How to create a table in Rstudio presentation - r

I'm trying to create a table in an RStudio .Rpres file. Below is what I have at this point from online searching but the alignment is not correct. Is this the best method? Any suggestions on the alignment?
Test
=========================================================
| Right | Left | Default | Center |
|------:|:-----|---------|:------:|
| 12 | 12 | 12 | 12 |
| 123 | 123 | 123 | 123 |
| 1 | 1 | 1 | 1 |
: Demonstration of simple table syntax.
Result:

You can use knitr::kable to print your data.frame
Test
========================================================
```{r, echo=FALSE}
my_df <- iris
knitr::kable(head(my_df))
```
#alignments:
I tried using align = c('l', 'r', 'c', 'r', 'l') as described in ?kable
but it did not work. Maybe this is a bug.
Output of
knitr::kable(head(iris), align = c('l', 'r', 'c', 'r', 'l'))
|Sepal.Length | Sepal.Width| Petal.Length | Petal.Width|Species |
|:------------|-----------:|:------------:|-----------:|:-------|
|5.1 | 3.5| 1.4 | 0.2|setosa |
|4.9 | 3.0| 1.4 | 0.2|setosa |
|4.7 | 3.2| 1.3 | 0.2|setosa |
|4.6 | 3.1| 1.5 | 0.2|setosa |
|5.0 | 3.6| 1.4 | 0.2|setosa |
|5.4 | 3.9| 1.7 | 0.4|setosa |

A pander example:
```{r}
df <- replicate(3, sample(letters, 3))
colnames(df) <- rep('foobar', 3)
pander::pander(df, justify = c('right', 'left', 'center'))
```
Or specifying a global alignment for all columns (which can be a smart function as well BTW):
```{r}
set.alignment('right')
pander::pander(df)
```
Both results in a correctly formatted markdown table that renders fine in HTML.

I managed to get align to work by including the format = "html" parameter in the function call, so in the example discussed above by FlooO:
knitr::kable(head(iris), format = "html", align = c('l', 'r', 'c', 'r', 'l'))
gave me the desired result

Related

Markdown table in Jupyter notebook not working

I know how to set to up a table in a jupyter notebook`. I even looked up internet and imitated it. However it is not working? Anyone can tell me what is wrong with my notebook, is there anything I should change while constructing markdown table
Tables | Are | Cool |
| ------------- |:-------------:| -----:|
| col 3 is | right-aligned | $1600 |
| col 2 is | centered | $12 |
| zebra stripes | are neat | $1 |
Two things:
the example code is missing the first | character
dollar signs need to be escaped with a backslash (\) since MathJax is enabled
Try this:
|Tables | Are | Cool |
| ------------- |:-------------:| ------:|
| col 3 is | right-aligned | \$1600 |
| col 2 is | centered | \$12 |
| zebra stripes | are neat | \$1 |

How to handle empty cells in R markdown?

I have an R analysis that I want to present in an R markdown table. The table's layout demands some empty cells:
x <- c(1:14)
Header1 | Header2 | Header3 | Header4
------- | ------- | -------- | -------
Label1 | LabelA | `r x[1]` | `r x[4]`
Label2 | LabelB | `r x[2]` | `r x[5]`
| LabelC | `r x[3]` | `r x[6]`
| LabelD | | `r x[7]`
------- | ------- | -------- | -------
Label3 | LabelA | `r x[8]` | `r x[11]`
Label4 | LabelB | `r x[9]` | `r x[12]`
| LabelC | `r x[10]`| `r x[13]`
| LabelD | | `r x[14]`
However, those empty cells are causing the layout to break, ie, LabelC appears directly under Label2 even though it is supposed to be one column over.
I know, from searching on this issue, that you can't merge table cells in R Markdown. But can I fill those cells with code such that they will present as empty? I tried filling them with r NULL but nothing happened.
The problem with this table is that it does not have the style required by rmarkdown. The table below has the good style and there's no issue with this table:
| Header1 | Header2 | Header3 | Header4 |
|:-------:|:-------:|:--------:|:---------:|
| Label1 | LabelA | `r x[1]` | `r x[4]` |
| Label2 | LabelB | `r x[2]` | `r x[5]` |
| | LabelC | `r x[3]` | `r x[6]` |
| | LabelD | | `r x[7]` |
| ------- | ------- | -------- | --------- |
| Label3 | LabelA | `r x[8]` | `r x[11]` |
| Label4 | LabelB | `r x[9]` | `r x[12]` |
| | LabelC | `r x[10]`| `r x[13]` |
| | LabelD | | `r x[14]` |
You can generate such a table with the pander package, function pandoc.table with the option style="rmarkdown", or with knitr::kable. Both have an option for dealing with the missing values.

