' @param main Image title, default "".
#' @param radii list - containing a, b, and ang (if wishing to plot half-mass
#' radii ellipse).
#' @param na.color String. Colour given to NA values in the image.
#' @param zlim Numeric array of length 2. Describing the numeric range of
#' colours in the image. Default is NA, in which the range will be described by
#' the minimum and maximum values in the image.
#' @param legend Boolean to determine if the colour bar axis should be printed
#' at the bottom of the image. Default is T.
#' @param titleshift Numeric. Describes the distance between the colour bar and
#' the units. Default is -4.
#' @param labN Numeric. Describes the minimum number of numeric labels added to
#' the colour bar. Default is 5.
#' @param radii_col String. Describing the colour of the ellipse drawn if
#' \code{radii} list is specified. Default is "red".
#' @param ... Further variables passed to magimage. See
#' \code{\link[magicaxis]{magimage}} for further details.
#' @return Returns an image to the plotting window of the input
#' \code{build_datacube} image.
#' @examples
#' ss_pd_gadget = system.file("extdata", "SimSpin_example_Gadget",
#' package = "SimSpin")
#' ss_gadget = make_simspin_file(ss_pd_gadget, write_to_file = FALSE)
#' cube = build_datacube(simspin_file = ss_gadget,
#' telescope = telescope(type="SAMI"),
#' observing_strategy = observing_strategy(),
#' method = "velocity", mass_flag=TRUE)
#' plot_mass(cube$raw_images$mass_image)
plot_mass <- function(mass_image, fig = c(0,1,0,1), new=F,
units = expression("Mass, M"["sol"]), main="",
radii = NA, na.color = "white", zlim = NA, legend = T,
titleshift = -4, labN=5, radii_col="red", ...){
Mass = mass_image
im_dim = dim(Mass)/2
mass_val = c(min(Mass, na.rm = T), max(Mass, na.rm = T))
if (all(mass_val == 0)){
stop("Image contains only '0'. No image can be produced in this case. \n
Please check your build_datacube function and try again.")
}
mass_map_cols = cmocean::cmocean("thermal", version = "2.0", start = .1, end=1)(50)
par(pty="s", fig=fig, xpd=FALSE, ps=12, cex=1, new=new); options(scipen = 1)
.image_nan(z = Mass, zlim = if(is.na(zlim[1])){mass_val}else{zlim}, col = mass_map_cols, na.color = na.color, xaxt="n",
yaxt="n", ann=FALSE, magmap=FALSE, family="mono", font=1, main = main, ...)
if (!is.na(radii[1])){
plotrix::draw.ellipse(im_dim[1], im_dim[2], radii$a, radii$b, radii$ang, border = radii_col, density = NULL, lwd=2)
}
if (legend){
.magcolbar(position = "bottom", range = if(is.na(zlim[1])){mass_val}else{zlim}, scale = c(1, 1/20),
col = mass_map_cols, orient = "h", inset = -1/20, labN=labN, title = units,
titleshift = titleshift)
}
}
#' Plotting pretty velocity images
#'
#' A function to produce a plot of the velocity image produced by
#' \code{build_datacube()} with associated colour bar and labels.
#'
#' @param velocity_image Numeric array containing the velocity image
#' @param fig Numeric array of length 4 describing the boundary of the image
#' @param new Boolean. Should the image be added to the existing plot? Default
#' is FALSE.
#' @param units String describing the units of the values contained
#' in the image.
#' @param main Image title, default "".
#' @param radii list - containing a, b, and ang (if wishing to plot half-mass
#' radii ellipse).
#' @param na.color String. Colour given to NA values in the image.
#' @param zlim Numeric array of length 2. Describing the numeric range of
#' colours in the image. Default is NA, in which the range will be described by
#' the minimum and maximum values in the image.
#' @param legend Boolean to determine if the colour bar axis should be printed
#' at the bottom of the image. Default is T.
#' @param titleshift Numeric. Describes the distance between the colour bar and
#' the units. Default is -4.
#' @param labN Numeric. Describes the minimum number of numeric labels added to
#' the colour bar. Default is 5.
#' @param radii_col String. Describing the colour of the ellipse drawn if
#' \code{radii} list is specified. Default is "red".
#' @param ... Further variables passed to magimage. See
#' \code{\link[magicaxis]{magimage}} for further details.
#' @return Returns an image to the plotting window of the input
#' \code{build_datacube} image.
#' @examples
#' ss_pd_gadget = system.file("extdata", "SimSpin_example_Gadget",
#' package = "SimSpin")
#' ss_gadget = make_simspin_file(ss_pd_gadget, write_to_file = FALSE)
#' cube = build_datacube(simspin_file = ss_gadget,
#' telescope = telescope(type="SAMI"),
#' observing_strategy = observing_strategy(),
#' method = "velocity")
#' plot_velocity(cube$observed_images$velocity_image)
plot_velocity <- function(velocity_image, fig = c(0,1,0,1), new=F,
units = expression("velocity"[LOS] * ", km s"^{-1}), main="",
radii = NA, na.color = "white", zlim = NA, legend = T,
titleshift = -4, labN=5, radii_col="red", ...){
V = velocity_image
im_dim = dim(V)/2
vel_val = max(c(abs(min(V, na.rm = T)), abs(max(V, na.rm = T))))
if (all(vel_val == 0)){
stop("Image contains only '0'. No image can be produced in this case. \n
Please check your build_datacube function and try again.")
}
velo_map_cols = cmocean::cmocean("balance", version = "2.0", start = .1, end=.9)(100)
par(pty="s", fig=fig, xpd=FALSE, ps=12, cex=1, new=new); options(scipen = 1)
.image_nan(z = V, zlim = if(is.na(zlim[1])){c(-vel_val,vel_val)}else{zlim}, col = velo_map_cols, na.color = na.color, xaxt="n",
yaxt="n", ann=FALSE, magmap=FALSE, family="mono", font=1, main = main, ...)
if (!is.na(radii[1])){
plotrix::draw.ellipse(im_dim[1], im_dim[2], radii$a, radii$b, radii$ang, border = radii_col, density = NULL, lwd=2)
}
if (legend){
.magcolbar(position = "bottom", range = if(is.na(zlim[1])){c(-vel_val,vel_val)}else{zlim}, scale = c(1, 1/20),
col = velo_map_cols, orient = "h", inset = -1/20, labN=labN, title = units,
titleshift = titleshift)
}
}
#' Plotting pretty dispersion images
#'
#' A function to produce a plot of the dispersion image produced by
#' \code{build_datacube()} with associated colour bar and labels.
#'
#' @param dispersion_image Numeric array containing the dispersion image
#' @param fig Numeric array of length 4 describing the boundary of the image
#' @param new Boolean. Should the image be added to the existing plot? Default
#' is FALSE.
#' @param units String describing the units of the values contained
#' in the image.
#' @param main Image title, default "".
#' @param radii list - containing a, b, and ang (if wishing to plot half-mass
#' radii ellipse).
#' @param na.color String. Colour given to NA values in the image.
#' @param zlim Numeric array of length 2. Describing the numeric range of
#' colours in the image. Default is NA, in which the range will be described by
#' the minimum and maximum values in the image.
#' @param legend Boolean to determine if the colour bar axis should be printed
#' at the bottom of the image. Default is T.
#' @param titleshift Numeric. Describes the distance between the colour bar and
#' the units. Default is -4.
#' @param labN Numeric. Describes the minimum number of numeric labels added to
#' the colour bar. Default is 5.
#' @param radii_col String. Describing the colour of the ellipse drawn if
#' \code{radii} list is specified. Default is "red".
#' @param ... Further variables passed to magimage. See
#' \code{\link[magicaxis]{magimage}} for further details.
#' @return Returns an image to the plotting window of the input
#' \code{build_datacube} image.
#' @examples
#' ss_pd_gadget = system.file("extdata", "SimSpin_example_Gadget",
#' package = "SimSpin")
#' ss_gadget = make_simspin_file(ss_pd_gadget, write_to_file = FALSE)
#' cube = build_datacube(simspin_file = ss_gadget,
#' telescope = telescope(type="SAMI"),
#' observing_strategy = observing_strategy(),
#' method = "velocity")
#' plot_dispersion(cube$observed_images$dispersion_image)
plot_dispersion <- function(dispersion_image, fig = c(0,1,0,1), new=F,
units = expression("dispersion"[LOS] * ", km s"^{-1}), main="",
radii = NA, na.color = "white", zlim = NA, legend=T,
titleshift = -4, labN=5, radii_col="red", ...){
disp_map = dispersion_image
im_dim = dim(disp_map)/2
disp_val = c(floor(min(disp_map, na.rm=T)), max(disp_map, na.rm=T))
if (all(disp_val == 0)){
stop("Image contains only '0'. No image can be produced in this case. \n
Please check your build_datacube function and try again.")
}
disp_map_cols = cmocean::cmocean("solar", version = "2.0", start = .1, end=.9)(100)
par(pty="s", fig=fig, xpd=FALSE, ps=12, cex=1, new=new); options(scipen = 1)
.image_nan(z = disp_map, zlim = if(is.na(zlim[1])){disp_val}else{zlim},
col = disp_map_cols, na.color = na.color, xaxt="n",
yaxt="n", ann=FALSE, magmap=FALSE, family="mono", font=1, main=main, ...)
if (!is.na(radii[1])){
plotrix::draw.ellipse(im_dim[1], im_dim[2], radii$a, radii$b, radii$ang, border = radii_col, density = NULL, lwd=2)
}
if (legend){
.magcolbar(position = "bottom", range = if(is.na(zlim[1])){disp_val}else{zlim}, scale = c(1, 1/20),
col = disp_map_cols, orient = "h", inset = -1/20, labN=labN, title = units,
titleshift = titleshift)
}
}
#' Plotting pretty higher-order kinematic (h3) images
#'
#' A function to produce a plot of the h3 image produced by
#' \code{build_datacube()} with associated colour bar and labels.
#'
#' @param h3_image Numeric array containing the h3 image
#' @param fig Numeric array of length 4 describing the boundary of the image
#' @param new Boolean. Should the image be added to the existing plot? Default
#' is FALSE.
