plot_upset_fishtissue: Plot Fish Study Upset

In leppott/ProjectTasks: Project Plots and Tables

Plot Fish Study Upset

Description

Upset plot for fish study projects

Usage

plot_upset_fishtissue(
  df_data,
  intersect = names(df_data)[-1],
  title_str = NA,
  title_custloc = FALSE,
  title_x = 0.2,
  title_y = 0.9,
  title_fontsize = 16,
  cap_str = NA,
  cap_custloc = FALSE,
  cap_x = 0.5,
  cap_y = 0.025,
  cap_fontsize = 8,
  ...
)

Arguments

intersect	Columns to be used to compose the intersection. Default = names(data)[-1]
title_str	Title string. Default = NA
title_custloc	Use a custom location for the title? Default = FALSE
title_x	Title x placement. Default = 0.2
title_y	Title y placement. Default = 0.9
title_fontsize	Title font size. Default = 16
cap_str	Caption string. Default = NA
cap_custloc	Use a custom location for the caption? Default = FALSE
cap_x	Caption x placement. Default = 0.5
cap_y	Caption y placement. Default = 0.025
cap_fontsize	Caption font size. Default = 8
...	Arguments to be passed on to ComplexUpset::upset
data	Data as data frame (variables are 1 or 0 as columns).

Details

Upset plot using the 'ComplexUpset' package.

Upset plots show co-occurrence of different variables. The left side sizes plot is turned on by default. This creates extra area in the upper left that can be used for an alternative location for the plot title. The function is set up to use the basic title as default but has input parameters to change the location (e.g., upper left).

A ggplot object is returned that the user can further modify and save. #' # 2023-07-20, moved code to package scripts. Derived for Great Lakes studies.

Value

A ggplot object is returned.

Examples

# Data
df_data <- data_gl2010_upset

# Parameters ----
namedata <- "Great Lakes, 2010"
fishconsumer <- "general"
sv_hg <- 300
sv_pfas <- 0.52
sv_pcb <- 12

# Plot Parts ----
title_str <- paste0(namedata
                    , "\n(n = ", nrow(df_data), ")"
                    , "\nExceeds Screening Value")
cap_str <- paste0("Screening Values for "
                  , fishconsumer
                  , " fish consumer; "
                  , "Mercury = "
                  , sv_hg
                  , ", "
                  , "PFAS = "
                  , sv_pfas
                  , ", "
                  , "Total PCBs = "
                  , sv_pcb
                  )

# Plot, title and caption, base location ----
p1 <- plot_upset_fishtissue(df_data = df_data
                           , title_str = title_str
                           , cap_str = cap_str)
p1

# Plot, title and caption, custom location ----
p2 <- plot_upset_fishtissue(df_data = df_data
                           , title_str = title_str
                           , title_custloc = TRUE
                           , title_x = 0.16
                           , title_y = 0.90
                           , title_fontsize = 16
                           , cap_str = cap_str
                           , cap_custloc = TRUE
                           , cap_x = 0.5
                           , cap_y = 0.025
                           , cap_fontsize = 8)
p2

leppott/ProjectTasks documentation built on Oct. 12, 2023, 1:18 a.m.