When creating a table with kable and kableExtra in a R markdown program, I want to group rows and generate a group header using the collapse_rows() function. This works fine. However, if the values in the variable used for grouping contain special characters, such as "(" and ")", the rendered pdf has inserted "\" in front of the special characters in the header line.
Is there any way how to fix this?
I am running R version 3.4.3 (2017-11-30) -- "Kite-Eating Tree" on
x86_64-pc-linux-gnu (64-bit).
R Studio is version 1.1.442.
Knitr is version 1.18.
KableExtra is version 0.9.0.
latex-engine is defaulted to pdflatex, but I also tried xelatex.
I also tried setting escape=T in kable() as well as column_spec(), the first has no effect and the second causes an error message in my environment.
---
output:
pdf_document:
fig_caption: yes
documentclass: article
fontsize: 11pt
geometry: "a4paper, portrait, left=3.00cm, right=1.98cm, bottom=3.81cm, top=2.01cm"
header-includes:
- \usepackage{booktabs}
- \usepackage{longtable}
- \usepackage{array}
- \usepackage{multirow}
- \usepackage{wrapfig}
- \usepackage{float}
- \usepackage{pdflscape}
- \usepackage[normalem]{ulem}
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
```{r prepcode, echo=FALSE, warning=FALSE, message=FALSE, include=FALSE}
rm(list=ls())
library(tidyverse)
options(kableExtra.latex.load_packages = FALSE)
library(kableExtra)
```
```{r tab, echo=FALSE, warning=FALSE, message=FALSE}
x <- rnorm(n=18)
t <- expand.grid(COL1=c("Stratum 1 (my first stratum)", "Stratum 2 (my second stratum)"),
COL2=c("A", "B", "C"),
COL3=c("x", "y", "z"))
xt <- cbind(t, COL4=x) %>% arrange(COL1, COL2, COL3)
knitr::kable(xt, format="latex", row.names=FALSE, booktabs=T) %>%
kable_styling(font_size=8, latex_options = c("repeat_header")) %>%
column_spec(1, bold=T) %>%
collapse_rows(1:2, row_group_label_position = 'stack', latex_hline = "major")
```
For example, "Stratum 1 (my first stratum)" is displayed as "Stratum 1 \(my first stratum\)" in the pdf.
You can prevent kableExtra from escaping special characters in stacked rows by changing the collapse_rows call to
collapse_rows(1:2, row_group_label_position = 'stack', latex_hline = "major",
row_group_label_fonts = list (list (escape = FALSE)))
Related
I have string like so:
"Job 1233:name_uuid (table n_Cars_1234567$20220316) done. Records: 24, with errors: 0."
I'd like to retieve the datte from the table name, so far I use:
"\$[0-9]+"
but this yields $20220316. How do I get only the date, without $?
I'd also like to get the table name: n_Cars_12345678$20220316
So far I have this:
pattern_table_info = "\(([^\)]+)\)"
pattern_table_name = "(?<=table ).*"
table_info = re.search(pattern_table_info, message).group(1)
table = re.search(pattern_table_name, table_info).group(0)
However I'd like to have a more simpler solution, how can I improve this?
EDIT:
Actually the table name should be:
n_Cars_12345678
So everything before the "$" sign and after "table"...how can this part of the string be retrieved?
You can use a regex with two capturing groups:
table\s+([^()]*)\$([0-9]+)
See the regex demo. Details:
table - a word
\s+ - one or more whitespaces
([^()]*) - Group 1: zero or more chars other than ( and )
\$ - a $ char
([0-9]+) - Group 2: one or more digits.
See the Python demo:
import re
text = "Job 1233:name_uuid (table n_Cars_1234567$20220316) done. Records: 24, with errors: 0."
rx = r"table\s+([^()]*)\$([0-9]+)"
m = re.search(rx, text)
if m:
print(m.group(1))
print(m.group(2))
Output:
n_Cars_1234567
20220316
You can write a single pattern with 2 capture groups:
\(table (\w+\$(\d+))\)
The pattern matches:
\(table
( Capture group 1
\w+\$ match 1+ word characters and $
(\d+) Capture group 2, match 1+ digits
) Close group 1
\) Match )
See a Regex demo and a Python demo.
import re
s = "Job 1233:name_uuid (table n_Cars_1234567$20220316) done. Records: 24, with errors: 0."
m = re.search(r"\(table (\w+\$(\d+))\)", s)
if m:
print(m.group(1))
print(m.group(2))
Output
n_Cars_1234567$20220316
20220316
How do I set indentation for string-based value spanning multiple lines in ConfigObj such that the second line, etc. does surpass the delimiter?