#' @param units String describing the units of the values contained
#' in the image.
#' @param main Image title, default "".
#' @param radii list - containing a, b, and ang (if wishing to plot half-mass
#' radii ellipse).
#' @param na.color String. Colour given to NA values in the image.
#' @param zlim Numeric array of length 2. Describing the numeric range of
#' colours in the image. Default is NA, in which the range will be described by
#' the minimum and maximum values in the image.
#' @param legend Boolean to determine if the colour bar axis should be printed
#' at the bottom of the image. Default is T.
#' @param titleshift Numeric. Describes the distance between the colour bar and
#' the units. Default is -4.
#' @param labN Numeric. Describes the minimum number of numeric labels added to
#' the colour bar. Default is 5.
#' @param radii_col String. Describing the colour of the ellipse drawn if
#' \code{radii} list is specified. Default is "red".
#' @param ... Further variables passed to magimage. See
#' \code{\link[magicaxis]{magimage}} for further details.
#' @return Returns an image to the plotting window of the input
#' \code{build_datacube} image.
#' @examples
#' ss_pd_gadget = system.file("extdata", "SimSpin_example_Gadget",
#' package = "SimSpin")
#' ss_gadget = make_simspin_file(ss_pd_gadget, write_to_file = FALSE)
#' cube = build_datacube(simspin_file = ss_gadget,
#' telescope = telescope(type="SAMI"),
#' observing_strategy = observing_strategy(),
#' method = "velocity")
#' plot_h3(cube$observed_images$h3_image)
plot_h3 <- function(h3_image, fig = c(0,1,0,1), new=F,
units = expression("h"[3]), main="",
radii = NA, na.color = "white", zlim = NA, legend = T,
titleshift = -4, labN=5, radii_col="red", ...){
V = h3_image
im_dim = dim(V)/2
vel_val = max(c(abs(min(V, na.rm = T)), abs(max(V, na.rm = T))))
if (all(vel_val == 0)){
stop("Image contains only '0'. No image can be produced in this case. \n
Please check your build_datacube function and try again.")
}
velo_map_cols = cmocean::cmocean("balance", version = "2.0", start = .1, end=.9)(100)
par(pty="s", fig=fig, xpd=FALSE, ps=12, cex=1, new=new); options(scipen = 1)
.image_nan(z = V, zlim = if(is.na(zlim[1])){c(-vel_val,vel_val)}else{zlim}, col = velo_map_cols, na.color = na.color, xaxt="n",
yaxt="n", ann=FALSE, magmap=FALSE, family="mono", font=1, main = main, ...)
if (!is.na(radii[1])){
plotrix::draw.ellipse(im_dim[1], im_dim[2], radii$a, radii$b, radii$ang, border = radii_col, density = NULL, lwd=2)
}
if (legend){
.magcolbar(position = "bottom", range = if(is.na(zlim[1])){c(-vel_val,vel_val)}else{zlim}, scale = c(1, 1/20),
col = velo_map_cols, orient = "h", inset = -1/20, labN=labN, title = units,
titleshift = titleshift)
}
}
#' Plotting pretty higher-order kinematic (h4) images
#'
#' A function to produce a plot of the h4 image produced by
#' \code{build_datacube()} with associated colour bar and labels.
#'
#' @param h4_image Numeric array containing the h4 image
#' @param fig Numeric array of length 4 describing the boundary of the image
#' @param new Boolean. Should the image be added to the existing plot? Default
#' is FALSE.
#' @param units String describing the units of the values contained
#' in the image.
#' @param main Image title, default "".
#' @param radii list - containing a, b, and ang (if wishing to plot half-mass
#' radii ellipse).
#' @param na.color String. Colour given to NA values in the image.
#' @param zlim Numeric array of length 2. Describing the numeric range of
#' colours in the image. Default is NA, in which the range will be described by
#' the minimum and maximum values in the image.
#' @param legend Boolean to determine if the colour bar axis should be printed
#' at the bottom of the image. Default is T.
#' @param titleshift Numeric. Describes the distance between the colour bar and
#' the units. Default is -4.
#' @param labN Numeric. Describes the minimum number of numeric labels added to
#' the colour bar. Default is 5.
#' @param radii_col String. Describing the colour of the ellipse drawn if
#' \code{radii} list is specified. Default is "red".
#' @param ... Further variables passed to magimage. See
#' \code{\link[magicaxis]{magimage}} for further details.
#' @return Returns an image to the plotting window of the input
#' \code{build_datacube} image.
#' @examples
#' ss_pd_gadget = system.file("extdata", "SimSpin_example_Gadget",
#' package = "SimSpin")
#' ss_gadget = make_simspin_file(ss_pd_gadget, write_to_file = FALSE)
#' cube = build_datacube(simspin_file = ss_gadget,
#' telescope = telescope(type="SAMI"),
#' observing_strategy = observing_strategy(),
#' method = "velocity")
#' plot_h4(cube$observed_images$h4_image)
plot_h4 <- function(h4_image, fig = c(0,1,0,1), new=F,
units = expression("h"[4]), main="",
radii = NA, na.color = "white", zlim = NA, legend = T,
titleshift = -4, labN=5, radii_col="red", ...){
V = h4_image
im_dim = dim(V)/2
vel_val = max(c(abs(min(V, na.rm = T)), abs(max(V, na.rm = T))))
if (all(vel_val == 0)){
stop("Image contains only '0'. No image can be produced in this case. \n
Please check your build_datacube function and try again.")
}
velo_map_cols = cmocean::cmocean("balance", version = "2.0", start = .1, end=.9)(100)
par(pty="s", fig=fig, xpd=FALSE, ps=12, cex=1, new=new); options(scipen = 1)
.image_nan(z = V, zlim = if(is.na(zlim[1])){c(-vel_val,vel_val)}else{zlim}, col = velo_map_cols, na.color = na.color, xaxt="n",
yaxt="n", ann=FALSE, magmap=FALSE, family="mono", font=1, main = main, ...)
if (!is.na(radii[1])){
plotrix::draw.ellipse(im_dim[1], im_dim[2], radii$a, radii$b, radii$ang, border = radii_col, density = NULL, lwd=2)
}
if (legend){
.magcolbar(position = "bottom", range = if(is.na(zlim[1])){c(-vel_val,vel_val)}else{zlim}, scale = c(1, 1/20),
col = velo_map_cols, orient = "h", inset = -1/20, labN=labN, title = units,
titleshift = titleshift)
}
}
#' Plotting pretty age images
#'
#' A function to produce a plot of the stellar age image produced by
#' \code{build_datacube()} with associated colour bar and labels.
#'
#' @param age_image Numeric array containing the age image
#' @param fig Numeric array of length 4 describing the boundary of the image
#' @param new Boolean. Should the image be added to the existing plot? Default
#' is FALSE.
#' @param units String describing the units of the values contained
#' in the image.
#' @param main Image title, default "".
#' @param radii list - containing a, b, and ang (if wishing to plot half-mass
#' radii ellipse).
#' @param na.color String. Colour given to NA values in the image.
#' @param zlim Numeric array of length 2. Describing the numeric range of
#' colours in the image. Default is NA, in which the range will be described by
#' the minimum and maximum values in the image.
#' @param legend Boolean to determine if the colour bar axis should be printed
#' at the bottom of the image. Default is T.
#' @param titleshift Numeric. Describes the distance between the colour bar and
#' the units. Default is -4.
#' @param labN Numeric. Describes the minimum number of numeric labels added to
#' the colour bar. Default is 5.
#' @param radii_col String. Describing the colour of the ellipse drawn if
#' \code{radii} list is specified. Default is "red".
#' @param ... Further variables passed to magimage. See
#' \code{\link[magicaxis]{magimage}} for further details.
#' @return Returns an image to the plotting window of the input
#' \code{build_datacube} image.
#' @examples
#' ss_pd_gadget = system.file("extdata", "SimSpin_example_Gadget",
#' package = "SimSpin")
#' ss_gadget = make_simspin_file(ss_pd_gadget, write_to_file = FALSE)
#' cube = build_datacube(simspin_file = ss_gadget,
#' telescope = telescope(type="SAMI"),
#' observing_strategy = observing_strategy(),
#' method = "velocity")
#' plot_age(cube$raw_images$age_image)
plot_age <- function(age_image, fig = c(0,1,0,1), new=F,
units = expression("Age, Gyr"), main="", radii = NA,
na.color = "white", zlim = NA, legend=T,
titleshift = -4, labN=5, radii_col="red", ...){
age_map = age_image
im_dim = dim(age_map)/2
age_val = c(floor(min(age_map, na.rm=T)/2), max(age_map, na.rm=T))
if (all(age_val == 0)){
stop("Image contains only '0'. No image can be produced in this case. \n
Please check your build_datacube function and try again.")
}
age_map_cols = cmocean::cmocean("deep", version = "2.0", start = .1, end=1)(50)
par(pty="s", fig=fig, xpd=FALSE, ps=12, cex=1, new=new); options(scipen = 1)
.image_nan(z = age_map, zlim = if(is.na(zlim[1])){age_val}else{zlim}, col = age_map_cols, na.color = na.color, xaxt="n",
yaxt="n", ann=FALSE, magmap=FALSE, family="mono", font=1, main=main, ...)
if (!is.na(radii[1])){
plotrix::draw.ellipse(im_dim[1], im_dim[2], radii$a, radii$b, radii$ang, border = radii_col, density = NULL, lwd=2)
}
if (legend){
.magcolbar(position = "bottom", range = if(is.na(zlim[1])){age_val}else{zlim}, scale = c(1, 1/20),
col = age_map_cols, orient = "h", inset = -1/20, labN=labN, title = units,
titleshift = titleshift)
}
}
#' Plotting pretty metallicity images
#'
#' A function to produce a plot of the stellar metallicity image produced by
#' \code{build_datacube()} with associated colour bar and labels.
#'
#' @param metallicity_image Numeric array containing the metallicity image.
#' @param fig Numeric array of length 4 describing the boundary of the image
#' @param new Boolean. Should the image be added to the existing plot? Default
#' is FALSE.
#' @param units String describing the units of the values contained
#' in the image.
