---
title: "Functions for Shiny app development"
author: "Zuguang Gu ( z.gu@dkfz.de )"
date: "`r Sys.Date()`"
output:
rmarkdown::html_vignette:
width: 8
fig_width: 5
toc: true
vignette: >
%\VignetteIndexEntry{3. Functions for Shiny app development}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
---
<style>
p {
margin: 1em 0;
}
img {
background-color: #FFFFFF;
padding: 2px;
border: 1px solid #DDDDDD;
border-radius: 3px;
border: 1px solid #CCCCCC;
margin: 0 5px;
}
</style>
```{r, echo = FALSE}
library(knitr)
knitr::opts_chunk$set(
error = FALSE,
tidy = FALSE,
message = FALSE,
warning = FALSE,
fig.align = "center"
)
```
## Usage
`htShiny()` can export heatmaps as a stand-alone Shiny app. **InteractiveComplexHeatmap** also provides two
functions for integrating the interactive heatmap widgets into other Shiny apps. The two functions are:
- `InteractiveComplexHeatmapOutput()`: for building UI on the client side.
- `makeInteractiveComplexHeatmap()`: for processing on the sever side.
### With one interactive heatmap widget
The usage is simple. Following is an example that you can directly copy and paste to your R session.
```{r, eval = FALSE}
library(ComplexHeatmap)
library(InteractiveComplexHeatmap)
library(shiny)
data(rand_mat) # simply a random matrix
ht1 = Heatmap(rand_mat, name = "mat",
show_row_names = FALSE, show_column_names = FALSE)
ht1 = draw(ht1)
ui = fluidPage(
h3("My first interactive ComplexHeatmap Shiny app"),
p("This is an interactive heatmap visualization on a random matrix."),
InteractiveComplexHeatmapOutput()
)
server = function(input, output, session) {
makeInteractiveComplexHeatmap(input, output, session, ht1)
}
shinyApp(ui, server)
```
<script>
document.write('<img src="https://jokergoo.github.io/images/app_demo1.png" width="100%" />');
</script>
### With multiple interactive heatmap widgets
You can also put multiple interactive heatmaps widgets in a single Shiny app,
but this time you must assign a "**heatmap ID**" for each one, so that
`makeInteractiveComplexHeatmap()` can find the correct heatmap to respond.
The heatmap ID should start with letters.
```{r, eval = FALSE}
mat2 = matrix(sample(letters[1:10], 100, replace = TRUE), 10)
ht2 = draw(Heatmap(mat2, name = "mat2"))
ui = fluidPage(
h3("The first heatmap"),
InteractiveComplexHeatmapOutput("heatmap_1"),
hr(),
h3("The second heatmap"),
InteractiveComplexHeatmapOutput("heatmap_2")
)
server = function(input, output, session) {
makeInteractiveComplexHeatmap(input, output, session, ht1, "heatmap_1")
makeInteractiveComplexHeatmap(input, output, session, ht2, "heatmap_2")
}
shinyApp(ui, server)
```
<script>
document.write('<img src="https://jokergoo.github.io/images/app_two.png" width=100% />');
</script>
Similarly, multiple interactive heatmap widgets can be arranged by a list of tabs:
```{r, eval = FALSE}
ui = tabsetPanel(
tabPanel("Numeric", InteractiveComplexHeatmapOutput("heatmap_1")),
tabPanel("character", InteractiveComplexHeatmapOutput("heatmap_2"))
)
server = function(input, output, session) {
makeInteractiveComplexHeatmap(input, output, session, ht1, "heatmap_1")
makeInteractiveComplexHeatmap(input, output, session, ht2, "heatmap_2")
}
shinyApp(ui, server)
```
## Customize the widgets
There are three main components in the interactive heatmap UI, _i.e._, the
orignal heatmap, the sub-heatmap and an output that shows information of the clicked cell or
the selected sub-heatmap. The original heatmap and sub-heatmap components can be resized by
dragging the two boxes, but still, `InteractiveComplexHeatmapOutput()`
provides arguments of `width1`, `width2`, `height1` and `height2` to control
the initial sizes of the two components. They can be manually set to make sure the
heatmap is well aligned, e.g. in `htShinyExample(2.2)`.
The initial style of the brush can be specified by `brush_opt` argument. The
value should be a list and the value will be sent to `shiny::brushOpts()`. Note,
the style of the brush can also be manually adjusted in the Shiny app.
