Embed LDAvis output to Rmarkdown #90

him4u324 · 2018-07-19T08:14:48Z

I am trying to embed LDAvis output to Rmarkdown and share the html output just like any other rmarkdown output with intact interactivity.

I have tried 2 approaches in rmarkdown

This does not produce anything in html output

        ```{r}
        data2 <- with(TwentyNewsgroups, createJSON(phi, theta, doc.length, vocab, 
        term.frequency))
        serVis(with(data2, createJSON(phi, theta, doc.length, vocab, 
        term.frequency,R = 25)))
        ```

with this, LDA interactive output appeared in Rstudio Viewer but does not show anything in browser

        ```{r}
        data2 <- with(TwentyNewsgroups, createJSON(phi, theta, doc.length,
        vocab, term.frequency))
        serVis(with(data2, createJSON(phi, theta, doc.length, vocab, 
        term.frequency, R = 25)), out.dir = "a")
        ```
        <iframe width="1200" height="1500" src="a/index.html" frameborder="0"></iframe>

I have tried open.browser = TRUE as well as FALSE but it didn't solve the problem.

Note: Shiny is not an option for me as I want to share the interactivity as an attachment.

I have also logged this issue on stackoverflow but no help so far.
https://stackoverflow.com/questions/51285861/embed-ldavis-output-to-rmarkdown

The text was updated successfully, but these errors were encountered:

ZHuang4270 · 2018-07-25T14:57:10Z

Did you check the Rmd file referenced in this thread?

#28

him4u324 · 2018-08-27T10:39:27Z

Hi ZHuang, Thanks for your response. I checked the thread but still I am not able to figure out how to embed it on RMD without Shiny.

o0oBluePhoenixo0o · 2018-12-11T14:43:45Z

Put these line before your <iframe></iframe>

Those files you can find in the LDAVis folder (out.dir)

<link rel="stylesheet" type="text/css" href="lda.css">
<script src="d3.v3.js"></script>
<script src="ldavis.js"></script>

him4u324 · 2019-07-26T12:00:13Z

Hello Trung Nguyen, I tried your suggestion but still no avail.

library(lda)
library(LDAvis)
 # data2 <- with(TwentyNewsgroups, createJSON(phi, theta, doc.length,
 #                                           vocab, term.frequency))
serVis(with(TwentyNewsgroups, createJSON(phi, theta, doc.length, vocab, 
                              term.frequency, R = 25)), out.dir = "a")

<link rel="stylesheet" type="text/css" href="a/lda.css">
<script src="a/d3.v3.js"></script>
<script src="a/ldavis.js"></script>

<iframe width="1200" height="1500" src="a/index.html" frameborder="0"></iframe>

BlakeList · 2019-12-02T23:53:15Z

@dselivanov has a great way of embedding them similar to what is described above.

See the code in his text2vec topic modelling tutorial here.

The graph can be saved then embedded after the code chunk using

<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<title>LDAvis</title>
<script src="topic_modeling_files/ldavis/d3.v3.js"></script>
<script src="topic_modeling_files/ldavis/ldavis.js"></script>
<link rel="stylesheet" type="text/css" href="topic_modeling_files/ldavis/lda.css">
</head>
<body>
<div id = "lda"></div>
<script>
var vis = new LDAvis("#lda", "topic_modeling_files/ldavis/lda.json");
</script>
</body>

valentinitnelav · 2020-06-29T15:38:06Z

I am curious if a solution was found as none of the proposed ones above worked in my case. As @him4u324 initially posted, I get the interactive visualization in the Rstudio Viewer, but still not in the html document.

BlakeList · 2020-06-29T21:18:23Z

You should be able to embed the dynamic graph using the html code above. Do you have a reproducible case?

valentinitnelav · 2020-06-30T07:28:35Z

Here is a Rmd simplified example and 2 imgur links showing what I see in the Rstudio Viewer and what in the browser:

      ---
      output: html_document
      ---

      ```{r global-options, include=FALSE}
      knitr::opts_chunk$set(echo=FALSE, warning=FALSE, message=FALSE, cache=TRUE)
      ```

