I'm having difficulty in getting pander tables to render in a slidify document (specifically with a call to pander.lm).
For example, the below works
```{r panderWorks, results = "asis"}
id <- rep(1:3, each = 2)
condition <- rep(c("A", "B"), 3)
score <- rnorm(6, 10, 3)
d <- data.frame(id, condition, score)
library(pander)
pander(d, style = "rmarkdown")
```
while the following does not
```{r panderFails, results = "asis"}
data(iris)
pander(lm(Sepal.Width ~ Species, data = iris),
style = "rmarkdown")
```
Note that I actually can get the first chunk to render correctly without the results = "asis" option, but that's worked for me in the past. I've tried changing many options and still no luck. It's also worth noting that I have no problem getting this to render in a standard rmarkdown document. It's only within slidify that I have issues.
I'm working within the io2012 framework, with the highlight.js highlighter and the zenburn highlight theme. I've loaded the mathjax widget and the mode is selfcontained.
Below I've attached my output from sessionInfo().
Any ideas?
Related
I am trying to a read data file within my Rmd file.
It works fine when I use the green arrow to "run current chunk" and when I run selected lines. It does not run when I knit.
I tried chunk option include=TRUE and others that I could think of. Did not work.
I started a new Rmd file using the prettydocs template, and I put the code into an existing chunk in that template that was running and producing output. That code chunk is below. The last two lines are what I added, and they run fine when I select and run or when I run current chunk. When I knit, everything else in the chunk runs, but not those two lines.
The other change I made to the template file was to add: library(tidyverse) and library(readxl).
Here's the code:
```{r fig.width=6, fig.height=6, fig.align='center'}
set.seed(123)
n <- 1000
x1 <- matrix(rnorm(n), ncol = 2)
x2 <- matrix(rnorm(n, mean = 3, sd = 1.5), ncol = 2)
x <- rbind(x1, x2)
head(x)
smoothScatter(x, xlab = "x1", ylab = "x2")
test <- read_excel("test_data.xlsx")
getwd()
```
I have a problem using summarytools packet. There is tutorial:https://cran.r-project.org/web/packages/summarytools/vignettes/Introduction.html with pretty plots of data:
My problem is that my code generate only TEXT GRAPH. This is chunk of code in my markdown to generate plot:
```{r summary, results='markup'}
library(summarytools)
my_data <- ...
dfSummary(my_data)
```
Unfortunately it generates something like this:
How can I generate this pretty report using summarytools?
Or have you better tools for this? (generate graph, mean, std, etc.)
I found the correct syntax to generate plot:
print(dfSummary(baseline_train), method = 'render')
And the results look like this:
A little update on this:
Always use knitr chunk option results='asis', as someone pointed in an earlier comment.
It is possible to generate summaries including png graphs using print():
print(dfSummary(iris), method = "render")
Starting with version 0.9.0 (available only on GitHub as of Feb. 2019), markdown summaries will also include png graphs provided you specify the following arguments:
plain.ascii = FALSE
style = "grid"
a physical location for temporary png's (tmp.img.dir)
dfSummary(iris, plain.ascii = FALSE, style = "grid", tmp.img.dir = "/tmp")
Additionnal tips
In both cases, you will (in all likelihood) need to adjust the size of the graphs with dfSummary()'s graph.magnif parameter (try values between .75 and .85).
Exclude a column or two to avoid overly wide summaries:
dfSummary(iris, [...], varnumbers = FALSE, valid.col = FALSE)
You need to use results = 'asis' for the code chunk. Here is minimal reproducible example:
---
title: "Untitled"
output: html_document
---
```{r, results='asis'}
library(summarytools)
dfSummary(iris, plain.ascii = FALSE, style = "grid")
```
produces
My visNetwork is not displayed at all when the displaying is attempted in a for loop. In a regular R script, I use the print function and it works just fine, but it does not work in an R Markdown document.
Here is a (hopefully) reproducible example:
---
title: "I want my beautiful networks back!"