### The layout
The layout of the three components are controlled by argument `layout`. It
supports following values:
- `"(1-2)|3"`: Original heatmap and sub-heatmap are in the same row, and output is in a
second row. This is the default layout.
- `"1|(2-3)"`: Original heatmap is in a single row, while sub-heatmap and output are in
a second row.
- `"1-2-3"`: All three components are in the same row.
- `"1|2|3"`: Each component is in a single row.
- `"1-(2|3)"`: Being different from the other four layouts, this is a
two-column layout. Original heatmap is in a single column. Sub-heatmap and output are
vertically aligned and the two are in the second column. An example can be
found at `htShinyExample(4.1)`.
Note the values for `layout` are in a special format to help to
understand the layout, where the three code `1`, `2` and `3` correspond to original heatmap, sub-heatmap and output respectively,
symbol `"-"` corresponds to horizontal
alignment and `"|"` corresponds to vertical alignment.
With different layouts, different default values are assigned to widths and
heights of the three components to make sure they are well aligned.
### Action on single heatmap cells
By default, to get the information of a single cell in the heatmap, a `"click"`
action is used. In `InteractiveComplexHeatmapOutput()`, the action can also be set
to `"hover"` or `"dblclick"`, then hovering or double clicking will trigger the response on the sever side.
The example in `htShinyExample(1.9)` demonstrates usages of these three actions.
### Which action to respond
The argument `response` can be set as a vector with values in `"click"`, `"hover"`, `"dblclick"`, `"brush"` and `"brush-output"`
to only respond to one or multiple events on heatmap. E.g. if `response` is only set to `"click"`, there will
be no response for the "brush event" in the interactive heatmap, also the sub-heatmap component
is removed from the app. Please go to Section ["Only respond to one event"](InteractiveComplexHeatmap.html#only-respond-to-one-event) for examples.
A brush on heatmap by default triggers two responses, one in the sub-heatmap and one in the output. If `"brush-output"`
is included in `response` instead of `"brush"`, you can still brush on the heatmap, but there is only response in the output,
and the sub-heatmap component is removed from the app.
### Separately specify the three UI components
`InteractiveComplexHeatmapOutput()` contains all three UI components. The three components can be
separately specified as three individual functions: `originalHeatmapOutput()`, `subHeatmapOutput()` and `HeatmapInfoOutput()`.
This provides flexibility for the UI arrangement, e.g. to integrate with package **shinydashboard** where each UI component
is wrapped within an individual box.
```{r, eval = FALSE}
body = dashboardBody(
fluidRow(
box(
title = "Original heatmap", width = 4, solidHeader = TRUE, status = "primary",
originalHeatmapOutput("ht", title = NULL)
),
box(
title = "Sub-heatmap", width = 4, solidHeader = TRUE, status = "primary",
subHeatmapOutput("ht", title = NULL)
),
box(
title = "Output", width = 4, solidHeader = TRUE, status = "primary",
HeatmapInfoOutput("ht", title = NULL)
)
)
)
ui = dashboardPage(
dashboardHeader(),
dashboardSidebar(),
body
)
server = function(input, output, session) {
makeInteractiveComplexHeatmap(input, output, session, ht, "ht")
}
shinyApp(ui, server)
```
<script>
document.write('<img src="https://jokergoo.github.io/images/shinydashboard.png" width="100%" />');
</script>
Please note, since now the three components are generated independently, to correctly connect the three components
as well as the server side, the heatmap ID must be explicitely specified in all functions.
More examples on integrating with **shinydashboard** can be found from `htShinyExample(10.1)` to `htShinyExample(10.5)`.
In vignette ["A Shiny app for visualizing DESeq2 results"](deseq2_app.html), we demonstrate a complex app where
the three UI components are specified separately to work with **shinydashboard**.