#' @param main Image title, default "".
#' @param radii list - containing a, b, and ang (if wishing to plot half-mass
#' radii ellipse).
#' @param na.color String. Colour given to NA values in the image.
#' @param zlim Numeric array of length 2. Describing the numeric range of
#' colours in the image. Default is NA, in which the range will be described by
#' the minimum and maximum values in the image.
#' @param legend Boolean to determine if the colour bar axis should be printed
#' at the bottom of the image. Default is T.
#' @param titleshift Numeric. Describes the distance between the colour bar and
#' the units. Default is -4.
#' @param labN Numeric. Describes the minimum number of numeric labels added to
#' the colour bar. Default is 5.
#' @param radii_col String. Describing the colour of the ellipse drawn if
#' \code{radii} list is specified. Default is "red".
#' @param ... Further variables passed to magimage. See
#' \code{\link[magicaxis]{magimage}} for further details.
#' @return Returns an image to the plotting window of the input
#' \code{build_datacube} image.
#' @examples
#' ss_pd_gadget = system.file("extdata", "SimSpin_example_Gadget",
#' package = "SimSpin")
#' ss_gadget = make_simspin_file(ss_pd_gadget, write_to_file = FALSE)
#' cube = build_datacube(simspin_file = ss_gadget,
#' telescope = telescope(type="SAMI"),
#' observing_strategy = observing_strategy(),
#' method = "velocity")
#' plot_metallicity(cube$raw_images$metallicity_image)
plot_metallicity <- function(metallicity_image, fig = c(0,1,0,1), new=F,
units = expression("log10(Z/Z"[solar]*")"), main="",
na.color = "white", zlim = NA, legend=T, radii = NA,
titleshift = -4, labN=5, radii_col="red", ...){
met_map = metallicity_image
im_dim = dim(met_map)/2
met_val = c(floor(min(met_map, na.rm=T)/2), max(met_map, na.rm=T))
if (all(met_val == 0)){
stop("Image contains only '0'. No image can be produced in this case. \n
Please check your build_datacube function and try again.")
}
met_map_cols = cmocean::cmocean("dense", version = "2.0", start = .1, end=1)(50)
par(pty="s", fig=fig, xpd=FALSE, ps=12, cex=1, new=new); options(scipen = 1)
.image_nan(z = met_map, zlim = if(is.na(zlim[1])){met_val}else{zlim},
col = met_map_cols, na.color = na.color, xaxt="n",
yaxt="n", ann=FALSE, magmap=FALSE, family="mono", font=1, main=main, ...)
if (!is.na(radii[1])){
plotrix::draw.ellipse(im_dim[1], im_dim[2], radii$a, radii$b, radii$ang, border = radii_col, density = NULL, lwd=2)
}
if (legend){
.magcolbar(position = "bottom", range = if(is.na(zlim[1])){met_val}else{zlim}, scale = c(1, 1/20),
col = met_map_cols, orient = "h", inset = -1/20, labN=labN, title = units,
titleshift = titleshift)
}
}
#' Plotting pretty particle number images
#'
#' A function to produce a plot of the particle per pixel image produced by
#' \code{build_datacube()} with associated colour bar and labels.
#'
#' @param particle_image Numeric array containing the particle per pixel image
#' @param fig Numeric array of length 4 describing the boundary of the image
#' @param new Boolean. Should the image be added to the existing plot? Default
#' is FALSE.
#' @param units String describing the units of the values contained
#' in the image.
#' @param main Image title, default "".
#' @param radii list - containing a, b, and ang (if wishing to plot half-mass
#' radii ellipse).
#' @param na.color String. Colour given to NA values in the image.
#' @param zlim Numeric array of length 2. Describing the numeric range of
#' colours in the image. Default is NA, in which the range will be described by
#' the minimum and maximum values in the image.
#' @param legend Boolean to determine if the colour bar axis should be printed
#' at the bottom of the image. Default is T.
#' @param titleshift Numeric. Describes the distance between the colour bar and
#' the units. Default is -4.
#' @param labN Numeric. Describes the minimum number of numeric labels added to
#' the colour bar. Default is 5.
#' @param radii_col String. Describing the colour of the ellipse drawn if
#' \code{radii} list is specified. Default is "red".
#' @param ... Further variables passed to magimage. See
#' \code{\link[magicaxis]{magimage}} for further details.
#' @return Returns an image to the plotting window of the input
#' \code{build_datacube} image.
#' @examples
#' ss_pd_gadget = system.file("extdata", "SimSpin_example_Gadget",
#' package = "SimSpin")
#' ss_gadget = make_simspin_file(ss_pd_gadget, write_to_file = FALSE)
#' cube = build_datacube(simspin_file = ss_gadget,
#' telescope = telescope(type="SAMI"),
#' observing_strategy = observing_strategy(),
#' method = "velocity")
#' plot_particles(cube$raw_images$particle_image)
plot_particles <- function(particle_image, fig = c(0,1,0,1), new=F,
units = expression("Number of particles"), main="", radii = NA,
na.color = "white", zlim = NA, legend=T,
titleshift = -4, labN=5, radii_col="red", ...){
part_map = particle_image
im_dim = dim(part_map)/2
part_val = c(floor(min(part_map, na.rm=T)/2), max(part_map, na.rm=T))
if (all(part_val == 0)){
stop("Image contains only '0'. No image can be produced in this case. \n
Please check your build_datacube function and try again.")
}
part_map_cols = cmocean::cmocean("deep", version = "2.0", start = .1, end=1)(50)
par(pty="s", fig=fig, xpd=FALSE, ps=12, cex=1, new=new); options(scipen = 1)
.image_nan(z = part_map, zlim = if(is.na(zlim[1])){part_val}else{zlim}, col = part_map_cols, na.color = na.color, xaxt="n",
yaxt="n", ann=FALSE, magmap=FALSE, family="mono", font=1, main=main, ...)
if (!is.na(radii[1])){
plotrix::draw.ellipse(im_dim[1], im_dim[2], radii$a, radii$b, radii$ang, border = radii_col, density = NULL, lwd=2)
}
if (legend){
.magcolbar(position = "bottom", range = if(is.na(zlim[1])){part_val}else{zlim}, scale = c(1, 1/20),
col = part_map_cols, orient = "h", inset = -1/20, labN=labN, title = units,
titleshift = titleshift)
}
}
#' Plotting pretty gas SFR images
#'
#' A function to produce a plot of the gas star formation rate image produced by
#' \code{build_datacube()} with associated colour bar and labels.
#'
#' @param SFR_image Numeric array containing the particle per pixel image
#' @param fig Numeric array of length 4 describing the boundary of the image
#' @param new Boolean. Should the image be added to the existing plot? Default
#' is FALSE.
#' @param units String describing the units of the values contained
#' in the image.
#' @param main Image title, default "".
#' @param radii list - containing a, b, and ang (if wishing to plot half-mass
#' radii ellipse).
#' @param na.color String. Colour given to NA values in the image.
#' @param zlim Numeric array of length 2. Describing the numeric range of
#' colours in the image. Default is NA, in which the range will be described by
#' the minimum and maximum values in the image.
#' @param legend Boolean to determine if the colour bar axis should be printed
#' at the bottom of the image. Default is T.
#' @param titleshift Numeric. Describes the distance between the colour bar and
#' the units. Default is -4.
#' @param labN Numeric. Describes the minimum number of numeric labels added to
#' the colour bar. Default is 5.
#' @param radii_col String. Describing the colour of the ellipse drawn if
#' \code{radii} list is specified. Default is "red".
#' @param ... Further variables passed to magimage. See
#' \code{\link[magicaxis]{magimage}} for further details.
#' @return Returns an image to the plotting window of the input
#' \code{build_datacube} image.
#' @examples
#' ss_pd_eagle = system.file("extdata", "SimSpin_example_EAGLE.hdf5",
#' package = "SimSpin")
#' ss_eagle = make_simspin_file(ss_pd_eagle, write_to_file = FALSE)
#' cube = build_datacube(simspin_file = ss_eagle,
#' telescope = telescope(type="SAMI"),
#' observing_strategy = observing_strategy(),
#' method = "gas")
#' plot_SFR(cube$raw_images$SFR_image)
plot_SFR <- function(SFR_image, fig = c(0,1,0,1), new=F,
units = expression("SFR, M"["sol"]*"/yr"), main="", radii = NA,
na.color = "white", zlim = NA, legend=T,
titleshift = -4, labN=5, radii_col="red",...){
part_map = SFR_image
im_dim = dim(part_map)/2
part_val = c(floor(min(part_map, na.rm=T)/2), max(part_map, na.rm=T))
if (all(part_val == 0)){
stop("Image contains only '0'. No image can be produced in this case. \n
Please check your build_datacube function and try again.")
}
part_map_cols = cmocean::cmocean("deep", version = "2.0", start = .1, end=1)(50)
par(pty="s", fig=fig, xpd=FALSE, ps=12, cex=1, new=new); options(scipen = 1)
.image_nan(z = part_map, zlim = if(is.na(zlim[1])){part_val}else{zlim}, col = part_map_cols, na.color = na.color, xaxt="n",
yaxt="n", ann=FALSE, magmap=FALSE, family="mono", font=1, main=main, ...)
if (!is.na(radii[1])){
plotrix::draw.ellipse(im_dim[1], im_dim[2], radii$a, radii$b, radii$ang, border = radii_col, density = NULL, lwd=2)
}
if (legend){
.magcolbar(position = "bottom", range = if(is.na(zlim[1])){part_val}else{zlim}, scale = c(1, 1/20),
col = part_map_cols, orient = "h", inset = -1/20, labN=labN, title = units,
titleshift = titleshift)
}
}
#' Plotting pretty log10(O/H) images
#'
#' A function to produce a plot of the gas log10(O/H) image produced by
#' \code{build_datacube()} with associated colour bar and labels.
#'
#' @param OH_image Numeric array containing the metallicity image.
#' @param fig Numeric array of length 4 describing the boundary of the image
#' @param new Boolean. Should the image be added to the existing plot? Default
#' is FALSE.
#' @param units String describing the units of the values contained
#' in the image.
