## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.width = 8,
  fig.height = 7,
  dpi = 110,
  fig.align = "center"
)

## ----setup--------------------------------------------------------------------
library(circlecorR)

## ----groups-------------------------------------------------------------------
groups <- list(
  Demographics = c("Age", "BMI"),
  Metrics      = c("Amplitude", "Fed-Fasted AR", "Frequency", "GA-RI"),
  Symptoms     = c("Nausea", "Early satiety", "Bloating",
                   "Upper GI pain", "Lower GI pain", "Heartburn"),
  Scores       = c("GCSI", "PAGI-SYM", "PAGI-QoL", "EQ-5D")
)

## ----raw-data-----------------------------------------------------------------
# `gastro_symptoms` is a synthetic per-row example dataset shipped with the package
head(gastro_symptoms[, 1:5])

corr_wheel(
  gastro_symptoms,             # raw data: one row per subject
  groups      = groups,
  method      = "pearson",     # correlation method
  adjust      = "hochberg",    # multiple-comparison adjustment (see below)
  sig_level   = 0.05,          # hide links with adjusted p > 0.05
  r_threshold = 0.3,           # ...and links with |r| < 0.3
  r_limits    = c(-0.6, 0.6)
)

## ----family-------------------------------------------------------------------
res <- corr_wheel(gastro_symptoms, groups = groups, adjust = "hochberg",
                  r_threshold = 0.3, r_limits = c(-0.6, 0.6))

k <- length(unlist(groups))
cat("Unique correlations in the full matrix:", k * (k - 1) / 2, "\n")
cat("Correlations actually tested (the family):", res$n_tests, "\n")

## ----power--------------------------------------------------------------------
p_raw <- 5e-4                       # a raw p-value for one correlation
k_all <- k * (k - 1) / 2

cat("Bonferroni across the full matrix:", signif(p_raw * k_all, 3), "\n")
cat("Bonferroni across the family only:", signif(p_raw * res$n_tests, 3), "\n")

## ----compute-correlations-----------------------------------------------------
cc <- compute_correlations(gastro_symptoms, method = "pearson")
str(cc)

## ----schemes-list-------------------------------------------------------------
corr_wheel_schemes()

## ----scheme-colorblind--------------------------------------------------------
corr_wheel(gastro_symptoms, groups = groups, r_threshold = 0.3,
          r_limits = c(-0.6, 0.6), scheme = "colorblind")

## ----scheme-alimetry----------------------------------------------------------
corr_wheel(gastro_symptoms, groups = groups, r_threshold = 0.3,
          r_limits = c(-0.6, 0.6), scheme = "alimetry")

## ----scheme-tweak-------------------------------------------------------------
s <- corr_wheel_scheme("ocean")
s$palette[2] <- "grey96"
corr_wheel(gastro_symptoms, groups = groups, r_threshold = 0.3,
          r_limits = c(-0.6, 0.6), scheme = s)

## ----scheme-custom------------------------------------------------------------
corr_wheel(gastro_symptoms, groups = groups, r_threshold = 0.3,
          r_limits = c(-0.6, 0.6),
          scheme = list(colors = c("#7B2CBF", "#2A9D8F", "#E76F51", "#264653"),
                       palette = c("#2A9D8F", "white", "#E76F51")))

## ----colours------------------------------------------------------------------
corr_wheel(
  gastro_symptoms, groups = groups, r_threshold = 0.3, r_limits = c(-0.6, 0.6),
  scheme = "colorblind",
  colors = c(Scores = "black"),          # override just one category
  labels = c("GA-RI" = "Rhythm index")
)

## ----sizes--------------------------------------------------------------------
corr_wheel(
  gastro_symptoms, groups = groups, r_threshold = 0.3, r_limits = c(-0.6, 0.6),
  tile_height = 0.12,   # thicker blocks
  link_lwd    = 3       # thicker lines
)

## ----palette------------------------------------------------------------------
corr_wheel(
  gastro_symptoms, groups = groups, r_threshold = 0.3,
  palette  = c("#2166AC", "white", "#B2182B"),   # blue - white - red
  r_limits = c(-0.5, 0.5)
)

## ----save, eval = FALSE-------------------------------------------------------
# png("correlation_wheel.png", width = 2500, height = 2000, res = 300)
# corr_wheel(gastro_symptoms, groups = groups, r_threshold = 0.3,
#            r_limits = c(-0.6, 0.6))
# dev.off()