One thing that needs to be noted when integrating with **shinydashboard** is that the width (via `width` argument in `box()`) is actually
measured as the relative fraction to parent `div` block, thus it is suggested to set the minimal width for parent block by adding
a self-defined CSS code:
```r
body = dashboardBody(
fluidRow(
box(
title = "Original heatmap", width = 4, solidHeader = TRUE, status = "primary",
originalHeatmapOutput("ht", title = NULL)
),
box(
title = "Sub-heatmap", width = 4, solidHeader = TRUE, status = "primary",
subHeatmapOutput("ht", title = NULL)
),
box(
title = "Output", width = 4, solidHeader = TRUE, status = "primary",
HeatmapInfoOutput("ht", title = NULL)
),
tags$style("
.content-wrapper, .right-side {
overflow-x: auto;
}
.content {
min-width:1500px;
}
")
)
)
```
## Work with R Markdown documents
It is very straightforward to integrate **InteractiveComplexHeatmap** in an
interactive R Markdown document, just in the same way of integrating normal Shiny
widgets. Following is an example and you can run a real interactive document
with heatmaps by `htShinyExample(7.1)`.
````markdown
---
title: "InteractiveComplexHeatmap in an Rmarkdown document"
author: "Zuguang Gu"
date: "16/12/2020"
output: html_document
runtime: shiny
---
`r ''````{r, echo = FALSE}
library(InteractiveComplexHeatmap)
m = matrix(rnorm(100*100), 100)
ht = Heatmap(m)
```
`r ''````{r, echo = FALSE}
ui = fluidPage(
InteractiveComplexHeatmapOutput()
)
server = function(input, output, session) {
makeInteractiveComplexHeatmap(input, output, session, ht)
}
shiny::shinyApp(ui, server)
```
````
<script>
document.write('<img src="https://jokergoo.github.io/images/rmarkdown.png" width="100%" />');
</script>
More simply, you can directly use `htShiny()` in the chunk:
````markdown
---
title: "InteractiveComplexHeatmap in an Rmarkdown document"
author: "Zuguang Gu"
date: "16/12/2020"
output: html_document
runtime: shiny
---
`r ''````{r, echo = FALSE}
library(InteractiveComplexHeatmap)
m = matrix(rnorm(100*100), 100)
ht = Heatmap(m)
```
`r ''````{r, echo = FALSE}
htShiny(ht)
```
````
## Self-define the output
Both the click and brush actions on the heatmap trigger an output below the
heatmaps. The output gives the information of which row(s) and columns(s) are
selected by users. The reponse for the two actions can be self-defined.
In `makeInteractiveComplexHeatmap()`, there are two arguments `click_action`
and `brush_action` which accept self-defined functions and define how to
respond after the heatmap is clicked or brushed. The input for the two
functions should accept two arguments, one is a `DataFrame` object which
contains the information of which row(s) and columns(s) selected by users,
and the second argument should always be `output` which is used in the Shiny
app. `click_action` and `brush_action` can also be functions with four arguments
which also includes `input` and `session`, in a form of `function(df, input, output, session) {...}`.
To use `click_action` or `brush_action`, a `htmlOutput` (or other similar
`*Output`) should be first set up in the UI, then the Shiny application knows where to
update the output. The output UI can replace the default output by directly assigning to argument
`output_ui` in `InteractiveComplexHeatmapOutput()`.
```{r, eval = FALSE}
ui = fluidPage(
InteractiveComplexHeatmapOutput(output_ui = htmlOutput("info"))
)
```
Or to create a new output UI independent to the interactive heatmap widget:
```{r, eval = FALSE}
ui = fluidPage(
InteractiveComplexHeatmapOutput(),
htmlOutput("info")
)
```
The `click_action` or `brush_action` is basically defined as follows (assume
the ID set in `htmlOutput()` is `"info"`):
```{r, eval = FALSE}
function(df, output) {
output[["info"]] = renderUI({ # or output$info = ...
if(is.null(df)) { # have not clicked or brushed into the heatmap body
...
} else {
...
}
})
}
```
If users didn't click or brush inside the heatmap body (e.g. clicked in the
dendrograms), `df` that is passed to the functions will be `NULL`. Users might
need to perform a sanity check here and print specific output when the heatmap
was not selected.
The format of `df` is slightly different between click and brush. If it is a
click action, `df` has the same format as the returned object of
`selectPosition()` function, which looks like follows. It always has one row.
```
## DataFrame with 1 row and 6 columns
## heatmap slice row_slice column_slice row_index
## <character> <character> <numeric> <numeric> <integer>
## 1 mat_a mat_a_heatmap_body_1_2 1 2 9
## column_index
## <integer>
## 1 1
```
If it is a brush action, `df` has the same format as the returned object of
`selectArea()` function, which looks like in the following chunk. Each line
contains row and column indices of the selected sub-matrix in a specific
heatmap slice of a specific heatmap.