#' @param main Image title, default "".
#' @param radii list - containing a, b, and ang (if wishing to plot half-mass
#' radii ellipse).
#' @param na.color String. Colour given to NA values in the image.
#' @param zlim Numeric array of length 2. Describing the numeric range of
#' colours in the image. Default is NA, in which the range will be described by
#' the minimum and maximum values in the image.
#' @param legend Boolean to determine if the colour bar axis should be printed
#' at the bottom of the image. Default is T.
#' @param titleshift Numeric. Describes the distance between the colour bar and
#' the units. Default is -4.
#' @param labN Numeric. Describes the minimum number of numeric labels added to
#' the colour bar. Default is 5.
#' @param radii_col String. Describing the colour of the ellipse drawn if
#' \code{radii} list is specified. Default is "red".
#' @param ... Further variables passed to magimage. See
#' \code{\link[magicaxis]{magimage}} for further details.
#' @return Returns an image to the plotting window of the input
#' \code{build_datacube} image.
#' @examples
#' ss_pd_eagle = system.file("extdata", "SimSpin_example_EAGLE.hdf5",
#' package = "SimSpin")
#' ss_eagle = make_simspin_file(ss_pd_eagle, write_to_file = FALSE)
#' cube = build_datacube(simspin_file = ss_eagle,
#' telescope = telescope(type="SAMI"),
#' observing_strategy = observing_strategy(),
#' method = "gas")
#' plot_OH(cube$raw_images$OH_image)
plot_OH <- function(OH_image, fig = c(0,1,0,1), new=F,
units = expression("log10(O/H) + 12"), main="",
na.color = "white", zlim = NA, legend=T, radii = NA,
titleshift = -4, labN=5, radii_col="red", ...){
met_map = OH_image
im_dim = dim(met_map)/2
met_val = c(floor(min(met_map, na.rm=T)/2), max(met_map, na.rm=T))
if (all(met_val == 0)){
stop("Image contains only '0'. No image can be produced in this case. \n
Please check your build_datacube function and try again.")
}
met_map_cols = cmocean::cmocean("dense", version = "2.0", start = .1, end=1)(50)
par(pty="s", fig=fig, xpd=FALSE, ps=12, cex=1, new=new); options(scipen = 1)
.image_nan(z = met_map, zlim = if(is.na(zlim[1])){met_val}else{zlim},
col = met_map_cols, na.color = na.color, xaxt="n",
yaxt="n", ann=FALSE, magmap=FALSE, family="mono", font=1, main=main, ...)
if (!is.na(radii[1])){
plotrix::draw.ellipse(im_dim[1], im_dim[2], radii$a, radii$b, radii$ang, border = radii_col, density = NULL, lwd=2)
}
if (legend){
.magcolbar(position = "bottom", range = if(is.na(zlim[1])){met_val}else{zlim}, scale = c(1, 1/20),
col = met_map_cols, orient = "h", inset = -1/20, labN=labN, title = units,
titleshift = titleshift)
}
}
#' Plotting pretty Voronoi bin images
#'
#' A function to produce a plot of the Voronoi bins produced by
#' \code{build_datacube()} with associated colour bar and labels.
#'
#' @param voronoi_bins Numeric array containing the metallicity image.
#' @param fig Numeric array of length 4 describing the boundary of the image
#' @param new Boolean. Should the image be added to the existing plot? Default
#' is FALSE.
#' @param main Image title, default "".
#' @param na.color String. Colour given to NA values in the image.
#' @param zlim Numeric array of length 2. Describing the numeric range of
#' colours in the image. Default is NA, in which the range will be described by
#' the minimum and maximum values in the image.
#' @param ... Further variables passed to magimage. See
#' \code{\link[magicaxis]{magimage}} for further details.
#' @return Returns an image to the plotting window of the input
#' \code{build_datacube} image.
#' @examples
#' ss_pd_eagle = system.file("extdata", "SimSpin_example_EAGLE.hdf5",
#' package = "SimSpin")
#' ss_eagle = make_simspin_file(ss_pd_eagle, write_to_file = FALSE)
#' cube = build_datacube(simspin_file = ss_eagle,
#' telescope = telescope(type="SAMI"),
#' observing_strategy = observing_strategy(),
#' method = "velocity", voronoi_bin = TRUE)
#' plot_voronoi(cube$raw_images$voronoi_bins)
plot_voronoi <- function(voronoi_bins, fig = c(0,1,0,1), new=F,
main="", na.color = "white", zlim = NA,
...){
bin_map = voronoi_bins
im_dim = dim(bin_map)/2
bin_val = c(min(bin_map, na.rm=T), max(bin_map, na.rm=T))
if (all(bin_val == 0)){
stop("Image contains only '0'. No image can be produced in this case. \n
Please check your build_datacube function and try again.")
}
bin_map_cols = cmocean::cmocean("phase", version = "2.0", start = .1, end=1)(max(bin_map, na.rm=T))
par(pty="s", fig=fig, xpd=FALSE, ps=12, cex=1, new=new); options(scipen = 1)
.image_nan(z = bin_map, zlim = if(is.na(zlim[1])){bin_val}else{zlim},
col = bin_map_cols, na.color = na.color, xaxt="n",
yaxt="n", ann=FALSE, magmap=FALSE, family="mono", font=1, main=main, ...)
}
.image_nan <- function(z, zlim, col, na.color='gray', ...){
# Function for plotting an image with NAs as a set colour
# z :==: array corresponding to the image to be plotted
# zlim :==: colour range associated with the image for
# the colour palette
# col :==: the colour palette to be used for the image
# na.color :==: string describing the color used for NA
zstep <- (zlim[2] - zlim[1]) / length(col); # step in the color palette
newz.na <- zlim[2] + zstep # new z for NA
z[which(is.na(z>zlim[2]))] <- newz.na # same for newz.na
zlim[2] <- zlim[2] + zstep # extend top limit to include the new value na
col <- c(col, na.color) # we construct the new color range by including: na.color
magicaxis::magimage(x=z, zlim=zlim, col=col, ...) # we finally call image(...)
}
.magcolbar <- # function modified from magicaxis to generate colour bars
function(position='topright',range=c(0,1),orient='v',log=FALSE,col=hcl.colors(21),scale=c(1/4,1/20), inset=1/40,labN=5,title='',titleshift=0,centrealign='rb',clip='',cex=1,...){
usercoord=par()$usr
xlogcheck=FALSE;ylogcheck=FALSE
xlo=usercoord[1];xhi=usercoord[2];ylo=usercoord[3];yhi=usercoord[4]
xdiff=xhi-xlo;ydiff=yhi-ylo
if(orient=='h'){
xl=xlo+xdiff/2-xdiff*scale[1]/2
yb=ylo+ydiff/2-ydiff*scale[2]/2
xr=xlo+xdiff/2+xdiff*scale[1]/2
yt=ylo+ydiff/2+ydiff*scale[2]/2
align=centrealign
if(length(grep('bottom',position))>0){aligntext='lt'; yb=ylo+ydiff*inset;yt=ylo+ydiff*inset+ydiff*scale[2]}
}
rangetemp=range
legend=magicaxis::maglab(rangetemp,labN,log=log,trim=F)
roughNscale=(max(legend$labat)-min(legend$labat))/(rangetemp[2]-rangetemp[1])
colremap=magicaxis::magmap(data=seq(min(legend$labat),max(legend$labat),length=length(col)*roughNscale),locut=rangetemp[1],hicut=rangetemp[2],type='num',range=c(1,length(col)),clip=clip)$map
col=col[round(colremap,digits=0)]
if(orient=='h'){plotrix::color.legend(xl,yb,xr,yt,legend=legend$exp,rect.col=col,cex=cex,align=align,gradient='x',...)}
if(orient=='h' & aligntext=='lt'){text((xl+xr)/2,yt+(titleshift)*ydiff/20, labels=title,adj=c(0.5,0.5),srt=0,cex=cex, xpd=NA)}
par(xlog=xlogcheck)
par(ylog=ylogcheck)
par(usr=usercoord)
}
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Defines functions .image_nan plot_voronoi plot_OH plot_SFR plot_particles plot_metallicity plot_age plot_h4 plot_h3 plot_dispersion plot_velocity plot_mass plot_flux
Documented in plot_age plot_dispersion plot_flux plot_h3 plot_h4 plot_mass plot_metallicity plot_OH plot_particles plot_SFR plot_velocity plot_voronoi
# Author: Kate Harborne
# Date: 25/10/2023
# Title: plot_images - a suite of function for plotting pretty images
#' Plotting pretty flux images
#'
#' A function to produce a plot of the flux image produced by
#' \code{build_datacube()} with associated colour bar and labels.
#'
#' @param flux_image Numeric array containing the flux image
#' @param fig Numeric array of length 4 describing the boundary of the image
#' @param new Boolean. Should the image be added to the existing plot? Default
#' is FALSE.
#' @param units String describing the units of the values contained
#' in the image.
#' @param main Image title, default "".
#' @param radii list - containing a, b, and ang (if wishing to plot half-mass
#' radii ellipse).
#' @param na.color String. Colour given to NA values in the image.
#' @param zlim Numeric array of length 2. Describing the numeric range of
#' colours in the image. Default is NA, in which the range will be described by
#' the minimum and maximum values in the image.
#' @param legend Boolean to determine if the colour bar axis should be printed
#' at the bottom of the image. Default is T.
#' @param titleshift Numeric. Describes the distance between the colour bar and
#' the units. Default is -4.
#' @param labN Numeric. Describes the minimum number of numeric labels added to
#' the colour bar. Default is 5.
#' @param radii_col String. Describing the colour of the ellipse drawn if
#' \code{radii} list is specified. Default is "red".
#' @param ... Further variables passed to magimage. See
#' \code{\link[magicaxis]{magimage}} for further details.
#' @return Returns an image to the plotting window of the input
#' \code{build_datacube} image.