Control digits in specific cells

I have a table that looks like this:
+-----------------------------------+-------+--------+------+
| | Male | Female | n |
+-----------------------------------+-------+--------+------+
| way more than my fair share | 2,4 | 21,6 | 135 |
| a little more than my fair share | 5,4 | 38,1 | 244 |
| about my fair share | 54,0 | 35,3 | 491 |
| a littles less than my fair share | 25,1 | 3,0 | 153 |
| way less than my fair share | 8,7 | 0,7 | 51 |
| Can't say | 4,4 | 1,2 | 31 |
| n | 541,0 | 564,0 | 1105 |
+-----------------------------------+-------+--------+------+
Everything is fine but what I would like to do is to show no digits in the last row at all since they show the margins (real cases). Is there any chance in R I can manipulate specific cells and their digits?
Thanks!
You could use ifelse to output the numbers in different formats in different rows, as in the example below. However, it will take some additional finagling to get the values in the last row to line up by place value with the previous rows:
library(knitr)
library(tidyverse)
# Fake data
set.seed(10)
dat = data.frame(category=c(LETTERS[1:6],"n"), replicate(3, rnorm(7, 100,20)))
dat %>%
mutate_if(is.numeric, funs(sprintf(ifelse(category=="n", "%1.0f", "%1.1f"), .))) %>%
kable(align="lrrr")
|category | X1| X2| X3|
|:--------|-----:|-----:|-----:|
|A | 100.4| 92.7| 114.8|
|B | 96.3| 67.5| 101.8|
|C | 72.6| 94.9| 80.9|
|D | 88.0| 122.0| 96.1|
|E | 105.9| 115.1| 118.5|
|F | 107.8| 95.2| 109.7|
|n | 76| 120| 88|
The huxtable package makes it easy to decimal-align the values (see the Vignette for more on table formatting):
library(huxtable)
tab = dat %>%
mutate_if(is.numeric, funs(sprintf(ifelse(category=="n", "%1.0f", "%1.1f"), .))) %>%
hux %>% add_colnames()
align(tab)[-1] = "."
tab
Here's what the PDF output looks like when knitted to PDF from an rmarkdown document:

R apply script output in different formats for similar inputs

I'm using a double apply function to get a list of p-values for cor.test between any two columns of two tables.
hel_plist<-apply(bc, 2, function(x) { apply(otud, 2, function(y) { if (cor.test(x,y,method="spearman", exact=FALSE)$p.value<0.05){cor.test(x,y,method="spearman", exact=FALSE)$p.value}}) })
The otud data.frame is 90X11 (90rows,11 colums or to say dim(otud) 90 11) and will be used with different data.frames.
bc and hel - are both 90X2 data.frame-s - so for both I get 2*11=22 p-values out of functions
bc_plist<-apply(bc, 2, function(x) { apply(otud, 2, function(y) { if (cor.test(x,y,method="spearman", exact=FALSE)$p.value<0.05){cor.test(x,y,method="spearman", exact=FALSE)$p.value}}) })
hel_plist<-apply(hel, 2, function(x) { apply(otud, 2, function(y) { if (cor.test(x,y,method="spearman", exact=FALSE)$p.value<0.05){cor.test(x,y,method="spearman", exact=FALSE)$p.value}}) })
For bc I will have an output with dim=NULL a list of elements of otunames$bcnames$ p-value (a format that I have always got from these scripts and are happy with)
But for hel I will get and output of dim(hel) 11 2 - an 11X2 table with p-values written inside.
Shortened examples of output.
hel_plist
+--------+--------------+--------------+
| | axis1 | axis2 |
+--------+--------------+--------------+
| Otu037 | 1.126362e-18 | 0.01158251 |
| Otu005 | 3.017458e-2 | NULL |
| Otu068 | 0.00476002 | NULL |
| Otu070 | 1.27646e-15 | 5.252419e-07 |
+--------+--------------+--------------+
bc_plist
$axis1
$axis1$Otu037
[1] 1.247717e-06
$axis1$Otu005
[1] 1.990313e-05
$axis1$Otu068
[1] 5.664597e-07
Why is it like that when the input formats are all the same? (Shortened examples)
bc
+-------+-----------+-----------+
| group | axis1 | axis2 |
+-------+-----------+-----------+
| 1B041 | 0.125219 | 0.246319 |
| 1B060 | -0.022412 | -0.030227 |
| 1B197 | -0.088005 | -0.305351 |
| 1B222 | -0.119624 | -0.144123 |
| 1B227 | -0.148946 | -0.061741 |
+-------+-----------+-----------+
hel
+-------+---------------+---------------+
| group | axis1 | axis2 |
+-------+---------------+---------------+
| 1B041 | -0.0667782322 | -0.1660606406 |
| 1B060 | 0.0214470932 | -0.0611351008 |
| 1B197 | 0.1761876858 | 0.0927570627 |
| 1B222 | 0.0681058251 | 0.0549292399 |
| 1B227 | 0.0516864361 | 0.0774155225 |
| 1B235 | 0.1205676221 | 0.0181712761 |
+-------+---------------+---------------+
How could I force my scripts to always produce "flat" outputs as in the case of bc
OK different output-s are caused because of the NULL results from conditional function in bc_plist case. If I'd to modify code to replace possible NULL-s with NA-s I'd get 2d tables in any case.
So to keep things constant :
bc_nmds_plist<-apply(bc_nmds, 2, function(x) { apply(stoma_otud, 2, function(y) { if (cor.test(x,y,method="spearman", exact=FALSE)$p.value<0.05){cor.test(x,y,method="spearman", exact=FALSE)$p.value}else NA}) })
And I get a 2d tabel out for bc_nmds_plist too.
So I guess this thing can be called solved - as I now have a piece of code that produces predictable output on any correct input.
If anyone has any idea how to force the output to conform to previos bc_plist format instead I would still be interested as I do actually prefer that form:
$axis1
$axis1$Otu037
[1] 1.247717e-06
$axis1$Otu005
[1] 1.990313e-05
$axis1$Otu068
[1] 5.664597e-07