```
## DataFrame with 4 rows and 6 columns
## heatmap slice row_slice column_slice row_index
## <character> <character> <numeric> <numeric> <IntegerList>
## 1 mat_a mat_a_heatmap_body_1_2 1 2 7,5,2,...
## 2 mat_a mat_a_heatmap_body_2_2 2 2 6,3
## 3 mat_b mat_b_heatmap_body_1_1 1 1 7,5,2,...
## 4 mat_b mat_b_heatmap_body_2_1 2 1 6,3
## column_index
## <IntegerList>
## 1 2,4,1,...
## 2 2,4,1,...
## 3 1,2,3,...
## 4 1,2,3,...
```
Note as demonstrated above, the values in column `row_index` and `column_index` might
be duplicated due to that the selected heatmap slices are in a same row slice or column slice,
_e.g._, in previous example, the first and the third rows correspond to selection in the first
row slice, but in the two column slices respectively, so they have the same value for `row_index`.
thus, to safely get the row indices and column indices of the selected heatmap, users
might need to perform:
```{r, eval = FALSE}
unique(unlist(df$row_index))
unique(unlist(df$column_index))
```
Note again, if users want to use the values in `input` or `session`, `click_action` and `brush_action` can also
be specified as functions with four arguments:
```{r, eval = FALSE}
function(df, input, output, session) {
output[["info"]] = renderUI({ # or output$info = ...
if(is.null(df)) { # have not clicked into the heatmap body
...
} else {
...
}
})
}
```
If `action` in `InteractiveComplexHeatmapOutput()` is set to `"hover"` or `"dblclick"`, the corresponding
argument for action is `hover_action` or `dblclick_action`. The usage is exactly the same as `click_action`.
### Examples of self-defining output
In this section, I will demonstrate several examples of implementing self-defined output.
In the first example, I replace the default ui with a new `htmlOutput("info")`.
On the sever side, I define a `click_action` to print a styled text and a
`brush_action` to print the table of the selected rows and columns from the
heatmap. This following example can be run by `htShinyExample(5.2)`.
```{r, eval = FALSE}
library(GetoptLong) # for the qq() function which does variable intepolation
data(rand_mat)
ht = Heatmap(rand_mat, show_row_names = FALSE, show_column_names = FALSE)
ht = draw(ht)
ui = fluidPage(
InteractiveComplexHeatmapOutput(output_ui = htmlOutput("info")),
)
click_action = function(df, output) {
output[["info"]] = renderUI({
if(!is.null(df)) {
HTML(qq("<p style='background-color:#FF8080;color:white;padding:5px;'>You have clicked on heatmap @{df$heatmap}, row @{df$row_index}, column @{df$column_index}</p>"))
}
})
}
suppressPackageStartupMessages(library(kableExtra))
brush_action = function(df, output) {
row_index = unique(unlist(df$row_index))
column_index = unique(unlist(df$column_index))
output[["info"]] = renderUI({
if(!is.null(df)) {
HTML(kable_styling(kbl(m[row_index, column_index, drop = FALSE], digits = 2, format = "html"), full_width = FALSE, position = "left"))
}
})
}
server = function(input, output, session) {
makeInteractiveComplexHeatmap(input, output, session, ht,
click_action = click_action, brush_action = brush_action)
}
shinyApp(ui, server)
```
<script>
document.write('<img src="https://jokergoo.github.io/images/customize_output.gif" width="100%" />');
</script>
The second example gives another scenario where the output needs to be
self-defined. In this example, an gene expression matrix is visualized and
clicking on the heatmap will print the corresponding gene and some other
annotations related to this gene (e.g. the corresponding gene symbol, RefSeq
IDs and UniProt IDs). Run `htShinyExample(5.3)` to see how this is implemented.
<script>
document.write('<img src="https://jokergoo.github.io/images/customize_output2.png" width="100%" />');
</script>
`htShinyExample(5.4)` gives an example where the heatmap visualizes
correlations of a list of Gene Ontology terms (The plot is generated by [the
**simplifyEnrichment**
package](https://bioconductor.org/packages/simplifyEnrichment/)). In this
example, the click and brush actions are self-defined so that the selected GO
IDs as well as their detailed descriptions are printed.
