---
title: "Interactivate heatmaps indirectly generated by pheatmap(), heatmap.2() and heatmap()"
author: "Zuguang Gu ( z.gu@dkfz.de )"
date: "`r Sys.Date()`"
output:
rmarkdown::html_vignette:
width: 8
fig_width: 5
vignette: >
%\VignetteIndexEntry{5. Interactivate heatmaps indirectly generated by pheatmap(), heatmap.2() and heatmap()}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
---
```{r, echo = FALSE}
library(knitr)
knitr::opts_chunk$set(
error = FALSE,
tidy = FALSE,
message = FALSE,
warning = FALSE,
fig.width = 6,
fig.height = 6,
fig.align = "center"
)
library(GetoptLong)
options(digits = 4)
```
<style>
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(SC3)
library(GOexpress)
```
With **InteractiveComplexHeatmap**, the following heatmaps can be exported as an interactive Shiny app:
1. heatmaps directly produced from **ComplexHeatmap**,
2. heatmaps from other functions or packages which are implemented with **ComplexHeatmap**,
3. heatmaps originally produced by `stats::heatmap()`, `gplots::heatmap.2()`
and `pheatmap::pheatmap()`, but can be reproduced by the "translation
functions": `ComplexHeatmap:::heatmap()`, `ComplexHeatmap:::heatmap.2()`
and `ComplexHeatmap::pheatmap()`.
All these types of heatmaps can be turned into interactive just by calling
`htShiny()` after the heatmaps are drawn. E.g.:
```{r eval = FALSE}
ComplexHeatmap::pheatmap(...)
htShiny()
```
which means you don't need to touch your heatmap code. After you see the heatmap in your R terminal or generated in a file,
directly calling `htShiny()` with no argument will produce an interactive heatmap, like magic. :P
Now there is a fourth scenario where the heatmap is produced by third-party
functions which internally use `stats::heatmap()`, `gplots::heatmap.2()` or
`pheatmap::pheatmap()`. Since now we cannot directly interact with
`heatmap()`, `heatmap.2()` or `pheatmap()`, how can we turn these heatmaps into
interactive? The solution is fairly simple. We just need to go to _e.g._ **pheatmap**
namespace and replace `pheatmap` with `ComplexHeatmap::pheatmap`.
The following example is from the **SC3** package where
function `sc3_plot_expression()` internally uses `pheatmap()`.
```{r, eval = FALSE}
library(SingleCellExperiment)
library(SC3)
library(scater)
sce <- SingleCellExperiment(
assays = list(
counts = as.matrix(yan),
logcounts = log2(as.matrix(yan) + 1)
),
colData = ann
)
rowData(sce)$feature_symbol <- rownames(sce)
sce <- sce[!duplicated(rowData(sce)$feature_symbol), ]
sce <- runPCA(sce)
sce <- sc3(sce, ks = 2:4, biology = TRUE)
sc3_plot_expression(sce, k = 3)
```
<script>
document.write('<img width="500px" src="https://user-images.githubusercontent.com/449218/105498918-0a871300-5cc1-11eb-92a6-ffed7460e4e1.png" />');
</script>
To replace the internally use of `pheatmap::pheatmap` with
`ComplexHeatmap::pheatmap`, we can use `assignInNamespace()` to directly
change the value of `pheatmap` in **pheatmap** namespace. After that,
recalling `sc3_plot_expression()` will directly use
`ComplexHeatmap::pheatmap()` and now you can use `htShiny()` to export it as
an interactive app. Of course, you need to regenerate the heatmap with the
same code.
```{r, eval = FALSE}
assignInNamespace("pheatmap", ComplexHeatmap::pheatmap, ns = "pheatmap")
library(InteractiveComplexHeatmap)
sc3_plot_expression(sce, k = 3)
htShiny()
```
<script>
document.write('<img width="100%" alt="pheatmap" src="https://user-images.githubusercontent.com/449218/105490976-e40faa80-5cb5-11eb-85f5-df2c80939aef.png" />');
</script>
If you check the source code of `sc3_plot_expression()`, `pheatmap()` is used
by explicitely adding its namespace (check the last few lines of the function definition):
```{r}
selectMethod("sc3_plot_expression", signature = "SingleCellExperiment")
```
In this case, changing `pheatmap` in **pheatmap** namespace directly affects `sc3_plot_expression()`.
However, if the heatmap function is called without adding the namespace (_e.g._, in previous example, the `pheatmap::` prefix), you
need to first unload the package, modify the heatmap function in the heatmap
namespace and later load the package back.
Let's look at the next example from **GOexpress** package where the function `heatmap_GO()` internally use `heatmap.2()`.
```{r, eval = FALSE}
library(GOexpress)
data(AlvMac)
set.seed(4543)
AlvMac_results <- GO_analyse(
eSet = AlvMac, f = "Treatment",
GO_genes=AlvMac_GOgenes, all_GO=AlvMac_allGO, all_genes=AlvMac_allgenes)
BP.5 <- subset_scores(
result = AlvMac_results.pVal,
namespace = "biological_process",
total = 5,
p.val=0.05)
heatmap_GO(
go_id = "GO:0034142", result = BP.5, eSet=AlvMac, cexRow=0.4,
cexCol=1, cex.main=1, main.Lsplit=30)
```
<script>
document.write('<img width="500px" src="https://user-images.githubusercontent.com/449218/105498979-212d6a00-5cc1-11eb-9911-6409b699257b.png" />');
</script>
Now note in `heatmap_GO()` function, `heatmap.2()` is used without **gplots** namespace (go to
the end of the function definition listed below).
```{r}
heatmap_GO
```
In this case, since we have already loaded the **GOexpress** namespace, the **GOexpress** namespace should firstly be removed by
`detach()`, or else `heatmap_GO()` will still use `gplots::heatmap.2()`.
```{r, eval = FALSE}
detach("package:GOexpress", unload = TRUE)
assignInNamespace("heatmap.2", ComplexHeatmap:::heatmap.2, ns = "gplots")
library(GOexpress)
library(InteractiveComplexHeatmap)
heatmap_GO(
go_id = "GO:0034142", result = BP.5, eSet=AlvMac, cexRow=0.4,
cexCol=1, cex.main=1, main.Lsplit=30)
htShiny()
```
<script>
document.write('<img width="100%" alt="heatmap 2" src="https://user-images.githubusercontent.com/449218/105490966-e114ba00-5cb5-11eb-8839-3ba1f25b5fa5.png">');
</script>
In the end, to safely change all `stats::heatmap()`, `gplots::heatmap.2()` and
`pheatmap::pheatmap()` to `ComplexHeatmap:::heatmap()`,
`ComplexHeatmap:::heatmap.2()` and `ComplexHeatmap::pheatmap()`, you can add following lines
to the start of your R session:
```{r, eval = FALSE}
library(pheatmap)
library(gplots)
assignInNamespace("heatmap", ComplexHeatmap:::heatmap, ns = "stats")
assignInNamespace("heatmap.2", ComplexHeatmap:::heatmap.2, ns = "gplots")
assignInNamespace("pheatmap", ComplexHeatmap::pheatmap, ns = "pheatmap")
```
You can find runnable examples in `htShinyExample(8.1)`, `htShinyExample(8.2)` and `htShinyExample(8.3)`.
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