kable function: "id" in the columns

When I trying print table with knitr::kable function "id" word apperas in the column names. How can I change it?
Example:
> x <- structure(c(42.3076923076923, 53.8461538461538, 96.1538461538462,
2.56410256410256, 1.28205128205128, 3.84615384615385,
44.8717948717949, 55.1282051282051, 100),
.Dim = c(3L, 3L),
.Dimnames = structure(list(Condition1 = c("Yes", "No", "Sum"),
Condition2 = c("Yes", "No", "Sum")),
.Names = c("Condition1", "Condition2")), class = c("table", "matrix"))
> print(x)
Condition2
Condition1 Yes No Sum
Yes 42,31 2,56 44,87
No 53,85 1,28 55,13
Sum 96,15 3,85 100,00
> library(knitr)
> kable(x)
|id | Yes| No| Sum|
|:----|-----:|-----:|------:|
|Yes | 42,3| 2,56| 44,9|
|No | 53,8| 1,28| 55,1|
|Sum | 96,2| 3,85| 100,0|
Edit: I find reason of this behavior in the knitr:::kable_mark function. But now I not understand how to make it more flexible.
An alternative to kable might be the general S3 method of pander:
> library(pander)
> pander(x, style = 'rmarkdown')
| | Yes | No | Sum |
|:---------:|:-----:|:-----:|:-----:|
| **Yes** | 42.31 | 2.564 | 44.87 |
| **No** | 53.85 | 1.282 | 55.13 |
| **Sum** | 96.15 | 3.846 | 100 |
If you need to set the decimal mark to comma, then set the relevant option before and use that in your R session:
> panderOptions('decimal.mark', ',')
> pander(x, style = 'rmarkdown')
| | Yes | No | Sum |
|:---------:|:-----:|:-----:|:-----:|
| **Yes** | 42,31 | 2,564 | 44,87 |
| **No** | 53,85 | 1,282 | 55,13 |
| **Sum** | 96,15 | 3,846 | 100 |
There are also some other possible tweaks: http://rapporter.github.io/pander/#pander-options
I think the easiest way is to rip out and replace kable_mark completely. Note: this is quite dirty – but it seems to work, and there is no current way to customise how kable_mark works (you could submit a patch to knitr though).
km <- edit(knitr:::kable_mark)
# Now edit the code and remove lines 7 and 8.
unlockBinding('kable_mark', environment(knitr:::kable_mark))
assign('kable_mark', km, envir=environment(knitr:::kable_mark))
Explanation: First we edit the function and store the amended definition in a temporary variable. We remove the two lines
if (grepl("^\\s*$", cn[1L]))
cn[1L] = "id"
… of course you can also hard-code the amended function rather than editing it, or change the function around completely.
Next we use unlockBinding to make knitr:::kable_mark overridable. If we don’t do this, the next assign command wouldn’t work.
Finally, we assign the patched function back to knitr:::kable_mark. Done.

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