<script>
document.write('<img src="https://jokergoo.github.io/images/customize_output3.png" width="100%" />');
</script>
`htShinyExample(5.5)` visualizes an correlation heatmap where clicking on the cell
generates a scatter plot of the two corresponding variables. In this example,
I set `response = "click"` in `InteractiveComplexHeatmapOutput()`, so that the sub-heatmap
is removed from the app and the scatterplot (the output) is directly placed on the right
of the original correlation heatmap.
<script>
document.write('<img src="https://jokergoo.github.io/images/corrheatmap.gif" width="100%" />');
</script>
`htShinyExample(5.6)` visualizes an a heatmap of pairwise Jaccard coefficients for
multiple lists of genomic regions. Clicking on the heatmap cell draws a Hilbert curve
(draw by [the **HilbertCurve** package](https://bioconductor.org/packages/HilbertCurve/)) which
shows how the two corresponding sets of genomic regions overlap.
<script>
document.write('<img src="https://jokergoo.github.io/images/hilbert_curve.gif" width="100%" />');
</script>
Instead of occupying static space, the output component can be floated to the
mouse positions by setting `output_ui_float = TRUE` in `InteractiveComplexHeatmapOutput()` so that clicking, hovering
or brushing from the heatmap opens a frame that contains the output.
There are two examples: `htShinyExample(9.1)` and `htShinyExample(9.2)`.
The demonstration is as follows:
<script>
document.write('<img src="https://jokergoo.github.io/images/float1.gif" width="100%" />');
</script>
The self-defined output can also be floated if the self-defined UI replaces the default UI by setting
`InteractiveComplexHeatmapOutput(..., output_ui = new_output_ui)`:
<script>
document.write('<img src="https://jokergoo.github.io/images/float2.gif" width="100%" />');
</script>
## Compact mode
In `InteractiveComplexHeatmapOutput()`, argument `compact` can be set to `TRUE`, so there is only the original heatmap
and the output is floating at the mouse positions if hovering/clicking on heatmap. The calling
```{r, eval = FALSE}
InteractiveComplexHeatmapOutput(..., compact = TRUE)
```
is actually identical to
```{r, eval = FALSE}
InteractiveComplexHeatmap(..., response = c(action, "brush-output"), output_ui_float = TRUE)
```
Self-defined output can still be used here, e.g.
```{r, eval = FALSE}
new_output_ui = ...
InteractiveComplexHeatmap(..., compact = TRUE, output_ui = new_output_ui)
```
See examples with `htShinyExample(1.11)`.
## Dynamically generate interactive heatmap widget
In previous examples, the heatmaps are already generated before making the
interactive app. There are also scenarios where the heatmaps are generated on
the fly, e.g. when the matrix is dynamically generated in the middle of an
analysis. There might be following scenarios:
- The heatmap is based on a subset of matrix which is filtered by users, _e.g._, the expression matrix
for differentially expressed genes filtered by different cutoffs.
- The annotations are dynamically provided by users.
- The heatmap parameters are changed by users, _e.g._, the clustering method or the splitting variable.
- If there are multiple heatmaps, which heatmaps are going to be drawn is dynamically selected.
In **InteractiveComplexHeatmap**, there are three ways to dynamically generate the interactive heatmap widgets
which I will explain one by one.
### Directly use `makeInteractiveComplexHeatmap()`
I first demonstrate use of `makeInteractiveComplexHeatmap()`. In the following
example, the matrix is reordered by a user-selected column:
```{r, eval = FALSE}
ui = fluidPage(
sliderInput("column", label = "Which column to order?",
value = 1, min = 1, max = 10),
InteractiveComplexHeatmapOutput()
)
server = function(input, output, session) {
m = matrix(rnorm(100), 10)
rownames(m) = 1:10
colnames(m) = 1:10
observeEvent(input$column, {
order = order(m[, input$column])
ht = Heatmap(m[order, , drop = FALSE],
cluster_rows = FALSE, cluster_columns = FALSE)
makeInteractiveComplexHeatmap(input, output, session, ht)
})
}
shiny::shinyApp(ui, server)
```
A similar but slightly complex example is as follows. It can be run by `htShinyExample(6.2)`.
<script>
document.write('<img src="https://jokergoo.github.io/images/dynamic_widget4.gif" width="100%" />');
</script>
The use is very natural. `makeInteractiveComplexHeatmap()` is put inside an `observeEvent()` or an `observe()`
so that every time `input$column` changes, it triggers an update of the interactive heatmap widgets.
