# == title
# Get row order from a heatmap list
#
# == param
# -object a `HeatmapList-class` object
#
# == value
# The format of the returned object depends on whether rows/columns of the heatmaps are split.
#
# == author
# Zuguang Gu <z.gu@dkfz.de>
#
# == example
# mat = matrix(rnorm(100), 10)
# ht_list = Heatmap(mat) + Heatmap(mat)
# ht_list = draw(ht_list)
# row_order(ht_list)
# ht_list = Heatmap(mat, row_km = 2) + Heatmap(mat)
# ht_list = draw(ht_list)
# row_order(ht_list)
# ht_list = Heatmap(mat, row_km = 2) %v% Heatmap(mat)
# ht_list = draw(ht_list)
# row_order(ht_list)
setMethod(f = "row_order",
signature = "HeatmapList",
definition = function(object) {
object = make_layout(object)
n = length(object@ht_list)
ht_index = which(sapply(seq_along(object@ht_list), function(i) inherits(object@ht_list[[i]], "Heatmap")))
if(length(ht_index) == 0) {
return(NULL)
}
if(object@direction == "horizontal") {
lt = object@ht_list[[ ht_index[1] ]]@row_order_list
if(length(lt) == 1) {
return(lt[[1]])
} else {
return(lt)
}
} else {
lt_rd = list()
for(i in ht_index) {
lt = object@ht_list[[i]]@row_order_list
lt_rd = c(lt_rd, list(lt))
}
names(lt_rd) = names(object@ht_list)[ht_index]
proper_format_lt(lt_rd)
}
})
# == title
# Get row order from a heatmap
#
# == param
# -object a `Heatmap-class` object
#
# == value
# The format of the returned object depends on whether rows/columns of the heatmaps are split.
#
# == author
# Zuguang Gu <z.gu@dkfz.de>
#
# == example
# mat = matrix(rnorm(100), 10)
# ht = Heatmap(mat)
# ht = draw(ht)
# row_order(ht)
# ht = Heatmap(mat, row_km = 2)
# ht = draw(ht)
# row_order(ht)
#
setMethod(f = "row_order",
signature = "Heatmap",
definition = function(object) {
object = prepare(object)
lt = object@row_order_list
if(length(lt) == 1) {
return(lt[[1]])
} else {
return(lt)
}
})
# == title
# Get column order from a heatmap list
#
# == param
# -object a `HeatmapList-class` object
#
# == value
# The format of the returned object depends on whether rows/columns of the heatmaps are split.
#
# == author
# Zuguang Gu <z.gu@dkfz.de>
#
# == example
# mat = matrix(rnorm(100), 10)
# ht_list = Heatmap(mat) + Heatmap(mat)
# ht_list = draw(ht_list)
# column_order(ht_list)
# ht_list = Heatmap(mat, column_km = 2) + Heatmap(mat, column_km = 2)
# ht_list = draw(ht_list)
# column_order(ht_list)
# ht_list = Heatmap(mat) %v% Heatmap(mat)
# ht_list = draw(ht_list)
# column_order(ht_list)
# ht_list = Heatmap(mat, column_km = 2) %v% Heatmap(mat)
# ht_list = draw(ht_list)
# column_order(ht_list)
setMethod(f = "column_order",
signature = "HeatmapList",
definition = function(object) {
object = make_layout(object)
n = length(object@ht_list)
ht_index = which(sapply(seq_along(object@ht_list), function(i) inherits(object@ht_list[[i]], "Heatmap")))
if(length(ht_index) == 0) {
return(NULL)
}
if(object@direction == "vertical") {
lt = object@ht_list[[ ht_index[1] ]]@column_order_list
if(length(lt) == 1) {
return(lt[[1]])
} else {
return(lt)
}
} else {
lt_rd = list()
for(i in ht_index) {
lt = object@ht_list[[i]]@column_order_list
lt_rd = c(lt_rd, list(lt))
}
names(lt_rd) = names(object@ht_list)[ht_index]
proper_format_lt(lt_rd)
}
})
# == title
# Get column order from a heatmap list
#
# == param
# -object a `Heatmap-class` object
#
# == value
# The format of the returned object depends on whether rows/columns of the heatmaps are split.
#
# == author
# Zuguang Gu <z.gu@dkfz.de>
#
# == example
# mat = matrix(rnorm(100), 10)
# ht = Heatmap(mat)
# ht = draw(ht)
# column_order(ht)
# ht = Heatmap(mat, column_km = 2)
# ht = draw(ht)
# column_order(ht)
setMethod(f = "column_order",
signature = "Heatmap",
definition = function(object) {
object = prepare(object)
lt = object@column_order_list
if(length(lt) == 1) {
return(lt[[1]])
} else {
return(lt)
}
})
