inst/examples/01.example-simple.R

In jokergoo/InteractiveComplexHeatmap: Make Interactive Complex Heatmaps

# Simple examples

####################################################################
# title: A single heatmap with minimal arguments.

m = matrix(rnorm(100*100), 100)
ht = Heatmap(m)
ht = draw(ht)

htShiny(ht)

####################################################################
# title: A single heatmap from a character matrix.

m = matrix(sample(letters[1:10], 100*100, replace = TRUE), 100)
ht = Heatmap(m)
ht = draw(ht)

htShiny(ht)

####################################################################
# title: A single heatmap with annotations on both rows and columns.

m = matrix(rnorm(100*100), 100)
rownames(m) = paste0("R", 1:100)
colnames(m) = paste0("C", 1:100)
ht = Heatmap(m, 
	top_annotation = HeatmapAnnotation(foo = runif(100)),
	left_annotation = rowAnnotation(bar = anno_points(1:100)),
	show_row_names = FALSE, show_column_names = FALSE)
ht = draw(ht)

htShiny(ht)

####################################################################
# title: A single heatmap where rows and columns are split.

m = matrix(rnorm(100*100), 100)
rownames(m) = paste0("R", 1:100)
colnames(m) = paste0("C", 1:100)
ht = Heatmap(m, 
	top_annotation = HeatmapAnnotation(foo = runif(100)),
	left_annotation = rowAnnotation(bar = anno_points(1:100)),
	show_row_names = FALSE, show_column_names = FALSE,
	row_km = 2, column_km = 3)
ht = draw(ht)

htShiny(ht)

####################################################################
# title: A list of two heatmaps.

m = matrix(rnorm(100*100), 100)
rownames(m) = paste0("R", 1:100)
colnames(m) = paste0("C", 1:100)
ht1 = Heatmap(m, 
	top_annotation = HeatmapAnnotation(foo1 = runif(100)),
	left_annotation = rowAnnotation(bar1 = anno_points(1:100)),
	show_row_names = FALSE, show_column_names = FALSE)

m = matrix(rnorm(100*100), 100)
rownames(m) = paste0("R", 1:100)
colnames(m) = paste0("C", 1:100)
ht2 = Heatmap(m, 
	bottom_annotation = HeatmapAnnotation(foo2 = runif(100)),
	right_annotation = rowAnnotation(bar2 = anno_points(1:100)),
	show_row_names = FALSE, show_column_names = FALSE)

ht_list = ht1 + ht2
ht_list = draw(ht_list)
htShiny(ht_list, width1 = 600)

################################################################
# title: A list of two vertically concatenated heatmaps

set.seed(123)
mat1 = matrix(rnorm(100), 10)
rownames(mat1) = colnames(mat1) = paste0("a", 1:10)
mat2 = matrix(sample(letters[1:10], 100, replace = TRUE), 10)
rownames(mat2) = colnames(mat2) = paste0("b", 1:10)

ht_list = Heatmap(mat1, name = "mat_a", row_km = 2, column_km = 2) %v%
    Heatmap(mat2, name = "mat_b")

htShiny(ht_list, height1 = 600)

###############################################################
# title: Use last generated heatmap, an example from cola package.

library(cola)
data(golub_cola)

res = golub_cola["ATC:skmeans"]

# In this example, the plot was first generated in a null device. You can also
# generate it in any other devices
pdf(NULL)
get_signatures(res, k = 3)
dev.off()

htShiny()

###############################################################
# title: Use last generated heatmap, an app with three interactive heatmaps

library(cola)
data(golub_cola)

res = golub_cola["ATC:skmeans"]

pdf(NULL)
consensus_heatmap(res, k = 3)
dev.off()
# Here we use `ComplexHeatmap:::get_last_ht()` to explicitely extract the heatmap object
ht1 = ComplexHeatmap:::get_last_ht()

pdf(NULL)
membership_heatmap(res, k = 3)
dev.off()
ht2 = ComplexHeatmap:::get_last_ht()

pdf(NULL)
get_signatures(res, k = 3)
dev.off()
ht3 = ComplexHeatmap:::get_last_ht()

# The three interactive complex heatmap widgets are put into three different tabs
ui = mainPanel(
    tabsetPanel(
        tabPanel("Consensus heatmap",  InteractiveComplexHeatmapOutput("heatmap_1")),
        tabPanel("Membership heatmap", InteractiveComplexHeatmapOutput("heatmap_2")),
        tabPanel("Signature heatmap",  InteractiveComplexHeatmapOutput("heatmap_3"))
    )
)

server = function(input, output, session) {
    makeInteractiveComplexHeatmap(input, output, session, ht1, "heatmap_1")
    makeInteractiveComplexHeatmap(input, output, session, ht2, "heatmap_2")
    makeInteractiveComplexHeatmap(input, output, session, ht3, "heatmap_3")
}

shinyApp(ui, server)

###############################################################
# title: Demonstrate hover, click and dblclick actions to select cells.

m = matrix(rnorm(10*10), 10)
ht = Heatmap(m)
ht = draw(ht)

# In each tab, you can only get the information of a single cell either by hovering, single clicking or double clicking.
ui = tabsetPanel(
    tabPanel("action = 'hover'",    InteractiveComplexHeatmapOutput("heatmap_1", action = "hover")),
    tabPanel("action = 'click'",    InteractiveComplexHeatmapOutput("heatmap_2", action = "click")),
    tabPanel("action = 'dblclick'", InteractiveComplexHeatmapOutput("heatmap_3", action = "dblclick"))
)

server = function(input, output, session) {
    makeInteractiveComplexHeatmap(input, output, session, ht, "heatmap_1")
    makeInteractiveComplexHeatmap(input, output, session, ht, "heatmap_2")
    makeInteractiveComplexHeatmap(input, output, session, ht, "heatmap_3")
}

shinyApp(ui, server)

################################################################
# title: Only response to one of click/hover/dblclick/hover events. Please use htShinyExample('1.10') to get this example (quote the index, or else htShinyExample(1.10) will be treated as the same as htShinyExample(1.1)).

m = matrix(rnorm(10*10), 10)
ht = Heatmap(m)
ht = draw(ht)

# Each tab only responds to one event on heatmap.
ui = tabsetPanel(
    tabPanel("response = 'hover'",    InteractiveComplexHeatmapOutput("heatmap_1", action = "hover", response = "hover")),
    tabPanel("response = 'click'",    InteractiveComplexHeatmapOutput("heatmap_2", action = "click", response = "click")),
    tabPanel("response = 'dblclick'", InteractiveComplexHeatmapOutput("heatmap_3", action = "dblclick", response = "dblclick")),
    tabPanel("response = 'brush-output'", InteractiveComplexHeatmapOutput("heatmap_4", response = "brush-output")),
    tabPanel("response = 'brush'",    InteractiveComplexHeatmapOutput("heatmap_5", response = "brush"))
)

server = function(input, output, session) {
    makeInteractiveComplexHeatmap(input, output, session, ht, "heatmap_1")
    makeInteractiveComplexHeatmap(input, output, session, ht, "heatmap_2")
    makeInteractiveComplexHeatmap(input, output, session, ht, "heatmap_3")
    makeInteractiveComplexHeatmap(input, output, session, ht, "heatmap_4")
    makeInteractiveComplexHeatmap(input, output, session, ht, "heatmap_5")
}

shinyApp(ui, server)


#########################################################
# title: Interactive heatmap under compact mode.

m = matrix(rnorm(10*10), 10)
ht = Heatmap(m)
ht = draw(ht)

htShiny(ht, compact = TRUE)