In the following code block defined in `server` function:
```{r, eval = FALSE}
...
observeEvent(input$column, {
order = order(m[, input$column])
ht = Heatmap(m[order, , drop = FALSE],
cluster_rows = FALSE, cluster_columns = FALSE)
makeInteractiveComplexHeatmap(input, output, session, ht)
})
...
```
`makeInteractiveComplexHeatmap()` internally creates a list of responses by
`observeEvent()`. Every time when `input$column` triggers the update of
`makeInteractiveComplexHeatmap()`, all the calls of `observeEvent()` will be
re-executed. Re-executing `observeEvent()` only adds the observations to the
current observation list while not overwrites them, thus, repeatedly executing
`makeInteractiveComplexHeatmap()` will make a same observatin running multiple
times. To solve this issue, `makeInteractiveComplexHeatmap()` saves all
the observations returned by `observeEvent()` and it tries to first destroies
all the avaiable observations that have been created. However, if user-defined
reponses via `click_action` and `brush_action` use `observe()` or `observeEvent()`,
they must manually recorded so that they can also be destroied when updating `makeInteractiveComplexHeatmap()`.
See the following example:
```{r, eval = FALSE}
click_action = function(df, input, output, session) {
obs = observeEvent(input$foo, {
...
})
record_observation(obs)
}
```
### Use `InteractiveComplexHeatmapModal()` and `InteractiveComplexHeatmapWidget()`
In the first example, the interactive heatmap is already generated when the
Shiny app is loaded. There is a second scenario where the complete interactive heatmap
widget is dynamically generated and inserted into the HTML document. There are
two other functions `InteractiveComplexHeatmapModal()` and
`InteractiveComplexHeatmapWidget()` which have very similar behaviors. These
two functions are normally put inside e.g. `shiny::observeEvent()` or
`shiny::observe()` and they generate UI as well as render the interactive
heatmaps.
First I will introduce the usage of `InteractiveComplexHeatmapModal()`. In the
following example, there is only an action button in the UI, and in the server
function, `InteractiveComplexHeatmapModal()` is called when receiving an `input$show_heatmap`
signal. This example can also be run by `htShinyExample(6.3)`.
```{r, eval = FALSE}
ui = fluidPage(
actionButton("show_heatmap", "Generate_heatmap"),
)
server = function(input, output, session) {
m = matrix(rnorm(100), 10)
ht = Heatmap(m)
observeEvent(input$show_heatmap, {
InteractiveComplexHeatmapModal(input, output, session, ht)
})
}
shiny::shinyApp(ui, server)
```
As shown in the following figure, `InteractiveComplexHeatmapModal()` will open
an "modal frame" which includes the interactive heatmap.
<script>
document.write('<img src="https://jokergoo.github.io/images/dynamic_widget.gif" width="100%" />');
</script>
In the next example which is also available in `htShinyExample(6.4)`, a different heatmap is generated
according to user's selection.
```{r, eval = FALSE}
ui = fluidPage(
radioButtons("select", "Select", c("Numeric" = 1, "Character" = 2)),
actionButton("show_heatmap", "Generate_heatmap"),
)
get_heatmap_fun = function(i) {
mat_list = list(
matrix(rnorm(100), 10),
matrix(sample(letters[1:10], 100, replace = TRUE), 10)
)
Heatmap(mat_list[[i]])
}
server = function(input, output, session) {
observeEvent(input$show_heatmap, {
i = as.numeric(input$select)
InteractiveComplexHeatmapModal(input, output, session,
get_heatmap = get_heatmap_fun(i))
})
}
shiny::shinyApp(ui, server)
```
<script>
document.write('<img src="https://jokergoo.github.io/images/dynamic_widget_radio_selection.gif" width="100%" />');
</script>
The usage of `InteractiveComplexHeatmapWidget()` is very similar as
`InteractiveComplexHeatmapModal()`, except that now for
`InteractiveComplexHeatmapWidget()`, user needs to allocate a place
defined by `shiny::htmlOutput()` in UI, and later the interactive heatmap widget is
put there.
