show_transect: Plot results for a seagrass transect by time and location

In tbep-tech/tbeptools: Data and Indicators for the Tampa Bay Estuary Program

Plot results for a seagrass transect by time and location

Description

Plot results for a seagrass transect by time and location

Usage

show_transect(
  transect,
  site,
  species = c("Halodule", "Syringodium", "Thalassia", "Halophila", "Ruppia", "Caulerpa",
    "Dapis", "Chaetomorpha"),
  yrrng = c(1998, 2024),
  varplo = c("Abundance", "Blade Length", "Short Shoot Density"),
  base_size = 12,
  facet = FALSE,
  ncol = NULL,
  plotly = FALSE,
  width = NULL,
  height = NULL,
  sppcol = NULL
)

Arguments

transect	data frame returned by read_transect
site	chr string indicating site results to plot
species	chr string indicating one to many of which species to plot
yrrng	numeric indicating year ranges to evaluate
varplo	chr string indicating which variable to plot
base_size	numeric indicating text scaling size for plot
facet	logical indicating if plots are separated into facets by species
ncol	numeric indicating number of columns if facet = TRUE
plotly	logical if plot is created using plotly
width	numeric for width of the plot in pixels, only applies of plotly = TRUE
height	numeric for height of the plot in pixels, only applies of plotly = TRUE
sppcol	character vector of alternative colors to use for each species, must have length of six

Details

All sites along a transect that were surveyed are shown in the plot, including those where the selected species were not found. The latter is colored in grey hollow points. Species options include Halodule, Syringodium, Thalassia, Halophila, Ruppia, Caulerpa (attached macroalgae), Dapis (cyanobacteria), and/or Chaetomorpha (drift green algae). Drift or attached macroalgae and cyanobacteria (Dapis) estimates may not be accurate prior to 2021.

Note that if plotly = TRUE, the size legend is not shown.

Value

A ggplot object

Examples

## Not run: 
transect <- read_transect()

## End(Not run)

# one species
show_transect(transect, site = 'S3T10', species = 'Halodule', varplo = 'Abundance')

# multiple species, one plot
show_transect(transect, site = 'S3T10',
  species = c('Halodule', 'Syringodium', 'Thalassia', 'Halophila', 'Ruppia',
    'Caulerpa', 'Dapis', 'Chaetomorpha'),
  varplo = 'Abundance')

# multiple species, multiple plots
show_transect(transect, site = 'S3T10',
  species = c('Halodule', 'Syringodium', 'Thalassia', 'Halophila', 'Ruppia',
    'Caulerpa', 'Dapis', 'Chaetomorpha'),
  varplo = 'Abundance', facet = TRUE)

tbep-tech/tbeptools documentation built on April 13, 2025, 4:50 p.m.