Related
In R Markdown, I would like to plot a decision tree horizontally, so that it fits better the entire PDF page. This code plots it vertically:
```{r, message=FALSE, warning = FALSE, echo=FALSE, cache = FALSE}
rpart.lrn <- makeLearner("classif.rpart", predict.type = "prob", fix.factors.prediction = FALSE)
model = train(rpart.lrn, task = classif.task, subset = train.set)
tree <- getLearnerModel(model)
rpart.plot(tree) # visualise the tree
```
How can I plot it horizontally instead?
Have you tried so set fig.height and fig.width, for example {r ggpair, echo=FALSE, message = FALSE, warning = FALSE, fig.height = 12, fig.width = 12}
The section of the bookdown manual on generating figures demonstrates a case where include_graphics() can be given a vector of paths of length > 1, producing a number of subplots with a single caption:
However, when I try this in my fork of thesisdown, in the PDF output I get the figure caption (and, judging by the spacing, the entire figure environment) repeated for each subplot. Here is a reproducible example:
---
output: bookdown::pdf_document2
toc: false
---
```{r, echo = FALSE}
for(i in 1:3){
jpeg(filename = paste0("temp_", i, ".jpg"), width = 600, height = 250)
plot(cars)
title(main = i)
dev.off()
}
```
```{r fig.cap = "Caption", out.width="100%", fig.ncol = 1, echo = FALSE}
knitr::include_graphics(paste0("temp_", 1:3, ".jpg"))
```
I was hoping more for the five images stacked, with a single caption at the bottom. This also appears to be breaking the figure cross-referencing, as each plot has its own figure number and cross-references to the chunk render as ??.
Getting subfigures requires a few additional settings to be set in the chunk header.
fig.subcap is a list of the captions for subfigures
fig.ncol: the number of columns of subfigures
out.width: the output width of the figures. You will normally set this 100% divided by the number of sub columns.
Subfigures are built using the subfig package. You can either include this within your LaTeX bookdown template, or alternative you can added it to the YAML as follows:
Here is an example:
---
output: bookdown::pdf_document2
toc: false
header-includes:
- \usepackage{subfig}
---
```{r, echo = FALSE}
for(i in 1:3){
jpeg(filename = paste0("temp_", i, ".jpg"), width = 600, height = 250)
plot(cars)
title(main = i)
dev.off()
}
```
```{r fig.cap = "Caption", out.width="100%", fig.ncol = 1, echo = FALSE, fig.subcap= c("First", "Second", "Third")}
knitr::include_graphics(paste0("temp_", 1:3, ".jpg"))
```
I would like to create a default chunk option for my documents, so that I can choose which chunks are included in the appendix. Here is my MWE:
```{r setup, include=FALSE, appendix=FALSE}
knitr::opts_chunk$set(echo=FALSE)
knitr::opts_chunk$set(appendix=TRUE)
```
```{r}
# some code included in the appendix
```
```{r appendix=FALSE}
# some code not included in the appendix
```
# Appendix
```{r, ref.label=knitr::all_labels(appendix), echo = T, eval = F}
```
I would like to include all the chunks that do not explicitly say appendix=TRUE. If I add that, it works as expected, but the default knitr::opts_chunk$set(appendix=TRUE) does not seem to work.
I am probably missing something in my setup. Any help is greatly appreciated.
You need to explicitly set:
Appendix <- TRUE in setOptions
you then set -
knitr::opts_chunk$set(appendix = TRUE)
now any chunk without Appendix = FALSE is included in the Appendix.
Note: It is important to include Appendix = FALSE in the Appendix chunk.
I hope the above helps, it is how I do this.
---
title: "47085866-2"
author: "Technophobe1"
date: "11/5/2017"
output:
html_document:
keep_md: yes
---
```{r setOptions, echo = FALSE, Appendix = FALSE}
Appendix <- TRUE
knitr::opts_chunk$set(echo = FALSE, message = FALSE, error = FALSE, warning = FALSE, results = 'hide')
knitr::opts_chunk$set(appendix = TRUE)
```
## Appendix = TRUE
```{r code}
# some code included in the appendix
setClass(
"CStruct",
slots = list(
powerLevel = "numeric",
size = "numeric"
)
)
CStructure <- new("CStruct", powerLevel = 5, size = 10)
CStructure
str(CStructure)
CStructure#powerLevel
CStructure#size
```
## Appendix = FALSE
```{r ref.label='code', Appendix = FALSE}
# some code not included in the appendix
setClass(
"CStruct2",
slots = list(
n = "numeric",
s = "character",
b = "logical"
)
)
CStructure2 <- new("CStruct2", n = c(2, 3, 5),
s = c("aa", "bb"),
b = c(TRUE, FALSE, TRUE) )
str(CStructure2)
CStructure2#n
CStructure2#s
CStructure2#b
```
# Code Appendix
```{r, ref.label=knitr::all_labels(Appendix), Appendix = FALSE, echo=TRUE, eval=FALSE}
## Code Appendix
```
Output:
I'm generating GIFs using the gganimate package within an RMarkdown file. When using output = github_document in the front matter, the GIF appears as expected in the output (github-document-output). However, when using output = html_document, the GIF generates with alt text, which defaults to the chunk name (html-document-output).
Is there a way to suppress this automatic caption? I've tried setting my own caption using the fig.cap chunk option, but that was unsuccessful.