#' @examples
#' ss_pd_gadget = system.file("extdata", "SimSpin_example_Gadget",
#' package = "SimSpin")
#' ss_gadget = make_simspin_file(ss_pd_gadget, write_to_file = FALSE)
#' cube = build_datacube(simspin_file = ss_gadget,
#' telescope = telescope(type="SAMI"),
#' observing_strategy = observing_strategy(),
#' method = "velocity")
#' plot_flux(cube$observed_images$flux_image)
plot_flux <- function(flux_image, fig = c(0,1,0,1), new=F,
units = expression("Flux, CGS"), main="",
radii = NA, na.color = "white", zlim = NA, legend = T,
titleshift = -4, labN=5, radii_col="red", ...){
Flux = flux_image
im_dim = dim(Flux)/2
flux_val = c(min(Flux, na.rm = T), max(Flux, na.rm = T))
if (all(flux_val == 0)){
stop("Image contains only '0'. No image can be produced in this case. \n
Please check your build_datacube function and try again.")
}
flux_map_cols = cmocean::cmocean("thermal", version = "2.0", start = .1, end=1)(50)
par(pty="s", fig=fig, xpd=FALSE, ps=12, cex=1, new=new); options(scipen = 1)
.image_nan(z = Flux, zlim = if(is.na(zlim[1])){flux_val}else{zlim}, col = flux_map_cols, na.color = na.color, xaxt="n",
yaxt="n", ann=FALSE, magmap=FALSE, family="mono", font=1, main = main, ...)
if (!is.na(radii[1])){
plotrix::draw.ellipse(im_dim[1], im_dim[2], radii$a, radii$b, radii$ang, border = radii_col, density = NULL, lwd=2)
}
if (legend){
.magcolbar(position = "bottom", range = if(is.na(zlim[1])){flux_val}else{zlim}, scale = c(1, 1/20),
col = flux_map_cols, orient = "h", inset = -1/20, labN=labN, title = units,
titleshift = titleshift)
}
}
#' Plotting pretty mass images
#'
#' A function to produce a plot of the mass image produced by
#' \code{build_datacube()} with associated colour bar and labels.
#'
#' @param mass_image Numeric array containing the mass image
#' @param fig Numeric array of length 4 describing the boundary of the image
#' @param new Boolean. Should the image be added to the existing plot? Default
#' is FALSE.
#' @param units String describing the units of the values contained
#' in the image.
#' @param main Image title, default "".
#' @param radii list - containing a, b, and ang (if wishing to plot half-mass
#' radii ellipse).
#' @param na.color String. Colour given to NA values in the image.
#' @param zlim Numeric array of length 2. Describing the numeric range of
#' colours in the image. Default is NA, in which the range will be described by
#' the minimum and maximum values in the image.
#' @param legend Boolean to determine if the colour bar axis should be printed
#' at the bottom of the image. Default is T.
#' @param titleshift Numeric. Describes the distance between the colour bar and
#' the units. Default is -4.
#' @param labN Numeric. Describes the minimum number of numeric labels added to
#' the colour bar. Default is 5.
#' @param radii_col String. Describing the colour of the ellipse drawn if
#' \code{radii} list is specified. Default is "red".
#' @param ... Further variables passed to magimage. See
#' \code{\link[magicaxis]{magimage}} for further details.
#' @return Returns an image to the plotting window of the input
#' \code{build_datacube} image.
#' @examples
#' ss_pd_gadget = system.file("extdata", "SimSpin_example_Gadget",
#' package = "SimSpin")
#' ss_gadget = make_simspin_file(ss_pd_gadget, write_to_file = FALSE)
#' cube = build_datacube(simspin_file = ss_gadget,
#' telescope = telescope(type="SAMI"),
#' observing_strategy = observing_strategy(),
#' method = "velocity", mass_flag=TRUE)
#' plot_mass(cube$raw_images$mass_image)
plot_mass <- function(mass_image, fig = c(0,1,0,1), new=F,
units = expression("Mass, M"["sol"]), main="",
radii = NA, na.color = "white", zlim = NA, legend = T,
titleshift = -4, labN=5, radii_col="red", ...){
Mass = mass_image
im_dim = dim(Mass)/2
mass_val = c(min(Mass, na.rm = T), max(Mass, na.rm = T))
if (all(mass_val == 0)){
stop("Image contains only '0'. No image can be produced in this case. \n
Please check your build_datacube function and try again.")
}
mass_map_cols = cmocean::cmocean("thermal", version = "2.0", start = .1, end=1)(50)
par(pty="s", fig=fig, xpd=FALSE, ps=12, cex=1, new=new); options(scipen = 1)
.image_nan(z = Mass, zlim = if(is.na(zlim[1])){mass_val}else{zlim}, col = mass_map_cols, na.color = na.color, xaxt="n",
yaxt="n", ann=FALSE, magmap=FALSE, family="mono", font=1, main = main, ...)
if (!is.na(radii[1])){
plotrix::draw.ellipse(im_dim[1], im_dim[2], radii$a, radii$b, radii$ang, border = radii_col, density = NULL, lwd=2)
}
if (legend){
.magcolbar(position = "bottom", range = if(is.na(zlim[1])){mass_val}else{zlim}, scale = c(1, 1/20),
col = mass_map_cols, orient = "h", inset = -1/20, labN=labN, title = units,
titleshift = titleshift)
}
}
#' Plotting pretty velocity images
#'
#' A function to produce a plot of the velocity image produced by
#' \code{build_datacube()} with associated colour bar and labels.
#'
#' @param velocity_image Numeric array containing the velocity image
#' @param fig Numeric array of length 4 describing the boundary of the image
#' @param new Boolean. Should the image be added to the existing plot? Default
#' is FALSE.
#' @param units String describing the units of the values contained
#' in the image.
#' @param main Image title, default "".
#' @param radii list - containing a, b, and ang (if wishing to plot half-mass
#' radii ellipse).
#' @param na.color String. Colour given to NA values in the image.
#' @param zlim Numeric array of length 2. Describing the numeric range of
#' colours in the image. Default is NA, in which the range will be described by
#' the minimum and maximum values in the image.
#' @param legend Boolean to determine if the colour bar axis should be printed
#' at the bottom of the image. Default is T.
#' @param titleshift Numeric. Describes the distance between the colour bar and
#' the units. Default is -4.
#' @param labN Numeric. Describes the minimum number of numeric labels added to
#' the colour bar. Default is 5.
#' @param radii_col String. Describing the colour of the ellipse drawn if
#' \code{radii} list is specified. Default is "red".
#' @param ... Further variables passed to magimage. See
#' \code{\link[magicaxis]{magimage}} for further details.
#' @return Returns an image to the plotting window of the input
#' \code{build_datacube} image.
#' @examples
#' ss_pd_gadget = system.file("extdata", "SimSpin_example_Gadget",
#' package = "SimSpin")
#' ss_gadget = make_simspin_file(ss_pd_gadget, write_to_file = FALSE)
#' cube = build_datacube(simspin_file = ss_gadget,
#' telescope = telescope(type="SAMI"),
#' observing_strategy = observing_strategy(),
#' method = "velocity")
#' plot_velocity(cube$observed_images$velocity_image)
plot_velocity <- function(velocity_image, fig = c(0,1,0,1), new=F,
units = expression("velocity"[LOS] * ", km s"^{-1}), main="",
radii = NA, na.color = "white", zlim = NA, legend = T,
titleshift = -4, labN=5, radii_col="red", ...){
V = velocity_image
im_dim = dim(V)/2
vel_val = max(c(abs(min(V, na.rm = T)), abs(max(V, na.rm = T))))
if (all(vel_val == 0)){
stop("Image contains only '0'. No image can be produced in this case. \n
Please check your build_datacube function and try again.")
}
velo_map_cols = cmocean::cmocean("balance", version = "2.0", start = .1, end=.9)(100)
par(pty="s", fig=fig, xpd=FALSE, ps=12, cex=1, new=new); options(scipen = 1)
.image_nan(z = V, zlim = if(is.na(zlim[1])){c(-vel_val,vel_val)}else{zlim}, col = velo_map_cols, na.color = na.color, xaxt="n",
yaxt="n", ann=FALSE, magmap=FALSE, family="mono", font=1, main = main, ...)
if (!is.na(radii[1])){
plotrix::draw.ellipse(im_dim[1], im_dim[2], radii$a, radii$b, radii$ang, border = radii_col, density = NULL, lwd=2)
}
if (legend){
.magcolbar(position = "bottom", range = if(is.na(zlim[1])){c(-vel_val,vel_val)}else{zlim}, scale = c(1, 1/20),
col = velo_map_cols, orient = "h", inset = -1/20, labN=labN, title = units,
titleshift = titleshift)
}
}
#' Plotting pretty dispersion images
#'
#' A function to produce a plot of the dispersion image produced by
#' \code{build_datacube()} with associated colour bar and labels.
#'
#' @param dispersion_image Numeric array containing the dispersion image
#' @param fig Numeric array of length 4 describing the boundary of the image
#' @param new Boolean. Should the image be added to the existing plot? Default
#' is FALSE.
#' @param units String describing the units of the values contained
#' in the image.
#' @param main Image title, default "".
#' @param radii list - containing a, b, and ang (if wishing to plot half-mass
#' radii ellipse).
#' @param na.color String. Colour given to NA values in the image.
#' @param zlim Numeric array of length 2. Describing the numeric range of
#' colours in the image. Default is NA, in which the range will be described by
#' the minimum and maximum values in the image.
#' @param legend Boolean to determine if the colour bar axis should be printed
#' at the bottom of the image. Default is T.
#' @param titleshift Numeric. Describes the distance between the colour bar and
#' the units. Default is -4.
#' @param labN Numeric. Describes the minimum number of numeric labels added to
#' the colour bar. Default is 5.
#' @param radii_col String. Describing the colour of the ellipse drawn if
#' \code{radii} list is specified. Default is "red".
#' @param ... Further variables passed to magimage. See
#' \code{\link[magicaxis]{magimage}} for further details.
#' @return Returns an image to the plotting window of the input
#' \code{build_datacube} image.