# == title
# Get row dendrograms from a heatmap list
#
# == param
# -object a `HeatmapList-class` object
#
# == value
# The format of the returned object depends on whether rows/columns of the heatmaps are split.
#
# == author
# Zuguang Gu <z.gu@dkfz.de>
#
# == example
# mat = matrix(rnorm(100), 10)
# ht_list = Heatmap(mat) + Heatmap(mat)
# ht_list = draw(ht_list)
# row_dend(ht_list)
# ht_list = Heatmap(mat, row_km = 2) + Heatmap(mat)
# ht_list = draw(ht_list)
# row_dend(ht_list)
# ht_list = Heatmap(mat, row_km = 2) %v% Heatmap(mat)
# ht_list = draw(ht_list)
# row_dend(ht_list)
setMethod(f = "row_dend",
signature = "HeatmapList",
definition = function(object) {
object = make_layout(object)
n = length(object@ht_list)
ht_index = which(sapply(seq_along(object@ht_list), function(i) inherits(object@ht_list[[i]], "Heatmap")))
if(length(ht_index) == 0) {
return(NULL)
}
if(object@direction == "horizontal") {
lt = object@ht_list[[ ht_index[1] ]]@row_dend_list
if(length(lt) == 1) {
return(lt[[1]])
} else {
return(lt)
}
} else {
lt_rd = list()
for(i in ht_index) {
lt = object@ht_list[[i]]@row_dend_list
lt_rd = c(lt_rd, list(lt))
}
names(lt_rd) = names(object@ht_list)[ht_index]
proper_format_lt(lt_rd)
}
})
# == title
# Get row dendrograms from a heatmap
#
# == param
# -object a `Heatmap-class` object
#
# == value
# The format of the returned object depends on whether rows/columns of the heatmaps are split.
#
# == author
# Zuguang Gu <z.gu@dkfz.de>
#
# == example
# mat = matrix(rnorm(100), 10)
# ht = Heatmap(mat)
# ht = draw(ht)
# row_dend(ht)
# ht = Heatmap(mat, row_km = 2)
# ht = draw(ht)
# row_dend(ht)
#
setMethod(f = "row_dend",
signature = "Heatmap",
definition = function(object) {
object = prepare(object)
lt = object@row_dend_list
if(length(lt) == 1) {
return(lt[[1]])
} else {
return(lt)
}
})
# == title
# Get column dendrograms from a heatmap list
#
# == param
# -object a `HeatmapList-class` object
#
# == value
# The format of the returned object depends on whether rows/columns of the heatmaps are split.
#
# == author
# Zuguang Gu <z.gu@dkfz.de>
#
# == example
# mat = matrix(rnorm(100), 10)
# ht_list = Heatmap(mat) + Heatmap(mat)
# ht_list = draw(ht_list)
# column_dend(ht_list)
# ht_list = Heatmap(mat, column_km = 2) + Heatmap(mat, column_km = 2)
# ht_list = draw(ht_list)
# column_dend(ht_list)
# ht_list = Heatmap(mat) %v% Heatmap(mat)
# ht_list = draw(ht_list)
# column_dend(ht_list)
# ht_list = Heatmap(mat, column_km = 2) %v% Heatmap(mat)
# ht_list = draw(ht_list)
# column_dend(ht_list)
setMethod(f = "column_dend",
signature = "HeatmapList",
definition = function(object) {
object = make_layout(object)
n = length(object@ht_list)
ht_index = which(sapply(seq_along(object@ht_list), function(i) inherits(object@ht_list[[i]], "Heatmap")))
if(length(ht_index) == 0) {
return(NULL)
}
if(object@direction == "vertical") {
lt = object@ht_list[[ ht_index[1] ]]@column_dend_list
if(length(lt) == 1) {
return(lt[[1]])
} else {
return(lt)
}
} else {
lt_rd = list()
for(i in ht_index) {
lt = object@ht_list[[i]]@column_dend_list
lt_rd = c(lt_rd, list(lt))
}
names(lt_rd) = names(object@ht_list)[ht_index]
proper_format_lt(lt_rd)
}
})
# == title
# Get column dendrograms from a heatmap
#
# == param
# -object a `Heatmap-class` object
#
# == value
# The format of the returned object depends on whether rows/columns of the heatmaps are split.
#
# == author
# Zuguang Gu <z.gu@dkfz.de>
#
# == example
# mat = matrix(rnorm(100), 10)
# ht = Heatmap(mat)
# ht = draw(ht)
# column_dend(ht)
# ht = Heatmap(mat, column_km = 2)
# ht = draw(ht)
# column_dend(ht)
#
setMethod(f = "column_dend",
signature = "Heatmap",
definition = function(object) {
object = prepare(object)
lt = object@column_dend_list
if(length(lt) == 1) {
return(lt[[1]])
} else {
return(lt)
}
})
proper_format_lt = function(lt) {
n_ht = length(lt)
# for a single heatmap
if(n_ht == 1) {
if(length(lt[[1]]) == 1) {
return(lt[[1]][[1]])
} else {
return(lt[[1]])
}
} else {
has_splitting = any(sapply(lt, function(x) length(x) != 1))
if(has_splitting) {
return(lt)
} else {
return(lapply(lt, function(x) x[[1]]))
}
}
}
