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

## ----setup--------------------------------------------------------------------
library(ggalign)

## ----setup_data---------------------------------------------------------------
set.seed(123)
small_mat <- matrix(rnorm(81), nrow = 9)
rownames(small_mat) <- paste0("row", seq_len(nrow(small_mat)))
colnames(small_mat) <- paste0("column", seq_len(ncol(small_mat)))

## ----align_group_top----------------------------------------------------------
ggheatmap(small_mat) +
    anno_top() +
    align_group(sample(letters[1:4], ncol(small_mat), replace = TRUE))

## ----align_group_left---------------------------------------------------------
ggheatmap(small_mat) +
    theme(strip.text = element_text()) +
    anno_left() +
    align_group(sample(letters[1:4], nrow(small_mat), replace = TRUE))

## ----align_order--------------------------------------------------------------
ggheatmap(small_mat) +
    anno_left() +
    align_order(rowMeans)

## ----align_order_integer_index------------------------------------------------
my_order <- sample(nrow(small_mat))
print(rownames(small_mat)[my_order])
ggheatmap(small_mat) +
    anno_left() +
    align_order(my_order)

## ----align_order_character_index----------------------------------------------
ggheatmap(small_mat) +
    anno_left() +
    align_order(rownames(small_mat)[my_order])

## ----align_order_reverse------------------------------------------------------
ggheatmap(small_mat) +
    anno_left() +
    align_order(rowMeans, reverse = TRUE)

## -----------------------------------------------------------------------------
ggheatmap(small_mat) +
    anno_top() +
    align_order(rowMeans)

## -----------------------------------------------------------------------------
ggheatmap(small_mat) +
    anno_top() +
    align_kmeans(3L)

## ----error=TRUE---------------------------------------------------------------
ggheatmap(small_mat) +
    anno_top() +
    align_group(sample(letters[1:4], ncol(small_mat), replace = TRUE)) +
    align_kmeans(3L)

## ----error=TRUE---------------------------------------------------------------
ggheatmap(small_mat) +
    anno_top() +
    align_kmeans(3L) +
    align_group(sample(letters[1:4], ncol(small_mat), replace = TRUE))

## ----align_dendro-------------------------------------------------------------
ggheatmap(small_mat) +
    anno_top() +
    align_dendro()

## ----align_dendro_distance_pearson--------------------------------------------
ggheatmap(small_mat) +
    anno_top() +
    align_dendro(distance = "pearson") +
    patch_titles(top = "pre-defined distance method (1 - pearson)")

## ----align_dendro_distance_function-------------------------------------------
ggheatmap(small_mat) +
    anno_top() +
    align_dendro(distance = function(m) dist(m)) +
    patch_titles(top = "a function that calculates distance matrix")

## -----------------------------------------------------------------------------
ggheatmap(small_mat) +
    anno_top() +
    align_dendro(method = "ward.D2")

## -----------------------------------------------------------------------------
ggheatmap(small_mat) +
    anno_top() +
    align_dendro(k = 3L)

## -----------------------------------------------------------------------------
ggheatmap(small_mat) +
    anno_top() +
    align_dendro() +
    geom_point(aes(y = y))

## -----------------------------------------------------------------------------
ggheatmap(small_mat) +
    anno_top() +
    align_dendro(aes(color = branch), k = 3) +
    geom_point(aes(color = branch, y = y))

## ----fig.width=10-------------------------------------------------------------
h1 <- ggheatmap(small_mat) +
    anno_top() +
    align_dendro(aes(color = branch), k = 3, reorder_dendrogram = TRUE) +
    ggtitle("reorder_dendrogram = TRUE")
h2 <- ggheatmap(small_mat) +
    anno_top() +
    align_dendro(aes(color = branch), k = 3) +
    ggtitle("reorder_dendrogram = FALSE")
align_plots(h1, h2)

## -----------------------------------------------------------------------------
set.seed(3L)
column_groups <- sample(letters[1:3], ncol(small_mat), replace = TRUE)
ggheatmap(small_mat) +
    anno_top() +
    align_group(column_groups) +
    align_dendro(aes(color = branch))

## -----------------------------------------------------------------------------
ggheatmap(small_mat) +
    anno_top() +
    align_group(column_groups) +
    align_dendro(aes(color = branch), reorder_group = TRUE)

## -----------------------------------------------------------------------------
ggheatmap(small_mat) +
    anno_top() +
    align_group(column_groups) +
    align_dendro(aes(color = branch), merge_dendrogram = TRUE)

## -----------------------------------------------------------------------------
ggheatmap(small_mat) +
    anno_top() +
    align_group(column_groups) +
    align_dendro(aes(color = branch),
        reorder_group = TRUE,
        merge_dendrogram = TRUE
    ) +
    anno_bottom() +
    align_dendro(aes(color = branch),
        reorder_group = FALSE,
        merge_dendrogram = TRUE
    )

## ----error=TRUE---------------------------------------------------------------
ggheatmap(small_mat) +
    anno_top() +
    align_group(column_groups) +
    align_dendro(k = 2L)

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