I modify the previous example with `InteractiveComplexHeatmapWidget()`. Now in the UI,
I add one line where I specify `htmlOutput()` with ID `"heatmap_output"`, and this ID is set
in `InteractiveComplexHeatmapWidget()` correspondingly.
```{r, eval = FALSE}
ui = fluidPage(
actionButton("show_heatmap", "Generate_heatmap"),
htmlOutput("heatmap_output")
)
server = function(input, output, session) {
m = matrix(rnorm(100), 10)
ht = Heatmap(m)
observeEvent(input$show_heatmap, {
InteractiveComplexHeatmapWidget(input, output, session, ht, output_id = "heatmap_output")
})
}
shiny::shinyApp(ui, server)
```
The app looks like follows:
<script>
document.write('<img src="https://jokergoo.github.io/images/dynamic_widget2.gif" width="100%" />');
</script>
`InteractiveComplexHeatmapModal()` and `InteractiveComplexHeatmapWidget()`
all accept an argument `js_code` where customized JavaScript code can be
inserted after the interactive UI. This is sometimes useful. In previous
example where the heatmap widget is triggered by clicking on the action
button, every time when clicking on the button, the widget is regenerated
although the heatmaps are actually the same. Actually we can change the
behavior of the button that from the second click it just switches the
visibility of the heatmap widget. See more examples in `htShinyExample(6.5)`
and `htShinyExample(6.7)`.
```{r, eval = FALSE}
ui = fluidPage(
actionButton("show_heatmap", "Generate_heatmap"),
htmlOutput("heatmap_output")
)
server = function(input, output, session) {
m = matrix(rnorm(100), 10)
ht = Heatmap(m)
observeEvent(input$show_heatmap1, {
InteractiveComplexHeatmapWidget(input, output, session, ht,
output_id = "heatmap_output", close_button = FALSE,
js_code = "
$('#show_heatmap').click(function() {
$('#heatmap_output').toggle('slow');
}).text('Show/hide heatmap').
attr('id', 'show_heatmap_toggle');
"
)
})
}
shiny::shinyApp(ui, server)
```
<script>
document.write('<img src="https://jokergoo.github.io/images/dynamic_widget3.gif" width="100%" />');
</script>
## Implement interactivity from scratch
**InteractiveComplexHeatmap** provides rich tools for interactively working with heatmaps. However, some people
might want to develop their own tools while they only need the information of which cells are selected. Next I demonstrate it
with a simple example. The following example is runnable.
```{r, eval = FALSE}
ui = fluidPage(
actionButton("action", "Generate heatmap"),
plotOutput("heatmap", width = 500, height = 500, click = "heatmap_click",
brush = "heatmap_brush"),
verbatimTextOutput("output")
)
server = function(input, output, session) {
ht_obj = reactiveVal(NULL)
ht_pos_obj = reactiveVal(NULL)
observeEvent(input$action, {
m = matrix(rnorm(100), 10)
rownames(m) = 1:10
colnames(m) = 1:10
output$heatmap = renderPlot({
ht = draw(Heatmap(m))
ht_pos = htPositionsOnDevice(ht)
ht_obj(ht)
ht_pos_obj(ht_pos)
})
})
observeEvent(input$heatmap_click, {
pos = getPositionFromClick(input$heatmap_click)
selection = selectPosition(ht_obj(), pos, mark = FALSE, ht_pos = ht_pos_obj(),
verbose = FALSE)
output$output = renderPrint({
print(selection)
})
})
observeEvent(input$heatmap_brush, {
lt = getPositionFromBrush(input$heatmap_brush)
selection = selectArea(ht_obj(), lt[[1]], lt[[2]], mark = FALSE, ht_pos = ht_pos_obj(),
verbose = FALSE)
output$output = renderPrint({
print(selection)
})
})
}
shinyApp(ui, server)
```
In this simple Shiny app, a click or a brush on heatmap prints the corresponding data frame that contains the information of the selected cells.
There are several points that need to be noticed:
1. `draw()` and `htPositionsOnDevice()` need to be put inside the `renderPlot()`.
2. To get the position of the click on heatmap, `getPositionFromClick()`
should be used. With knowing the position of the click, it can be sent to
`selectPosition()` to correspond to the original matrix.
3. Similarly, to get the positions of the area that was brushed on heatmap, `getPositionFromBrush()` should be used.
This method also works for complex heatmaps, e.g. with row or column splitting, or with multiple heatmaps.
<br>
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