I have a dataframe dataof nobservations of several numeric and factor variables. I would like to produce a html report in which class and describe are reported and a histogram (qplotor ggplot) is plotted for every variable.
How can I do that?
Is it possible in R Markdown to produce an automatic header preceding every variable analysis?
Thank you for your help.
Corrado
You can put a loop in your R chunks in Markdown files. Something like that for example :
```{r, echo=FALSE}
library(ggplot2)
```
This is an introductory sentence with absolutely no interest.
```{r, results="asis", eval=TRUE, echo=FALSE}
data(cars)
for (varname in names(cars)) {
var <- cars[,varname]
cat(paste0("<h2>",varname,"</h2>"))
cat(paste0("Class : <pre>",class(var),"</pre>"))
cat("Summary : <pre>")
print(summary(var))
cat("</pre>")
if (is.numeric(var)) print(qplot(var, binwidth=diff(range(var))/30))
}
```
This is an astonishing conclusion.
Which gives the following result : http://rpubs.com/juba/mdloop
Related
I create an Rmarkdown document where I would like to create a plot at the start of the document, and then print it at the end of the document.
I thought the best way to achieve this would be to save the plot in the environment and then recall it later, I save this as follows:
plot(1:5, 1:5) ; plot1 <- recordPlot() # I create a plot and save it as plot1
This plot is saved under "Data" in the environment.
If I enter plot1 into the console, my plot is reproduced, but when I try to display it directly in Rmarkdown as follows I get the following error:
plot(plot1)
Error in xy.coords(x, y, xlabel, ylabel, log) :
'x' is a list, but does not have components 'x' and 'y'
How I can take the plot that I saved into Data and print it anywhere I would like in my Rmarkdown document?
p.s. I know it's tempting to say to repeat the plot again later in the document, but the parameters that build the plot are subsequently altered for another part of my analysis.
Re-producible example:
x = 1
plot_later <- function() {
plot(x)
}
plot_later()
x = -10
plot_later()
X starts at 1 then changes to -10 on the Y axis, I want it to stay at the initial value of 1.
Solution based on https://bookdown.org/yihui/rmarkdown-cookbook/reuse-chunks.html :
---
title: plot now, render later
output: html_document
---
We put some plot expression here to evaluate it later:
```{r, deja-vu, eval=FALSE}
x = 1
plot(x)
```
Here we change `x` - but only within the corresponding chunk's scope:
```{r}
x = 10
```
... moving on
Here, we evaluate and plot the expression defined earlier; x is taken from that chunk's scope, so it still evaluates to `1`:
```{r, deja-vu, eval=TRUE}
```
One option could be saving the plot as grob object using as.grob function from ggplotify and then print it elsewhere.
---
title: "Saving A Plot"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## R Markdown
```{r}
library(ggplotify)
library(grid)
show_captured_plot <- function(grb) {
grid::grid.newpage()
grid::grid.draw(grb)
}
```
```{r}
x <- 1
p <- as.grob(~plot(x))
```
Now we can plot the figure here.
```{r}
x <- 10
show_captured_plot(p)
```
here, check out this link: https://bookdown.org/yihui/rmarkdown-cookbook/fig-chunk.html
It has a lot of instructions on how to get started with rmarkdown.
Specifically answering your question:
We generate a plot in this code chunk but do not show it:
```{r cars-plot, dev='png', fig.show='hide'}
plot(cars)
```
After another paragraph, we introduce the plot:
`)
Basically you have to save your graph as a variable and then call on it using the knitr::fig_chunk() function.
I am trying to print a simple plot with knitr markdown.
below is my code.
```{Simple plot}
library(datasets)
with(airquality, plot(Wind, Ozone))
```
If I run this in r code file, it returns the plot properly.
However, when running this in a markdown file, it only shows code but no plot to the printed document.
what am I doing wrong?