      ```{r load-packages}
      library(stm)
      library(LDAvis)
      ```

      ```{r}
      mod <- stm(documents = poliblog5k.docs,
                 vocab= poliblog5k.voc,
                 K = 10,
                 prevalence = ~ rating,
                 max.em.its = 2, # set very low to gain speed for this example
                 data = poliblog5k.meta) 

      stm::toLDAvis(mod = mod, docs = poliblog5k.docs, out.dir = "ldavis")
      ```

      <head>
        <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
        <title>LDAvis</title>
        <script src="ldavis/d3.v3.js"></script>
        <script src="ldavis/ldavis.js"></script>
        <link rel="stylesheet" type="text/css" href="ldavis/lda.css">
      </head>

      <body>
        <div id = "lda"></div>
        <script>
         var vis = new LDAvis("#lda", "ldavis/lda.json");
        </script>
      </body>

What I see in the Rstudio Viewer (LDAvis works)

What I see in the browser - tested on Chrome, Firefox, Brave and Internet explorer (no LDAvis output)

sessionInfo()

## R version 4.0.0 (2020-04-24)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 18362)
## 
## Matrix products: default
## 
## locale:
## [1] LC_COLLATE=English_United States.1252 
## [2] LC_CTYPE=English_United States.1252   
## [3] LC_MONETARY=English_United States.1252
## [4] LC_NUMERIC=C                          
## [5] LC_TIME=English_United States.1252    
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] ggcorrplot_0.1.3  plotly_4.9.2.1    ggdendro_0.1-20   ggplot2_3.3.2    
##  [5] tidyr_1.1.0       magrittr_1.5      dplyr_1.0.0       data.table_1.12.8
##  [9] LDAvis_0.3.2      textmineR_3.0.4   Matrix_1.2-18     stm_1.3.5        
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.4.6       compiler_4.0.0     pillar_1.4.4       tools_4.0.0       
##  [5] stopwords_2.0      digest_0.6.25      viridisLite_0.3.0  jsonlite_1.7.0    
##  [9] evaluate_0.14      lifecycle_0.2.0    tibble_3.0.1       gtable_0.3.0      
## [13] lattice_0.20-41    pkgconfig_2.0.3    rlang_0.4.6        rstudioapi_0.11   
## [17] yaml_2.2.1         xfun_0.15          httr_1.4.1         withr_2.2.0       
## [21] stringr_1.4.0      knitr_1.29         htmlwidgets_1.5.1  generics_0.0.2    
## [25] fs_1.4.1           vctrs_0.3.1        grid_4.0.0         tidyselect_1.1.0  
## [29] glue_1.4.1         R6_2.4.1           rmarkdown_2.3      purrr_0.3.4       
## [33] MASS_7.3-51.5      scales_1.1.1       htmltools_0.5.0    ellipsis_0.3.1    
## [37] RcppProgress_0.4.2 usethis_1.6.1      colorspace_1.4-1   stringi_1.4.6     
## [41] lazyeval_0.2.2     munsell_0.5.0      crayon_1.3.4

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Embed LDAvis output to Rmarkdown #90

Embed LDAvis output to Rmarkdown #90

him4u324 commented Jul 19, 2018

ZHuang4270 commented Jul 25, 2018

him4u324 commented Aug 27, 2018

o0oBluePhoenixo0o commented Dec 11, 2018 •

edited

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him4u324 commented Jul 26, 2019 •

edited

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BlakeList commented Dec 2, 2019

valentinitnelav commented Jun 29, 2020

BlakeList commented Jun 29, 2020

valentinitnelav commented Jun 30, 2020 •

edited

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Embed LDAvis output to Rmarkdown #90

Embed LDAvis output to Rmarkdown #90

Comments

him4u324 commented Jul 19, 2018

ZHuang4270 commented Jul 25, 2018

him4u324 commented Aug 27, 2018

o0oBluePhoenixo0o commented Dec 11, 2018 • edited Loading

him4u324 commented Jul 26, 2019 • edited Loading

BlakeList commented Dec 2, 2019

valentinitnelav commented Jun 29, 2020

BlakeList commented Jun 29, 2020

valentinitnelav commented Jun 30, 2020 • edited Loading

o0oBluePhoenixo0o commented Dec 11, 2018 •

edited

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him4u324 commented Jul 26, 2019 •

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valentinitnelav commented Jun 30, 2020 •

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