plot_var_nc: Plot variables from a .nc file

In USGS-R/glmtools: Tools for working with the General Lake Model (GLM)

Plot variables from a .nc file

Description

Plots variables directly from a .nc file output from a GLM simulation. Replaces function plot_var.

Usage

plot_var_nc(
  nc_file = "output.nc",
  var_name = "temp",
  fig_path = NULL,
  reference = "surface",
  legend.title = NULL,
  interval = 0.5,
  text.size = 12,
  show.legend = TRUE,
  legend.position = "right",
  plot.title = NULL,
  color.palette = "RdYlBu",
  color.direction = -1,
  zlim = NULL,
  ...
)

plot_var(
  nc_file = "output.nc",
  var_name = "temp",
  fig_path = NULL,
  reference = "surface",
  legend.title = NULL,
  interval = 0.5,
  text.size = 12,
  show.legend = TRUE,
  legend.position = "right",
  plot.title = NULL,
  color.palette = "RdYlBu",
  color.direction = -1,
  zlim = NULL,
  ...
)

Arguments

nc_file	a string with the path to the netcdf output from GLM
var_name	a character vector of valid variable names (see sim_vars)
fig_path	Default is NULL (only plots to screen). Enter string path to save as output file. File type can be anything supported by ggplot2:ggsave. See examples.
reference	String; 'surface' or 'bottom'. Only used for heatmap plots. We recommend using 'bottom' if surface levels are fluctuating. This will present a more realistic representation of surface conditions.
legend.title	Vector string; Default ('NULL') will use variable and units from netcdf file
interval	Positive number indicating the depth interval in meters to interpolate output data. Must be less than max depth of lake. Default = 0.5 m.
text.size	Integer; Default is 12. Higher values will increase text size in plot.
show.legend	Logical; TRUE to show legend (default), FALSE to hide legend
legend.position	String; Legend position. Default is 'right'. Options: 'left','right','top','bottom'
plot.title	Vector string; Default is no title.
color.palette	See ggplot2:scale_color_distiller . If a string, will use that named palette. Default is 'RdYlBu'. If a number, will index into the list of palettes of appropriate. Palettes available include: Diverging: BrBG, PiYG, PRGn, PuOr, RdBu, RdGy, RdYlBu, RdYlGn. Spectral. Qualitative: Accent, Dark2, Paired, Pastel1, Pastel2, Set1, Set2, Set3. Sequential: Blues, BuGn, BuPu, GnBu, Greens, Greys, Oranges, OrRd, PuBu, PuBuGn, PuRd, Purples, RdPu, Reds, YlGn, YlGnBu, YlOrBr, YlOrRd.
color.direction	Sets the order of colors in the scale. If 1, colors are as output by brewer.pal. If -1, the order of colors is reversed (default).
zlim	Color palette limits for z-variable. Default is maximum range of variable. Set as c(value,value).
...	additional arguments passed to ggplot2:ggsave

Functions

• plot_var: Deprecated. Use plot_var_nc

Author(s)

Jordan S. Read, Luke A. Winslow, Hilary A. Dugan

See Also

get_temp, sim_var_longname, sim_vars, plot_temp, get_var

Examples

nc_file <- system.file("extdata", "output/output.nc", package = "glmtools")
plot_var_nc(nc_file, 'temp')

#Plotting two variables
plot_var_nc(nc_file, var_name = c('temp','wind'), show.legend = FALSE, 
text.size = 14, plot.title = c('My Lake: Temp','My Lake: Wind'))

#Change color palette
plot_var_nc(nc_file, var_name = 'temp', color.palette = 'PuBuGn', 
color.direction = 1, show.legend = FALSE)

## Not run: 
#'#How to save a plot
plot_var_nc(nc_file,var_name = c('temp', 'u_mean'),
fig_path = './figtest.png', width = 6, height = 2, units = 'in')

# need to specify a valid .nc file here: 
plot_var_nc(file = fabm_sim_nc.nc,
var_name = 'aed_oxygen_oxy', 
fig_path = 'aed_out.png')

## End(Not run)

USGS-R/glmtools documentation built on March 26, 2024, 5:43 p.m.