Use ```{r} where r means R langage :
```{r}
library(datasets)
with(airquality, plot(Wind, Ozone))
```
I'm analyzing some data and would like to do a Simpsons paradox on R. I've installed the Simpsons package and loaded the library. Here is an example based on the package documentation:
---
output: html_document
---
```{r}
library(Simpsons)
#generating data
Coffee1=rnorm(100,100,15)
Neuroticism1=(Coffee1*.8)+rnorm(100,15,8)
g1=cbind(Coffee1, Neuroticism1)
Coffee2=rnorm(100,170,15)
Neuroticism2=(300-(Coffee2*.8)+rnorm(100,15,8))
g2=cbind(Coffee2, Neuroticism2)
Coffee3=rnorm(100,140,15)
Neuroticism3=(200-(Coffee3*.8)+rnorm(100,15,8))
g3=cbind(Coffee3, Neuroticism3)
data2=data.frame(rbind(g1,g2,g3))
colnames(data2) <- c("Coffee","Neuroticism")
example <- Simpsons(Coffee,Neuroticism,data=data2)
plot(example)
```
This is returning a plot with 3 clusters (exactly what I need). However, when I Knit the Rmd file to HTML, I'm getting a lot of equals signs (======) with a percentage next to it like a loading grid which I would like to remove from my final output.
You can suppress any output messages in R by setting the knitr chunk option. If we wish to hide all code output other than plots, we can use the following solution:
---
output: html_document
---
```{r echo=FALSE, results='hide', fig.keep='all', message = FALSE}
library(Simpsons)
#generating data
Coffee1=rnorm(100,100,15)
Neuroticism1=(Coffee1*.8)+rnorm(100,15,8)
g1=cbind(Coffee1, Neuroticism1)
Coffee2=rnorm(100,170,15)
Neuroticism2=(300-(Coffee2*.8)+rnorm(100,15,8))
g2=cbind(Coffee2, Neuroticism2)
Coffee3=rnorm(100,140,15)
Neuroticism3=(200-(Coffee3*.8)+rnorm(100,15,8))
g3=cbind(Coffee3, Neuroticism3)
data2=data.frame(rbind(g1,g2,g3))
colnames(data2) <- c("Coffee","Neuroticism")
example <- Simpsons(Coffee,Neuroticism,data=data2)
plot(example)
```
I would note that this package seems to print out a lot more content that most packages, and therefore the combination of options are quite long.
An easier method would probably be to move the plot to a separate chunk and have all the analysis run before it. The include argument can be used to suppress all outputs, but this includes plots, hence why we must use two chunks:
```{r, include = FALSE}
# your code to build model
```
```{r}
plot(example)
```
Check out the full list of knitr chunk options here
I'm using rmarkdown via R-Studio and want to plot a heatmap by the heatmap.2. When I change the angle of column labels via the strCol option I get a NULL message printed before the heatmap in the output PDF file.
Attached a minimal code reproduce the problem:
{r, message=FALSE,warning=FALSE, echo=FALSE}
require(gplots)
data(mtcars)
x <- as.matrix(mtcars)
heatmap.2(x,srtCol=0)
The PDF look like
Is there any way to remove this NULL from the PDF output?
Try the following modification using capture.output. This did not print NULL for me.
```{r, message=FALSE,warning=FALSE, echo=FALSE}
require(gplots)
data(mtcars)
x <- as.matrix(mtcars)
res <- capture.output(heatmap.2(x,srtCol=0))
```
There may be a better way with some option to heatmap.2 but I didn't see it in the documentation. This was based off of the following SO post Suppress one command's output in R.
I have a print statement in R as a macro in Markdown
```{r chunk_name, echo=FALSE}
if ( any(so.results$Duration <0.0))
{print("there are non-positive durations")
} else
{print("all durations are fine!")}
```
and I want to generate a PDF, not an XML! How can I print "all durations are fine!" in colour for example green or red?
Using HERE and HERE and the hints given by User I wrote the following:
```{r, results='asis', echo=FALSE}
if ( any(so.results$Duration <0.0))
{cat("\n") print("\textcolor{blue}
{print("there are non-positive durations}")
} else
{cat("\n") print("\textcolor{red}{print("all durations are fine!}")}
```
which solves the problem.