2020/05/31/word-cloud-as-heatmap-annotation/

[utterances-bot]

Word cloud as heatmap annotation - A Bioinformagician

https://jokergoo.github.io/2020/05/31/word-cloud-as-heatmap-annotation/

[Paul-Yuchao-Dong]

Really cool blog on stretching what is possible. I find the trick of using "Show/hide Output" button really neat, how do you achieve that with RMarkdown?

[jokergoo]

You can put the following code to the end of your R markdown file:

<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.5.1/jquery.min.js"></script>

<script>
$(document).ready(function(){
    $("pre").not(".r").prepend("<input class='switch_hljs' type='button' value='show/hide output' />");
    $(".switch_hljs").next().hide();
    $(".switch_hljs").click(function() {
        $(this).next().toggle();
    })
});
</script>

It adds a button before every non-r code block and switches the visibility of the next code block.

[Paul-Yuchao-Dong]

Many thanks! that is very clear!

[nfancy]

Hi, really nice package. I was wondering, how can I add the text annotation using anno_link instead of word cloud. So, for example if I want to add the actual pathways instead of the key words in the text box.

[jokergoo]

@nfancy First you need to install the newest version of simplifyEnrichment from GitHub.

Then try the following code:

mat = matrix(rnorm(100*10), nrow = 100)

term = lapply(letters[1:10], function(x) {
    data.frame(c("this is sentence 1", "this is sentence 2"), 1:2)
})
names(term) = letters[1:10]
Heatmap(mat, row_split = split, 
    right_annotation = rowAnnotation(wc = anno_word_cloud(split, term, add_new_line = TRUE, 
        value_range = c(1, 2), fontsize_range = c(10, 12)))
)

I have added some examples in the vignette. You can find in the bottom part of https://jokergoo.github.io/simplifyEnrichment/articles/word_cloud_anno.html

[nfancy]

Thank you very much for your solution.

[hsiaoyi0504]

Is there a way to control the color of each sentences directly (rather than depending on font size)? Like I have a GSEA result and would like to put them in the right hand side of the heatmap by setting font size based on NES score and change colors based on p-value.

[jokergoo]

Then you may directly use anno_text_box(). Note this is a new function and I haven't written the documentation for it.

[WandeRum]

Thank you for implementing this nice feature which is super useful for biological data analysis. However, I've met problems using the same script on top as well as my own data. I found the annotation rows are not corresponding to the correcct rows but clumping to the upper-right part of the heatmap. I tested it on multiple computers which showed the same problem. Any potential reasons or solutions? Thank you!

[jokergoo]

@WandeRum are you using Rstudio? Did you see any message when you use the function? There must be some messages specifically for Rstudio to tell you want to do.