#' @examples
#' ss_pd_gadget = system.file("extdata", "SimSpin_example_Gadget",
#' package = "SimSpin")
#' ss_gadget = make_simspin_file(ss_pd_gadget, write_to_file = FALSE)
#' cube = build_datacube(simspin_file = ss_gadget,
#' telescope = telescope(type="SAMI"),
#' observing_strategy = observing_strategy(),
#' method = "velocity")
#' plot_dispersion(cube$observed_images$dispersion_image)
plot_dispersion <- function(dispersion_image, fig = c(0,1,0,1), new=F,
units = expression("dispersion"[LOS] * ", km s"^{-1}), main="",
radii = NA, na.color = "white", zlim = NA, legend=T,
titleshift = -4, labN=5, radii_col="red", ...){
disp_map = dispersion_image
im_dim = dim(disp_map)/2
disp_val = c(floor(min(disp_map, na.rm=T)), max(disp_map, na.rm=T))
if (all(disp_val == 0)){
stop("Image contains only '0'. No image can be produced in this case. \n
Please check your build_datacube function and try again.")
}
disp_map_cols = cmocean::cmocean("solar", version = "2.0", start = .1, end=.9)(100)
par(pty="s", fig=fig, xpd=FALSE, ps=12, cex=1, new=new); options(scipen = 1)
.image_nan(z = disp_map, zlim = if(is.na(zlim[1])){disp_val}else{zlim},
col = disp_map_cols, na.color = na.color, xaxt="n",
yaxt="n", ann=FALSE, magmap=FALSE, family="mono", font=1, main=main, ...)
if (!is.na(radii[1])){
plotrix::draw.ellipse(im_dim[1], im_dim[2], radii$a, radii$b, radii$ang, border = radii_col, density = NULL, lwd=2)
}
if (legend){
.magcolbar(position = "bottom", range = if(is.na(zlim[1])){disp_val}else{zlim}, scale = c(1, 1/20),
col = disp_map_cols, orient = "h", inset = -1/20, labN=labN, title = units,
titleshift = titleshift)
}
}
#' Plotting pretty higher-order kinematic (h3) images
#'
#' A function to produce a plot of the h3 image produced by
#' \code{build_datacube()} with associated colour bar and labels.
#'
#' @param h3_image Numeric array containing the h3 image
#' @param fig Numeric array of length 4 describing the boundary of the image
#' @param new Boolean. Should the image be added to the existing plot? Default
#' is FALSE.
#' @param units String describing the units of the values contained
#' in the image.
#' @param main Image title, default "".
#' @param radii list - containing a, b, and ang (if wishing to plot half-mass
#' radii ellipse).
#' @param na.color String. Colour given to NA values in the image.
#' @param zlim Numeric array of length 2. Describing the numeric range of
#' colours in the image. Default is NA, in which the range will be described by
#' the minimum and maximum values in the image.
#' @param legend Boolean to determine if the colour bar axis should be printed
#' at the bottom of the image. Default is T.
#' @param titleshift Numeric. Describes the distance between the colour bar and
#' the units. Default is -4.
#' @param labN Numeric. Describes the minimum number of numeric labels added to
#' the colour bar. Default is 5.
#' @param radii_col String. Describing the colour of the ellipse drawn if
#' \code{radii} list is specified. Default is "red".
#' @param ... Further variables passed to magimage. See
#' \code{\link[magicaxis]{magimage}} for further details.
#' @return Returns an image to the plotting window of the input
#' \code{build_datacube} image.
#' @examples
#' ss_pd_gadget = system.file("extdata", "SimSpin_example_Gadget",
#' package = "SimSpin")
#' ss_gadget = make_simspin_file(ss_pd_gadget, write_to_file = FALSE)
#' cube = build_datacube(simspin_file = ss_gadget,
#' telescope = telescope(type="SAMI"),
#' observing_strategy = observing_strategy(),
#' method = "velocity")
#' plot_h3(cube$observed_images$h3_image)
plot_h3 <- function(h3_image, fig = c(0,1,0,1), new=F,
units = expression("h"[3]), main="",
radii = NA, na.color = "white", zlim = NA, legend = T,
titleshift = -4, labN=5, radii_col="red", ...){
V = h3_image
im_dim = dim(V)/2
vel_val = max(c(abs(min(V, na.rm = T)), abs(max(V, na.rm = T))))
if (all(vel_val == 0)){
stop("Image contains only '0'. No image can be produced in this case. \n
Please check your build_datacube function and try again.")
}
velo_map_cols = cmocean::cmocean("balance", version = "2.0", start = .1, end=.9)(100)
par(pty="s", fig=fig, xpd=FALSE, ps=12, cex=1, new=new); options(scipen = 1)
.image_nan(z = V, zlim = if(is.na(zlim[1])){c(-vel_val,vel_val)}else{zlim}, col = velo_map_cols, na.color = na.color, xaxt="n",
yaxt="n", ann=FALSE, magmap=FALSE, family="mono", font=1, main = main, ...)
if (!is.na(radii[1])){
plotrix::draw.ellipse(im_dim[1], im_dim[2], radii$a, radii$b, radii$ang, border = radii_col, density = NULL, lwd=2)
}
if (legend){
.magcolbar(position = "bottom", range = if(is.na(zlim[1])){c(-vel_val,vel_val)}else{zlim}, scale = c(1, 1/20),
col = velo_map_cols, orient = "h", inset = -1/20, labN=labN, title = units,
titleshift = titleshift)
}
}
#' Plotting pretty higher-order kinematic (h4) images
#'
#' A function to produce a plot of the h4 image produced by
#' \code{build_datacube()} with associated colour bar and labels.
#'
#' @param h4_image Numeric array containing the h4 image
#' @param fig Numeric array of length 4 describing the boundary of the image
#' @param new Boolean. Should the image be added to the existing plot? Default
#' is FALSE.
#' @param units String describing the units of the values contained
#' in the image.
#' @param main Image title, default "".
#' @param radii list - containing a, b, and ang (if wishing to plot half-mass
#' radii ellipse).
#' @param na.color String. Colour given to NA values in the image.
#' @param zlim Numeric array of length 2. Describing the numeric range of
#' colours in the image. Default is NA, in which the range will be described by
#' the minimum and maximum values in the image.
#' @param legend Boolean to determine if the colour bar axis should be printed
#' at the bottom of the image. Default is T.
#' @param titleshift Numeric. Describes the distance between the colour bar and
#' the units. Default is -4.
#' @param labN Numeric. Describes the minimum number of numeric labels added to
#' the colour bar. Default is 5.
#' @param radii_col String. Describing the colour of the ellipse drawn if
#' \code{radii} list is specified. Default is "red".
#' @param ... Further variables passed to magimage. See
#' \code{\link[magicaxis]{magimage}} for further details.
#' @return Returns an image to the plotting window of the input
#' \code{build_datacube} image.
#' @examples
#' ss_pd_gadget = system.file("extdata", "SimSpin_example_Gadget",
#' package = "SimSpin")
#' ss_gadget = make_simspin_file(ss_pd_gadget, write_to_file = FALSE)
#' cube = build_datacube(simspin_file = ss_gadget,
#' telescope = telescope(type="SAMI"),
#' observing_strategy = observing_strategy(),
#' method = "velocity")
#' plot_h4(cube$observed_images$h4_image)
plot_h4 <- function(h4_image, fig = c(0,1,0,1), new=F,
units = expression("h"[4]), main="",
radii = NA, na.color = "white", zlim = NA, legend = T,
titleshift = -4, labN=5, radii_col="red", ...){
V = h4_image
im_dim = dim(V)/2
vel_val = max(c(abs(min(V, na.rm = T)), abs(max(V, na.rm = T))))
if (all(vel_val == 0)){
stop("Image contains only '0'. No image can be produced in this case. \n
Please check your build_datacube function and try again.")
}
velo_map_cols = cmocean::cmocean("balance", version = "2.0", start = .1, end=.9)(100)
par(pty="s", fig=fig, xpd=FALSE, ps=12, cex=1, new=new); options(scipen = 1)
.image_nan(z = V, zlim = if(is.na(zlim[1])){c(-vel_val,vel_val)}else{zlim}, col = velo_map_cols, na.color = na.color, xaxt="n",
yaxt="n", ann=FALSE, magmap=FALSE, family="mono", font=1, main = main, ...)
if (!is.na(radii[1])){
plotrix::draw.ellipse(im_dim[1], im_dim[2], radii$a, radii$b, radii$ang, border = radii_col, density = NULL, lwd=2)
}
if (legend){
.magcolbar(position = "bottom", range = if(is.na(zlim[1])){c(-vel_val,vel_val)}else{zlim}, scale = c(1, 1/20),
col = velo_map_cols, orient = "h", inset = -1/20, labN=labN, title = units,
titleshift = titleshift)
}
}
#' Plotting pretty age images
#'
#' A function to produce a plot of the stellar age image produced by
#' \code{build_datacube()} with associated colour bar and labels.
#'
#' @param age_image Numeric array containing the age image
#' @param fig Numeric array of length 4 describing the boundary of the image
#' @param new Boolean. Should the image be added to the existing plot? Default
#' is FALSE.
#' @param units String describing the units of the values contained
#' in the image.
#' @param main Image title, default "".
#' @param radii list - containing a, b, and ang (if wishing to plot half-mass
#' radii ellipse).
#' @param na.color String. Colour given to NA values in the image.
#' @param zlim Numeric array of length 2. Describing the numeric range of
#' colours in the image. Default is NA, in which the range will be described by
#' the minimum and maximum values in the image.
#' @param legend Boolean to determine if the colour bar axis should be printed
#' at the bottom of the image. Default is T.
#' @param titleshift Numeric. Describes the distance between the colour bar and
#' the units. Default is -4.
#' @param labN Numeric. Describes the minimum number of numeric labels added to
#' the colour bar. Default is 5.
#' @param radii_col String. Describing the colour of the ellipse drawn if
#' \code{radii} list is specified. Default is "red".
#' @param ... Further variables passed to magimage. See
#' \code{\link[magicaxis]{magimage}} for further details.
#' @return Returns an image to the plotting window of the input
#' \code{build_datacube} image.