RMarkdown code
---
output:
html_document: default
github_document: default
---
```{r}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "output/test-fig-",
cache.path = "output/test-cache-"
)
```
```{r cache = FALSE}
library(knitr)
library(animation)
ani.options(autobrowse = FALSE, interval = 1)
opts_knit$set(animation.fun = function(x, options, format = "gif") {
x = c(knitr:::sans_ext(x), knitr:::file_ext(x))
fig.num = options$fig.num
format = sub("^[.]", "", format)
fig.fname = paste0(sub(paste0(fig.num, "$"), "*", x[1]),
".", x[2])
mov.fname = paste0(sub(paste0(fig.num, "$"), "", x[1]), ".",
format)
# order correctly
figs <- Sys.glob(fig.fname)
figs <- figs[order(as.numeric(stringr::str_match(figs, paste0("(\\d+)\\.", x[2]))[, 2]))]
animation::im.convert(figs, output = mov.fname)
sprintf("", options$label, paste0(opts_knit$get("base.url"), mov.fname))
})
opts_chunk$set(cache = TRUE, message = FALSE, warning = FALSE, fig.show = "animate")
```
```{r pkgs, cache = FALSE}
library(gapminder)
library(ggplot2)
theme_set(theme_bw())
```
```{r setup}
p <- ggplot(gapminder, aes(gdpPercap, lifeExp, size = pop, color = continent, frame = year)) +
geom_point() +
scale_x_log10()
```
```{r dependson = "setup"}
library(gganimate)
gg_animate(p)
```
The problem here is that you include the resulting animation with markdown syntax. This introduces some iiritations I guess.
Taking a look at hook_plot_html we can simulate the default output for standard plots:
sprintf(paste0('<div class="figure %s">',
'<img src="%s">',
'<p class="caption">%s</p>',
'</div>'), options$fig.align, mov.fname, options$fig.cap)
I want to display two charts with the rCharts package, one next to the other, more or less like the two pies are displayed in this link:
http://nvd3.org/examples/pie.html
I have a partial solution using <iframe>, but the solution has three problems:
It is too case specific
Including controls becomes a complicated task
It does not look too nice
Minimum working example:
---
title: "Example"
output: html_document
---
```{r rcht, message=FALSE, echo=FALSE, results='asis'}
library(rCharts)
df<-data.frame(label=c("One","Two","Three"),valuea=c(1,2,3),othera=c(10,11,12),
valueb=c(4,5,6),otherb=c(10,11,12),stringsAsFactors = FALSE)
p1 <- nPlot(valuea~ label, data = df, type = 'pieChart',height = 225, width = 300)
p2<- nPlot(valueb~ label, data = df, type = 'pieChart',height = 225, width = 300)
p1$show('inline', include_assets = TRUE, cdn = F)
p2$show('inline', include_assets = TRUE, cdn = F)
```
```{r message=FALSE, echo=FALSE}
p1$save("pie1.html", standalone = TRUE)
p2$save("pie2.html", standalone = TRUE)
```
<div align="center">
<font size="10" color="black" face="sans-serif">Both Pies</font><br>
<p>
<iframe src="pie1.html" height="400" width="400"></iframe>
<iframe src="pie2.html" height="400" width="400"></iframe>
</p>
<div>
I know pie charts should not be used and that I could use a multi-bar chart. However, I want to use this type of layout with other kinds of charts in the rCharts package.
Additionally, I would like to include controls in the charts whilst they are shown next to each other. Including the following code before the $save() function adds the controls:
```{r message=FALSE, echo=FALSE}
p1$addControls('y','valuea',values=c('valuea','othera'))
p2$addControls('y','valueb',values=c('valueb','otherb'))
```
This issue is less relevant to me, but if someone has a solution (preferably with only one control for both charts), it would be great.
I understand all this might be too much to handle from R. Any help/advice is appreciated.
Not elegant, but functional (I did not try it with controls):
---
title: "Example"
output: html_document
---
```{r rcht, message=FALSE, echo=FALSE, results='asis'}
library(rCharts)
library(htmltools)
df <- data.frame(label=c("One","Two","Three"),valuea=c(1,2,3),othera=c(10,11,12),
valueb=c(4,5,6),otherb=c(10,11,12),stringsAsFactors = FALSE)
p1 <- nPlot(valuea~ label, data = df, type = 'pieChart',height = 225, width = 300)
p2 <- nPlot(valueb~ label, data = df, type = 'pieChart',height = 225, width = 300)
```
```{r echo=FALSE, results="asis"}
cat("<table width='100%'><tr style='width:100%'><td width='50%'>")
```
```{r echo=FALSE, results="asis"}
p1$show('inline', include_assets = TRUE, cdn = FALSE)
```
```{r echo=FALSE, results="asis"}
cat("</td><td>")
```
```{r echo=FALSE, results="asis"}
p2$show('inline', include_assets = TRUE, cdn = FALSE)
```
```{r echo=FALSE, results="asis"}
cat("</td></tr></table>")
```
Hi I am having the same problem with controls it looks that in the viewer of R-studio everything works fine but not when I compile with Rmarkdown it doesn't show the plot at all.
```{r results = 'asis', comment = NA}
require(rCharts)
require(datasets)
p2 <- nPlot(mpg ~ cyl, group = 'wt',
data = mtcars, type = 'scatterChart')
p2$xAxis(axisLabel = 'Log2')
p2$yAxis(axisLabel = 'Log2')
p2$chart(tooltipContent = "#! function(key, x, y, e){
return '<b>Name:</b> ' + e.point.GeneID
} !#")
p2$chart(color = c('red', 'green'))
p2$addControls("x", value = 'mpg', values = names(mtcars))
p2$addControls("y", value = 'cyl', values = names(mtcars))
cat('<style>.nvd3{height: 400px;}</style>')
p2$print('chart2', include_assets = TRUE)
```
The code above is the addControls are removed actually works also in the rmarkdown.
Also, if you try to run the code above in Rstudio console (just from p2<-nPlot to cat command) and then calling p2 I can actually see the controls.