params <-
list(test = FALSE)

## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  warning = FALSE
)
library(BiocStyle)

## ----eval = FALSE-------------------------------------------------------------
#  if (!require("BiocManager")) {
#    install.packages("BiocManager")
#  }
#  BiocManager::install("spicyR")

## ----warning=FALSE, message=FALSE---------------------------------------------
# load required packages
library(spicyR)
library(ggplot2)
library(SingleCellExperiment)
library(SpatialExperiment)
library(imcRtools)

## -----------------------------------------------------------------------------
data("diabetesData")
diabetesData

## ----message=FALSE------------------------------------------------------------
spicyTestPair <- spicy(
  diabetesData,
  condition = "stage",
  subject = "case",
  from = "beta",
  to = "delta"
)

topPairs(spicyTestPair)

## ----message=FALSE------------------------------------------------------------
spicyTest <- spicy(
  diabetesData,
  condition = "stage",
  subject = "case"
)

topPairs(spicyTest)

## -----------------------------------------------------------------------------
bind(spicyTest)[1:5, 1:5]

## -----------------------------------------------------------------------------
signifPlot(
  spicyTest,
  breaks = c(-3, 3, 1),
  marksToPlot = c(
    "alpha", "beta", "gamma", "delta",
    "B", "naiveTc", "Th", "Tc", "neutrophil", "macrophage"
  )
)

## -----------------------------------------------------------------------------
spicyBoxPlot(results = spicyTest,
             # from = "beta",
             # to = "delta",
             rank = 1)

## -----------------------------------------------------------------------------
diabetesData_SPE <- SpatialExperiment(diabetesData,
                                      colData = colData(diabetesData)) 

spatialCoords(diabetesData_SPE) <- data.frame(colData(diabetesData_SPE)$x, colData(diabetesData_SPE)$y) |> as.matrix()
spatialCoordsNames(diabetesData_SPE) <- c("x", "y")

diabetesData_SPE <- imcRtools::buildSpatialGraph(diabetesData_SPE, img_id = "imageID", type = "knn", k = 20, coords = c("x", "y"))

pairAbundances <- convPairs(diabetesData_SPE,
                  colPair = "knn_interaction_graph")

head(pairAbundances["delta__delta"])

## -----------------------------------------------------------------------------
spicyTestColPairs <- spicy(
  diabetesData_SPE,
  condition = "stage",
  subject = "case",
  alternateResult = pairAbundances,
  weights = FALSE
)

topPairs(spicyTestColPairs)

## -----------------------------------------------------------------------------
signifPlot(
  spicyTestColPairs,
  marksToPlot = c(
    "alpha", "acinar", "ductal", "naiveTc", "neutrophil", "Tc",
    "Th", "otherimmune"
  )
)

## -----------------------------------------------------------------------------
sessionInfo()