For example:
about = {'Info' : {'Purpose': 'blabla continues for fixed chars ...\
\n and another line of bla ... etc.'}} # here nicely aligned under "b" from bla.
# 11 white-spaces.
config = ConfigObj(indent_type= 3*' ', interpolation=True, encoding='utf8')
config.filename = 'lol.ini'
config['About'] = about
config.write()
this result shows in the ini file as:
[About]
[[Info]]
Purpose = '''blabla continues for fixed chars ...
and another line of bla ... etc.''' # here the indentation goes sub-optimal/wrong.
# 11 white spaces but missing the indentations (6 white-spaces)
For two levels the indentation shift would be 6 white-spaces to add (for "About"and for "Info" 3 earch). Apparently, "interpolation=True" is not what does the trick. Any suggestions?
Configobj ver. = 5.0.6
Py = 3.9
I need to compose a simple rmarkdown file, with text, code and the results of executed code included in a resulting PDF file. I would prefer if the source file is executable and self sifficient, voiding the need for a makefile.
This is the best I have been able to achieve, and it is far from good:
#!/usr/bin/env Rscript
library(knitr)
pandoc('hw_ch4.rmd', format='latex')
# TODO: how to NOT print the above commands to the resulting .pdf?
# TODO: how to avoid putting everyting from here on in ""s?
# TODO: how to avoid mentioning the file name above?
# TODO: how to render special symbols, such as tilde, miu, sigma?
# Unicode character (U+3BC) not set up for use with LaTeX.
# See the inputenc package documentation for explanation.
# nano hw_ch4.rmd && ./hw_ch4.rmd && evince hw_ch4.pdf
"
4E1. In the model definition below, which line is the likelihood?
A: y_i is the likelihood, based on the expectation and deviation.
4M1. For the model definition below, simulate observed heights from the prior (not the posterior).
A:
```{r}
points <- 10
rnorm(points, mean=rnorm(points, 0, 10), sd=runif(points, 0, 10))
```
4M3. Translate the map model formula below into a mathematical model definition.
A:
```{r}
flist <- alist(
y tilda dnorm( mu , sigma ),
miu tilda dnorm( 0 , 10 ),
sigma tilda dunif( 0 , 10 )
)
```
"
Result:
What I eventually came to use is the following header. At first it sounded neat, but later I realized
+ is indeed easy to compile in one step
- this is code duplication
- mixing executable script and presentation data in one file is a security risk.
Code:
#!/usr/bin/env Rscript
#<!---
library(rmarkdown)
argv <- commandArgs(trailingOnly=FALSE)
fname <- sub("--file=", "", argv[grep("--file=", argv)])
render(fname, output_format="pdf_document")
quit(status=0)
#-->
---
title:
author:
date: "compiled on: `r Sys.time()`"
---
The quit() line is supposed to guarantee that the rest of the file is treated as data. The <!--- and --> comments are to render the executable code as comments in the data interpretation. They are, in turn, hidden by the #s from the shell.
I want to plot a simplified heatmap that is not so difficult to edit with the scalar vector graphics program I am using (inkscape). The original heatmap as produced below contains lots of rectangles, and I wonder if they could be merged together in the different sectors to simplify the output pdf file:
nentries=100000
ci=rainbow(nentries)
set.seed=1
mean=10
## Generate some data (4 factors)
i = data.frame(
a=round(abs(rnorm(nentries,mean-2))),
b=round(abs(rnorm(nentries,mean-1))),
c=round(abs(rnorm(nentries,mean+1))),
d=round(abs(rnorm(nentries,mean+2)))
)
minvalue = 10
# Discretise values to 1 or 0
m0 = matrix(as.numeric(i>minvalue),nrow=nrow(i))
# Remove rows with all zeros
m = m0[rowSums(m0)>0,]
# Reorder with 1,1,1,1 on top
ms =m[order(as.vector(m %*% matrix(2^((ncol(m)-1):0),ncol=1)), decreasing=TRUE),]
rowci = rainbow(nrow(ms))
colci = rainbow(ncol(ms))
colnames(ms)=LETTERS[1:4]
limits=c(which(!duplicated(ms)),nrow(ms))
l=length(limits)
toname=round((limits[-l]+ limits[-1])/2)
freq=(limits[-1]-limits[-l])/nrow(ms)
rn=rep("", nrow(ms))
for(i in toname) rn[i]=paste(colnames(ms)[which(ms[i,]==1)],collapse="")
rn[toname]=paste(rn[toname], ": ", sprintf( "%.5f", freq ), "%")
heatmap(ms,
Rowv=NA,
labRow=rn,
keep.dendro = FALSE,
col=c("black","red"),
RowSideColors=rowci,
ColSideColors=colci,
)
dev.copy2pdf(file="/tmp/file.pdf")
Why don't you try RSvgDevice? Using it you could save your image as svg file, which is much convenient to Inkscape than pdf
I use the Cairo package for producing svg. It's incredibly easy. Here is a much simpler plot than the one you have in your example:
require(Cairo)
CairoSVG(file = "tmp.svg", width = 6, height = 6)
plot(1:10)
dev.off()
Upon opening in Inkscape, you can ungroup the elements and edit as you like.
