Skip to contents

Plot saving

Source: R/aux_save.R
plot_save.Rd

Functions to save plots to directory of interest. all_plots_save_function() is used for plot saving operations. gpsparam() is used to generate a set of save parameters and filepath based on available parameter and giottoInstructions values.

Usage

all_plots_save_function(
  gobject,
  plot_object,
  save_dir = NULL,
  save_folder = NULL,
  save_name = NULL,
  default_save_name = "giotto_plot",
  save_format = NULL,
  show_saved_plot = FALSE,
  ncol = 1,
  nrow = 1,
  scale = 1,
  base_width = NULL,
  base_height = NULL,
  base_aspect_ratio = NULL,
  units = NULL,
  dpi = NULL,
  limitsize = TRUE,
  plot_count = NULL,
  GPSPARAM = NULL,
  ...
)

gpsparam(
  instructions,
  type = c("gg", "plotly", "general"),
  save_dir = NULL,
  save_folder = NULL,
  save_name = NULL,
  default_save_name = "giotto_plot",
  save_format = NULL,
  dpi = NULL,
  base_width = NULL,
  base_height = NULL,
  base_aspect_ratio = NULL,
  units = NULL,
  plot_count = NULL,
  ...
)

Arguments

gobject

giotto object or giottoInstructions

plot_object

ggplot object to plot

save_dir

directory to save to

save_folder

folder in save_dir to save to

save_name

name of plot

default_save_name

default name to save a plot

save_format

format (e.g. png, tiff, pdf, ...)

show_saved_plot

load & display the saved plot

ncol

number of columns for multiplots

nrow

number of rows for multiplot

scale

scale of plots

base_width

width of plot

base_height

height of plot

base_aspect_ratio

aspect ratio of plot

units

plotting units (e.g. in)

dpi

dpi for each plot if plot is in raster format

limitsize

When TRUE (the default), ggsave will not save images larger than 50x50 inches, to prevent the common error of specifying dimensions in pixels.

plot_count

manually set the plot count that is appended to a default_save_name

GPSPARAM

giotto_plot_save_param object. If provided, will be used instead of most other general save params. (save_dir, save_folder, save_name, default_save_name, save_format, base_width, base_height, base_aspect_ratio, units, dpi, plot_count)

...

additional parameters to pass downstream save functions. cowplot::save_plot() is used for ggplot2 plots. grDevices png, tiff svg, pdf is used for base and general saving

instructions

giotto or giottoInstructions object

type

character. One of "gg"', '"plotly"', '"general" to designate which type of plot to save. This affects which types of outputs are possible.

Value

all_plots_save_function returns a plot file. gpsparam returns a giotto_plot_save_param object

See also

showSaveParameters save_plot png tiff pdf svg

Examples

g <- GiottoData::loadGiottoMini("vis")
#> 1. read Giotto object
#> 2. read Giotto feature information
#> 3. read Giotto spatial information
#> 3.1 read Giotto spatial shape information
#> 3.2 read Giotto spatial centroid information
#> 3.3 read Giotto spatial overlap information
#> 4. read Giotto image information
#> python already initialized in this session
#>  active environment : '/usr/bin/python3'
#>  python version : 3.10
#> checking default envname 'giotto_env'
#> a system default python environment was found
#> Using python path:
#>  "/usr/bin/python3"
df <- data.frame(x = rnorm(5), y = rnorm(5))
g_plot <- ggplot2::ggplot(df, ggplot2::aes(x,y)) + ggplot2::geom_point()
all_plots_save_function(g, g_plot)