---
# First example that works
```{r}
require(visNetwork, quietly = TRUE)
# minimal example
nodes <- data.frame(id = 1:3)
edges <- data.frame(from = c(1,2), to = c(1,3))
vn <- visNetwork(nodes, edges, width = "100%")
vn # Or print(vn)
```
# When does it not work?
## In a for loop
```{r}
for (i in 1) vn
```
## In a for loop + using print
This will display the network in the Viewer.
```{r}
for (i in 1) print(vn)
```
## And also in functions
Same remark...
```{r}
foo <- function(x) print(x)
foo(vn)
```
I'm using Rstudio version Version 1.1.383 and
here is the result of a sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6
other attached packages:
[1] visNetwork_2.0.2
I just found a little workaround, consisting the following steps:
Save plot as HTML
Include the HTML code in RMD file
Here an example:
```{r}
for (i in 1:3){
visSave(vn, file = paste0("test",i,".html"))
}
```
```{r, results='asis'}
for (i in 1:3){
cat(htmltools::includeHTML(paste0("test",i,".html")))
}
```
Another solution is to use print(htmltools::tagList())
This prevents the !DOCTOOLS showing in the output.
```{r}
for (i in 1) print(htmltools::tagList(vn))
```
I came across the same issue / solution when working with Datatables and the solution was provided here by #Yihui: https://github.com/rstudio/DT/issues/67
Edit I've since realised that you need at least one visnetwork plotted outside of the loop, i.e. outside of print(htmltools::taglist()), otherwise the script to render is not added to the html file.
You can remove the !DOCTYPE by operating on the string.
cat (as.character(htmltools::includeHTML(paste0("vn",".html"))) %>%
{gsub("<!DOCTYPE html>","",.,fixed = TRUE)} %>%
{sub("\n","",.)}
)
I had the same problem but also wanted to knit my Rmd from the command line, not within RStudio, to easily generate reports for many different parameters, e.g.:
Rscript -e "rmarkdown::render('graphical-res-vis-reports.Rmd', \
params = list(tissue = '${tissue}'), \
output_file = sprintf('graphical-analysis-results_%s.html','${tissue}'))"
The htmltools::includeHTML(html_path) trick worked well when knitting from within RStudio, but it spat out a pandoc error when I tried to knit it from the command line because it's effectively concatenating multiple standalone HTMLs, which does not result in a valid HTML format. (EDIT: the pandoc error may have also been because R from the command line was using a much older version of pandoc than RStudio, but using iframes is still much cleaner.)
I finally found a solution using iframes that works well. Here is a minimal reproducible example:
---
title: "Finally, a way to print visNetworks in a loop!"
---
```{r make networks}
require(visNetwork, quietly = TRUE)
# minimal example
nodes <- data.frame(id = 1:3)
edges <- data.frame(from = c(1,2), to = c(1,3))
html_list <- c()
for (i in 1:3){
vn <- visNetwork(nodes, edges)
outfile <- sprintf("vn_%s.html", i)
visSave(vn, file=outfile)
html_list <- c(html_list, outfile)
}
```
```{r plot networks, results="asis"}
for (i in html_list){
print(htmltools::tags$iframe(title = "My embedded document",
src = f, height = "650", width = "900", frameBorder = "0"))
}
```
EDIT: Note that changing the iframe height and width doesn't resize the object from the HTML file. However, you can increase the size of the visNetwork HTML object with a simple text replacement. In this example, I remove the whitespace padding and change the size from 960x500 to 960x960:
visSave(v1, file = out_html)
# adjust browser window size
cmd = sprintf('sed -i \'s|"browser":{"width":960,"height":500,"padding":40,"fill":false}|"browser":{"width":960,"height":960,"padding":0,"fill":false}|\' %s', out_html)
system(cmd)
Question: How to place xtable object to the left side of page or how to disable centering globally.
I'm struggling to figure out how to place xtable object on the left side. I have got a *.Rmd file and all this goes to the relevant r chunk.
require(xtable)
df <- data.frame(x=seq(1,10,1),y=rnorm(10))
Xtab <- xtable(df, digits=0, caption="\\textbf{MINIMAL/IDEAL}",
floating=FALSE, latex.environments = c("left"))
print(Xtab, size = "small", include.colnames=FALSE)
I have included the following after reading various sources (print.xtable; xtable manual etc.)