Example (point moved, swirl added):
I don't think we (the internet) are being clear enough on this one.
Let me just start off with a successful export example
png("heatmap.png") #Ruby dev's think of this as kind of like opening a `File.open("asdfsd") do |f|` block
heatmap(sample_matrix, Rowv=NA, Colv=NA, col=terrain.colors(256), scale="column", margins=c(5,10))
dev.off()
The dev.off() bit, in my mind, reminds me of an end call to a ruby block or method, in that, the last line of the "nested" or enclosed (between png() and dev.off()) code's output is what gets dumped into the png file.
For example, if you ran this code:
png("heatmap4.png")
heatmap(sample_matrix, Rowv=NA, Colv=NA, col=terrain.colors(32), scale="column", margins=c(5,15))
heatmap(sample_matrix, Rowv=NA, Colv=NA, col=greenred(32), scale="column", margins=c(5,15))
dev.off()
it would output the 2nd (greenred color scheme, I just tested it) heatmap to the heatmap4.png file, just like how a ruby method returns its last line by default
I hope this question is not too simple for this board.
I have created a data.frame df:
CAS Name CID
89 13010-47-4 Lomustine 3950
90 130209-82-4 Latanoprost 5311221,5282380,46705340,3890
91 130636-43-0 Nifekalant 268083
92 130929-57-6 Entacapone 5281081
and a vector vec
[1] 5282380 18471829 45923789 44308022 44266812 24883465 24867475 24867460
I would like to extract the rows of df which contains any number of vec. I tried to solve this problem by this code:
df$GC[(df$CID %in% vec)] = 1
df[df$GC==1,]
But the problem with this solution is, that I only get the rows, which contain only one number in the CID column. Rows which contain several values in CID like line 90 do not appear.
Is there an elegant solution for this problem?
Thanks in advance
Given your comment on EDi's answer (which I like) I thought I'd make a suggestion.
Squeezing comma separated values into a single column of a data frame is awkward and (in my experience) just leads to frustration. I often find it simpler to keep it in a separate data structure, a list:
dat <- read.table(text = " CAS Name CID
13010-47-4 Lomustine 3950
130209-82-4 Latanoprost 5311221,5282380,46705340,3890
130636-43-0 Nifekalant 268083
130929-57-6 Entacapone 5281081",sep = "",header = TRUE)
cid <- sapply(dat$CID,strsplit,",",USE.NAMES = FALSE)
In this form, things are often easier to work with:
ID <- c(5282380, 18471829, 45923789, 44308022, 44266812, 24883465, 24867475, 24867460, 3950)
dat[sapply(cid,function(x) {any(x %in% as.character(ID))}),]
CAS Name CID
1 13010-47-4 Lomustine 3950
2 130209-82-4 Latanoprost 5311221,5282380,46705340,3890
You can always use rownames in dat and the names of the list to keep each item straight, if you're worried about orderings changing.
(Also note that my anonymous function is assuming that ID will be found eventually by R's scoping rules; you can alter the function to pass in ID explicitly if you like.)
One way is to use grep():
> txt <- " CAS Name CID
+ 13010-47-4 Lomustine 3950
+ 130209-82-4 Latanoprost 5311221,5282380,46705340,3890
+ 130636-43-0 Nifekalant 268083
+ 130929-57-6 Entacapone 5281081
+ "
> con <- textConnection(txt)
> df <- read.table(con, header = TRUE)
> close(con)
> ID <- c(5282380, 18471829, 45923789, 44308022, 44266812, 24883465, 24867475, 24867460, 3950)
> grep(paste("\\b", ID, "\\b", sep="", collapse = "|"), dat$CID)
[1] 1 2