R HTML Output File

Question

I am producing a HTML report output using R and when i get the output html file and open it I can see the charts i created using ggplot no problem but if i send the html file to anyone else the charts are missing and they only see the text. My code is below, any advice on what I am missing would be great.

Also i have an image from my local drive that isn't showing up.

---
title: "title"
 ``author: 
- "X"
date: "`r format(Sys.time(), '%d %B %Y')`"
output: 
  html_document: 
 number_sections: yes
toc: yes
runtime: shiny    
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE,message=FALSE, warning=FALSE)
```

{r libraries, include=FALSE} library(plyr) library(dplyr) library(tidyverse) library(ggplot2) library(forcats) library(reshape) library(png)

```{r, fig.width=12, fig.height=6, fig.align="center"}
# read in data file
lj= read.csv("LJ_Final.csv")  # read csv file

#rename variables to fit charts
names(lj)[names(lj) == "2015"] <- "15"

myvars <- c("HB","15")
newdatajoiner <- lj[myvars]

newdatajoiners.long<-melt(newdatajoiner,id.vars="HB")

aggdatajoiners <-aggregate(value ~ HB + variable, data = 
newdatajoiners.long, sum)

#plot the data
aggdatajoiners%>%
ggplot(aes(x=variable,y=value,fill=factor(HB)))+
 geom_bar(stat="identity",position="dodge")+
 labs(x="", y="")+
 theme_bw()+
 facet_wrap(~HB)
```
```{r,fig.align="center",out.width = "3000px"}
knitr::include_graphics('./tablefife.png')
```

Len Greski · Accepted Answer · 2017-11-23 21:26:45Z

1

@user3018495 The other thread describes how to exclude the charts. To include the charts in the output HTML document, one sets self_contained to yes rather than no in the Rmd output options.

---
title: "your title goes here"
output:
   html_document:
   self_contained: yes
   toc: yes
   toc_float: yes
---

If you are using RStudio with knitr, this is configured in RStudio options. First select the gear in the code editor window.

Next, select the Advanced tab, and

click Standalone HTML
then press `OK'.

When you knit the document the resulting HTML file will contain the charts, as illustrated by a test HTML document that I posted in a Github repository so it can be viewed by the Github HTML Previewer.

regards,

Len

edited Nov 23, 2017 at 21:26

answered Nov 23, 2017 at 21:19

Len Greski

11k2 gold badges26 silver badges37 bronze badges

Sign up to request clarification or add additional context in comments.

Comments

Rodrigo Rodrigues · Accepted Answer · 2017-11-23 17:30:20Z

1

When your HTML is generated from the Markdown file an image folder is generated with the HTML, your images are referenced by the HTML, not included in the html file itself, You need to send this folder as well.

You could convert the image to a base64 string and embed in the html file, however I don't know how to do that automatically in R

answered Nov 23, 2017 at 17:30

Rodrigo Rodrigues

1088 bronze badges

4 Comments

Rodrigo Rodrigues Over a year ago

This was solved on this other thread: stackoverflow.com/questions/14870589/…

user3018495 Over a year ago

Does that mean there's no way of including images in a HTML Output using markdown?

Rodrigo Rodrigues Over a year ago

There is, if you are using the command line you need to use the base64 parameter like in the link above, if you ate using RStudio, click on the gear next to Knit, Output Options, Advanced and check "Create a standalone HTML document", images should now be embeded as a base64 url

user3018495 Over a year ago

The images show up for me when I run it but if I share the html file, the charts from the code above don't show up. Even when I have create stand alone ticked

Collectives™ on Stack Overflow

R HTML Output File

2 Answers 2

Comments

4 Comments

Your Answer

Linked

Hot Network Questions

Collectives™ on Stack Overflow

2 Answers 2

Comments

4 Comments

Your Answer

Sign up or log in

Post as a guest

Linked

Related