#' @examples
#' ss_pd_gadget = system.file("extdata", "SimSpin_example_Gadget",
#' package = "SimSpin")
#' ss_gadget = make_simspin_file(ss_pd_gadget, write_to_file = FALSE)
#' cube = build_datacube(simspin_file = ss_gadget,
#' telescope = telescope(type="SAMI"),
#' observing_strategy = observing_strategy(),
#' method = "velocity")
#' plot_age(cube$raw_images$age_image)
plot_age <- function(age_image, fig = c(0,1,0,1), new=F,
units = expression("Age, Gyr"), main="", radii = NA,
na.color = "white", zlim = NA, legend=T,
titleshift = -4, labN=5, radii_col="red", ...){
age_map = age_image
im_dim = dim(age_map)/2
age_val = c(floor(min(age_map, na.rm=T)/2), max(age_map, na.rm=T))
if (all(age_val == 0)){
stop("Image contains only '0'. No image can be produced in this case. \n
Please check your build_datacube function and try again.")
}
age_map_cols = cmocean::cmocean("deep", version = "2.0", start = .1, end=1)(50)
par(pty="s", fig=fig, xpd=FALSE, ps=12, cex=1, new=new); options(scipen = 1)
.image_nan(z = age_map, zlim = if(is.na(zlim[1])){age_val}else{zlim}, col = age_map_cols, na.color = na.color, xaxt="n",
yaxt="n", ann=FALSE, magmap=FALSE, family="mono", font=1, main=main, ...)
if (!is.na(radii[1])){
plotrix::draw.ellipse(im_dim[1], im_dim[2], radii$a, radii$b, radii$ang, border = radii_col, density = NULL, lwd=2)
}
if (legend){
.magcolbar(position = "bottom", range = if(is.na(zlim[1])){age_val}else{zlim}, scale = c(1, 1/20),
col = age_map_cols, orient = "h", inset = -1/20, labN=labN, title = units,
titleshift = titleshift)
}
}
#' Plotting pretty metallicity images
#'
#' A function to produce a plot of the stellar metallicity image produced by
#' \code{build_datacube()} with associated colour bar and labels.
#'
#' @param metallicity_image Numeric array containing the metallicity image.
#' @param fig Numeric array of length 4 describing the boundary of the image
#' @param new Boolean. Should the image be added to the existing plot? Default
#' is FALSE.
#' @param units String describing the units of the values contained
#' in the image.
#' @param main Image title, default "".
#' @param radii list - containing a, b, and ang (if wishing to plot half-mass
#' radii ellipse).
#' @param na.color String. Colour given to NA values in the image.
#' @param zlim Numeric array of length 2. Describing the numeric range of
#' colours in the image. Default is NA, in which the range will be described by
#' the minimum and maximum values in the image.
#' @param legend Boolean to determine if the colour bar axis should be printed
#' at the bottom of the image. Default is T.
#' @param titleshift Numeric. Describes the distance between the colour bar and
#' the units. Default is -4.
#' @param labN Numeric. Describes the minimum number of numeric labels added to
#' the colour bar. Default is 5.
#' @param radii_col String. Describing the colour of the ellipse drawn if
#' \code{radii} list is specified. Default is "red".
#' @param ... Further variables passed to magimage. See
#' \code{\link[magicaxis]{magimage}} for further details.
#' @return Returns an image to the plotting window of the input
#' \code{build_datacube} image.
#' @examples
#' ss_pd_gadget = system.file("extdata", "SimSpin_example_Gadget",
#' package = "SimSpin")
#' ss_gadget = make_simspin_file(ss_pd_gadget, write_to_file = FALSE)
#' cube = build_datacube(simspin_file = ss_gadget,
#' telescope = telescope(type="SAMI"),
#' observing_strategy = observing_strategy(),
#' method = "velocity")
#' plot_metallicity(cube$raw_images$metallicity_image)
plot_metallicity <- function(metallicity_image, fig = c(0,1,0,1), new=F,
units = expression("log10(Z/Z"[solar]*")"), main="",
na.color = "white", zlim = NA, legend=T, radii = NA,
titleshift = -4, labN=5, radii_col="red", ...){
met_map = metallicity_image
im_dim = dim(met_map)/2
met_val = c(floor(min(met_map, na.rm=T)/2), max(met_map, na.rm=T))
if (all(met_val == 0)){
stop("Image contains only '0'. No image can be produced in this case. \n
Please check your build_datacube function and try again.")
}
met_map_cols = cmocean::cmocean("dense", version = "2.0", start = .1, end=1)(50)
par(pty="s", fig=fig, xpd=FALSE, ps=12, cex=1, new=new); options(scipen = 1)
.image_nan(z = met_map, zlim = if(is.na(zlim[1])){met_val}else{zlim},
col = met_map_cols, na.color = na.color, xaxt="n",
yaxt="n", ann=FALSE, magmap=FALSE, family="mono", font=1, main=main, ...)
if (!is.na(radii[1])){
plotrix::draw.ellipse(im_dim[1], im_dim[2], radii$a, radii$b, radii$ang, border = radii_col, density = NULL, lwd=2)
}
if (legend){
.magcolbar(position = "bottom", range = if(is.na(zlim[1])){met_val}else{zlim}, scale = c(1, 1/20),
col = met_map_cols, orient = "h", inset = -1/20, labN=labN, title = units,
titleshift = titleshift)
}
}
#' Plotting pretty particle number images
#'
#' A function to produce a plot of the particle per pixel image produced by
#' \code{build_datacube()} with associated colour bar and labels.
#'
#' @param particle_image Numeric array containing the particle per pixel image
#' @param fig Numeric array of length 4 describing the boundary of the image
#' @param new Boolean. Should the image be added to the existing plot? Default
#' is FALSE.
#' @param units String describing the units of the values contained
#' in the image.
#' @param main Image title, default "".
#' @param radii list - containing a, b, and ang (if wishing to plot half-mass
#' radii ellipse).
#' @param na.color String. Colour given to NA values in the image.
#' @param zlim Numeric array of length 2. Describing the numeric range of
#' colours in the image. Default is NA, in which the range will be described by
#' the minimum and maximum values in the image.
#' @param legend Boolean to determine if the colour bar axis should be printed
#' at the bottom of the image. Default is T.
#' @param titleshift Numeric. Describes the distance between the colour bar and
#' the units. Default is -4.
#' @param labN Numeric. Describes the minimum number of numeric labels added to
#' the colour bar. Default is 5.
#' @param radii_col String. Describing the colour of the ellipse drawn if
#' \code{radii} list is specified. Default is "red".
#' @param ... Further variables passed to magimage. See
#' \code{\link[magicaxis]{magimage}} for further details.
#' @return Returns an image to the plotting window of the input
#' \code{build_datacube} image.
#' @examples
#' ss_pd_gadget = system.file("extdata", "SimSpin_example_Gadget",
#' package = "SimSpin")
#' ss_gadget = make_simspin_file(ss_pd_gadget, write_to_file = FALSE)
#' cube = build_datacube(simspin_file = ss_gadget,
#' telescope = telescope(type="SAMI"),
#' observing_strategy = observing_strategy(),
#' method = "velocity")
#' plot_particles(cube$raw_images$particle_image)
plot_particles <- function(particle_image, fig = c(0,1,0,1), new=F,
units = expression("Number of particles"), main="", radii = NA,
na.color = "white", zlim = NA, legend=T,
titleshift = -4, labN=5, radii_col="red", ...){
part_map = particle_image
im_dim = dim(part_map)/2
part_val = c(floor(min(part_map, na.rm=T)/2), max(part_map, na.rm=T))
if (all(part_val == 0)){
stop("Image contains only '0'. No image can be produced in this case. \n
Please check your build_datacube function and try again.")
}
part_map_cols = cmocean::cmocean("deep", version = "2.0", start = .1, end=1)(50)
par(pty="s", fig=fig, xpd=FALSE, ps=12, cex=1, new=new); options(scipen = 1)
.image_nan(z = part_map, zlim = if(is.na(zlim[1])){part_val}else{zlim}, col = part_map_cols, na.color = na.color, xaxt="n",
yaxt="n", ann=FALSE, magmap=FALSE, family="mono", font=1, main=main, ...)
if (!is.na(radii[1])){
plotrix::draw.ellipse(im_dim[1], im_dim[2], radii$a, radii$b, radii$ang, border = radii_col, density = NULL, lwd=2)
}
if (legend){
.magcolbar(position = "bottom", range = if(is.na(zlim[1])){part_val}else{zlim}, scale = c(1, 1/20),
col = part_map_cols, orient = "h", inset = -1/20, labN=labN, title = units,
titleshift = titleshift)
}
}
#' Plotting pretty gas SFR images
#'
#' A function to produce a plot of the gas star formation rate image produced by
#' \code{build_datacube()} with associated colour bar and labels.
#'
#' @param SFR_image Numeric array containing the particle per pixel image
#' @param fig Numeric array of length 4 describing the boundary of the image
#' @param new Boolean. Should the image be added to the existing plot? Default
#' is FALSE.
#' @param units String describing the units of the values contained
#' in the image.
#' @param main Image title, default "".
#' @param radii list - containing a, b, and ang (if wishing to plot half-mass
#' radii ellipse).
#' @param na.color String. Colour given to NA values in the image.
#' @param zlim Numeric array of length 2. Describing the numeric range of
#' colours in the image. Default is NA, in which the range will be described by
#' the minimum and maximum values in the image.
#' @param legend Boolean to determine if the colour bar axis should be printed
#' at the bottom of the image. Default is T.
#' @param titleshift Numeric. Describes the distance between the colour bar and
#' the units. Default is -4.
#' @param labN Numeric. Describes the minimum number of numeric labels added to
#' the colour bar. Default is 5.
#' @param radii_col String. Describing the colour of the ellipse drawn if
#' \code{radii} list is specified. Default is "red".
#' @param ... Further variables passed to magimage. See
#' \code{\link[magicaxis]{magimage}} for further details.
#' @return Returns an image to the plotting window of the input
#' \code{build_datacube} image.