1) floating=FALSE
2) latex.environments = c("left")
I have searched SO and used some of the hints but all failed.
It seems to make quite a difference whether you pass a parameter to xtable() or to print(xtable()). The following chunk creates a table according to your data that is aligned at the left of the page in the pdf file.
```{r, results='asis',echo=FALSE}
library(xtable)
df <- data.frame(x=seq(1, 10, 1),y = rnorm(10))
print(xtable(df,digits=0, caption="\\textbf{MINIMAL/IDEAL}"), include.colnames=FALSE, size = "small", comment=FALSE, latex.environments="flushleft")
```
However, as you can see, the caption remains at the center of the page.
I'm presently trying to replicate a few different types of rCharts using my own data. The first is a HighCharts graph with the following code:
````{r}
setwd("C:/Users/ypetscher/Dropbox/R fun")
blah<-read.csv("g8a.csv")`
require(slidify)
require(rCharts)
require(rHighcharts)
```
```{r}
x<-data.frame(blah,stringsAsFactors=TRUE)
colnames(x)<-substr(colnames(x),2,5)
a<-rHighcharts:::Chart$new()
a$chart(type="column")
a$title(text="Percent of Students on Grade Level on G8 FCAT for Reading (1), Math (2), Writing (3), and Science (4)")
a$xAxis(categories=rownames(x))
a$yAxis(title=list(text="Percent Proficient"))
a$data(x)
```
When this is run as a chunk, the graph is produced nicely, but when I use Knit HTML in markdown, it sticks at the preview stage for a while and when I terminate it, it gives a "status 15" message, which I'm unclear what that means and how it should be resolved.
A second graph I'm trying is a Morris.js graph in Markdown with knitr. I took my R code and put into R Markdown which looks like:
```{r}
library(slidify)
library(knitr)
library(rCharts)
library(RColorBrewer)
library(reshape2)
setwd("C:/Users/ypetscher/Dropbox/R fun")
blah<-read.csv("g8.csv")
blah
```
```{r}
m2<-mPlot(x="year",y=colnames(blah)[-1],data=blah, type="Bar")
m2$set(barColors=brewer.pal(4,"Spectral"))
m2$set(xlab="Year")
m2$set(postUnits="%")
m2$set(hideHover="auto")
m2
```
When I run the chunks, it produces a nice graph the way I expected with an html file of (file:///C:/Users/ypetscher/AppData/Local/Temp/RtmpW4q3ka/filed284f137718.html); however, when I click on Knit HTML, I obtain a file which includes the code, but doesn't produce the graph. Additionally, when Google Chrome comes up I receive an error of :
"No webpage was found for the web address:
file:///C:/Users/YPETSC~1/AppData/Local/Temp/Rtmpk1Pfbp/filee0c383670e0.html
Error 6 (net::ERR_FILE_NOT_FOUND): The file or directory could not be
found."
Any help would be greatly appreciated in diagnosing these issues. Thank you much!
NOTE: This is the same solution I posted in the knitr google group.
To get rCharts to work with knit2html, you will need to use the print method with the argument include_assets = TRUE. This is because knitr will not add the js and css assets required by an rCharts plot automatically. Here is a minimal working example.
## MorrisJS with Knit2HTML
```{r results = 'asis', comment = NA}
require(rCharts)
data(economics, package = 'ggplot2')
econ <- transform(economics, date = as.character(date))
m1 <- mPlot(x = 'date', y = c('psavert', 'uempmed'), type = 'Line',
data = econ)
m1$set(pointSize = 0, lineWidth = 1)
m1$print('chart2', include_assets = TRUE)
```
Note that you need to use m1$print('chart2', include_assets = TRUE, cdn = TRUE) if you intend to publish your chart on RPubs, for otherwise the JS and CSS assets will be served from your local library.
Hope this helps.