#' @examples
#' ss_pd_eagle = system.file("extdata", "SimSpin_example_EAGLE.hdf5",
#' package = "SimSpin")
#' ss_eagle = make_simspin_file(ss_pd_eagle, write_to_file = FALSE)
#' cube = build_datacube(simspin_file = ss_eagle,
#' telescope = telescope(type="SAMI"),
#' observing_strategy = observing_strategy(),
#' method = "gas")
#' plot_SFR(cube$raw_images$SFR_image)
plot_SFR <- function(SFR_image, fig = c(0,1,0,1), new=F,
units = expression("SFR, M"["sol"]*"/yr"), main="", radii = NA,
na.color = "white", zlim = NA, legend=T,
titleshift = -4, labN=5, radii_col="red",...){
part_map = SFR_image
im_dim = dim(part_map)/2
part_val = c(floor(min(part_map, na.rm=T)/2), max(part_map, na.rm=T))
if (all(part_val == 0)){
stop("Image contains only '0'. No image can be produced in this case. \n
Please check your build_datacube function and try again.")
}
part_map_cols = cmocean::cmocean("deep", version = "2.0", start = .1, end=1)(50)
par(pty="s", fig=fig, xpd=FALSE, ps=12, cex=1, new=new); options(scipen = 1)
.image_nan(z = part_map, zlim = if(is.na(zlim[1])){part_val}else{zlim}, col = part_map_cols, na.color = na.color, xaxt="n",
yaxt="n", ann=FALSE, magmap=FALSE, family="mono", font=1, main=main, ...)
if (!is.na(radii[1])){
plotrix::draw.ellipse(im_dim[1], im_dim[2], radii$a, radii$b, radii$ang, border = radii_col, density = NULL, lwd=2)
}
if (legend){
.magcolbar(position = "bottom", range = if(is.na(zlim[1])){part_val}else{zlim}, scale = c(1, 1/20),
col = part_map_cols, orient = "h", inset = -1/20, labN=labN, title = units,
titleshift = titleshift)
}
}
#' Plotting pretty log10(O/H) images
#'
#' A function to produce a plot of the gas log10(O/H) image produced by
#' \code{build_datacube()} with associated colour bar and labels.
#'
#' @param OH_image Numeric array containing the metallicity image.
#' @param fig Numeric array of length 4 describing the boundary of the image
#' @param new Boolean. Should the image be added to the existing plot? Default
#' is FALSE.
#' @param units String describing the units of the values contained
#' in the image.
#' @param main Image title, default "".
#' @param radii list - containing a, b, and ang (if wishing to plot half-mass
#' radii ellipse).
#' @param na.color String. Colour given to NA values in the image.
#' @param zlim Numeric array of length 2. Describing the numeric range of
#' colours in the image. Default is NA, in which the range will be described by
#' the minimum and maximum values in the image.
#' @param legend Boolean to determine if the colour bar axis should be printed
#' at the bottom of the image. Default is T.
#' @param titleshift Numeric. Describes the distance between the colour bar and
#' the units. Default is -4.
#' @param labN Numeric. Describes the minimum number of numeric labels added to
#' the colour bar. Default is 5.
#' @param radii_col String. Describing the colour of the ellipse drawn if
#' \code{radii} list is specified. Default is "red".
#' @param ... Further variables passed to magimage. See
#' \code{\link[magicaxis]{magimage}} for further details.
#' @return Returns an image to the plotting window of the input
#' \code{build_datacube} image.
#' @examples
#' ss_pd_eagle = system.file("extdata", "SimSpin_example_EAGLE.hdf5",
#' package = "SimSpin")
#' ss_eagle = make_simspin_file(ss_pd_eagle, write_to_file = FALSE)
#' cube = build_datacube(simspin_file = ss_eagle,
#' telescope = telescope(type="SAMI"),
#' observing_strategy = observing_strategy(),
#' method = "gas")
#' plot_OH(cube$raw_images$OH_image)
plot_OH <- function(OH_image, fig = c(0,1,0,1), new=F,
units = expression("log10(O/H) + 12"), main="",
na.color = "white", zlim = NA, legend=T, radii = NA,
titleshift = -4, labN=5, radii_col="red", ...){
met_map = OH_image
im_dim = dim(met_map)/2
met_val = c(floor(min(met_map, na.rm=T)/2), max(met_map, na.rm=T))
if (all(met_val == 0)){
stop("Image contains only '0'. No image can be produced in this case. \n
Please check your build_datacube function and try again.")
}
met_map_cols = cmocean::cmocean("dense", version = "2.0", start = .1, end=1)(50)
par(pty="s", fig=fig, xpd=FALSE, ps=12, cex=1, new=new); options(scipen = 1)
.image_nan(z = met_map, zlim = if(is.na(zlim[1])){met_val}else{zlim},
col = met_map_cols, na.color = na.color, xaxt="n",
yaxt="n", ann=FALSE, magmap=FALSE, family="mono", font=1, main=main, ...)
if (!is.na(radii[1])){
plotrix::draw.ellipse(im_dim[1], im_dim[2], radii$a, radii$b, radii$ang, border = radii_col, density = NULL, lwd=2)
}
if (legend){
.magcolbar(position = "bottom", range = if(is.na(zlim[1])){met_val}else{zlim}, scale = c(1, 1/20),
col = met_map_cols, orient = "h", inset = -1/20, labN=labN, title = units,
titleshift = titleshift)
}
}
#' Plotting pretty Voronoi bin images
#'
#' A function to produce a plot of the Voronoi bins produced by
#' \code{build_datacube()} with associated colour bar and labels.
#'
#' @param voronoi_bins Numeric array containing the metallicity image.
#' @param fig Numeric array of length 4 describing the boundary of the image
#' @param new Boolean. Should the image be added to the existing plot? Default
#' is FALSE.
#' @param main Image title, default "".
#' @param na.color String. Colour given to NA values in the image.
#' @param zlim Numeric array of length 2. Describing the numeric range of
#' colours in the image. Default is NA, in which the range will be described by
#' the minimum and maximum values in the image.
#' @param ... Further variables passed to magimage. See
#' \code{\link[magicaxis]{magimage}} for further details.
#' @return Returns an image to the plotting window of the input
#' \code{build_datacube} image.
#' @examples
#' ss_pd_eagle = system.file("extdata", "SimSpin_example_EAGLE.hdf5",
#' package = "SimSpin")
#' ss_eagle = make_simspin_file(ss_pd_eagle, write_to_file = FALSE)
#' cube = build_datacube(simspin_file = ss_eagle,
#' telescope = telescope(type="SAMI"),
#' observing_strategy = observing_strategy(),
#' method = "velocity", voronoi_bin = TRUE)
#' plot_voronoi(cube$raw_images$voronoi_bins)
plot_voronoi <- function(voronoi_bins, fig = c(0,1,0,1), new=F,
main="", na.color = "white", zlim = NA,
...){
bin_map = voronoi_bins
im_dim = dim(bin_map)/2
bin_val = c(min(bin_map, na.rm=T), max(bin_map, na.rm=T))
if (all(bin_val == 0)){
stop("Image contains only '0'. No image can be produced in this case. \n
Please check your build_datacube function and try again.")
}
bin_map_cols = cmocean::cmocean("phase", version = "2.0", start = .1, end=1)(max(bin_map, na.rm=T))
par(pty="s", fig=fig, xpd=FALSE, ps=12, cex=1, new=new); options(scipen = 1)
.image_nan(z = bin_map, zlim = if(is.na(zlim[1])){bin_val}else{zlim},
col = bin_map_cols, na.color = na.color, xaxt="n",
yaxt="n", ann=FALSE, magmap=FALSE, family="mono", font=1, main=main, ...)
}
.image_nan <- function(z, zlim, col, na.color='gray', ...){
# Function for plotting an image with NAs as a set colour
# z :==: array corresponding to the image to be plotted
# zlim :==: colour range associated with the image for
# the colour palette
# col :==: the colour palette to be used for the image
# na.color :==: string describing the color used for NA
zstep <- (zlim[2] - zlim[1]) / length(col); # step in the color palette
newz.na <- zlim[2] + zstep # new z for NA
z[which(is.na(z>zlim[2]))] <- newz.na # same for newz.na
zlim[2] <- zlim[2] + zstep # extend top limit to include the new value na
col <- c(col, na.color) # we construct the new color range by including: na.color
magicaxis::magimage(x=z, zlim=zlim, col=col, ...) # we finally call image(...)
}
.magcolbar <- # function modified from magicaxis to generate colour bars
function(position='topright',range=c(0,1),orient='v',log=FALSE,col=hcl.colors(21),scale=c(1/4,1/20), inset=1/40,labN=5,title='',titleshift=0,centrealign='rb',clip='',cex=1,...){
usercoord=par()$usr
xlogcheck=FALSE;ylogcheck=FALSE
xlo=usercoord[1];xhi=usercoord[2];ylo=usercoord[3];yhi=usercoord[4]
xdiff=xhi-xlo;ydiff=yhi-ylo
if(orient=='h'){
xl=xlo+xdiff/2-xdiff*scale[1]/2
yb=ylo+ydiff/2-ydiff*scale[2]/2
xr=xlo+xdiff/2+xdiff*scale[1]/2
yt=ylo+ydiff/2+ydiff*scale[2]/2
align=centrealign
if(length(grep('bottom',position))>0){aligntext='lt'; yb=ylo+ydiff*inset;yt=ylo+ydiff*inset+ydiff*scale[2]}
}
rangetemp=range
legend=magicaxis::maglab(rangetemp,labN,log=log,trim=F)
roughNscale=(max(legend$labat)-min(legend$labat))/(rangetemp[2]-rangetemp[1])
colremap=magicaxis::magmap(data=seq(min(legend$labat),max(legend$labat),length=length(col)*roughNscale),locut=rangetemp[1],hicut=rangetemp[2],type='num',range=c(1,length(col)),clip=clip)$map
col=col[round(colremap,digits=0)]
if(orient=='h'){plotrix::color.legend(xl,yb,xr,yt,legend=legend$exp,rect.col=col,cex=cex,align=align,gradient='x',...)}
if(orient=='h' & aligntext=='lt'){text((xl+xr)/2,yt+(titleshift)*ydiff/20, labels=title,adj=c(0.5,0.5),srt=0,cex=cex, xpd=NA)}
par(xlog=xlogcheck)
par(ylog=ylogcheck)
par(usr=usercoord)
}
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