This vignette will introduce tidyverse patterns that are useful for making full
use of the CellBench framework. CellBench was developed with tidyverse
compatibility as a fundamental goal. `purrr`

provides functional programming
tools to manipulate the methods and lists produced in this framework. `dplyr`

is
very useful for working with the `tibble`

-based structures produced by
CellBench. Since the outputs are mostly in `tibble`

structure, they are very
easily visualised using `ggplot2`

.

For detailed explanations of tidyverse packages please see resources at https://www.tidyverse.org/learn/, in particular R for Data Science.

For quick concise references of tidyverse features and functions I recommend all of the cheatsheets available at https://www.rstudio.com/resources/cheatsheets/.

In CellBench we require methods to take in only a single argument. The idea is
that all methods within a single pipeline step should take the same kind of
input and produce the same type of output. In practice most methods have
additional parameters that can be tuned, and we may use `purrr::partial()`

to
help pre-fill these parameters.

`partial()`

takes a function, some variable values, and returns the function
with the specified arguments pre-filled. This reduces the number of free
parameters in your function.

We demonstrate a trivial application of `partial()`

:

```
library(CellBench)
library(purrr)
# function to raise number to a power
pow <- function(x, n) {
x^n
}
pow2 <- partial(pow, n = 2)
pow3 <- partial(pow, n = 3)
pow2(2)
```

`## [1] 4`

`pow3(2)`

`## [1] 8`

Here `partial()`

allowed us to turn a two-parameter function into a single
parameter function. Using `partial()`

is good practice compared to the two
alternatives:

- Writing duplicate functions
- Writing function wrappers

Consider writing duplicate functions

```
pow2 <- function(x) {
x^2
}
pow3 <- function(x) {
x^3
}
```

Now say you wanted to add an argument check `stopifnot(is.numeric(x))`

, you
would need to edit the code in two places. The chances for errors leading to
inconsistencies increases dramatically with the number of duplications and
changes required.

Consider writing function wrappers

```
pow <- function(x, n) {
x^n
}
pow2 <- function(x) {
pow(x, 2)
}
pow3 <- function(x) {
pow(x, 3)
}
```

The issue here is that these functions can contain much more in their bodies
than the simple function call. When working in collaboration or sharing the code
in general, it’s not immediately clear that the intention of the derived
functions is only to pre-fill certain variables. Using `partial()`

is concise
and unambiguous in purpose.

See also:

`?partial`

in the example section for more ways to use partial`?fn_arg_seq`

for the CellBench utility to construct a list of functions with varying parameter values

When functions have just one argument, they can easily be composed to create
new functions. We use `purrr::compose()`

for this, and it takes a series of
functions as input. `compose()`

will then return a function that applies
the functions given to it in a right-to-left fashion, such that the right-most
function is applied first and the left-most is applied last in succession.

```
# find the maximum absolute value
max_absolute <- compose(max, abs)
max_absolute(rnorm(100))
```

`## [1] 2.932003`

This is useful for stitching together steps of a pipeline manually, for example if some methods require normalisation but some do not, then you may write wrappers as follows

```
method1 <- function(x) {
x <- normalise(x)
method_func1(x)
}
method2 <- function(x) {
method_func2(x)
}
method3 <- function(x) {
x <- normalise(x)
method_func3(x)
}
```

alternatively you could write

```
# identity simply returns its argument, useful here for code consistency
method1 <- compose(method_func1, normalise)
method2 <- compose(method_func2, identity)
method3 <- compose(method_func3, normalise)
```

which is more succinct and likely to be less error-prone. This is useful when two or more steps in a pipeline would only work in specific combinations, then these combinations can be fused together to form a single step in the desired combinations.

The majority of `purrr`

’s functionality revolves around mapping functions over
a list of inputs. This is a represented by the `map()`

family of functions that
usually take a list and a function as arguments, returning the result of
applying the function to each element of the list.

`map()`

is the primary function which performs basic mapping of lists and
returns list. It functions almost identically to `lapply`

, but is accompanied by
a family of suffixed variants that are useful for various situations.

```
x <- list(1, 2, 3)
map(x, function(x) { x * 2 })
```

```
## [[1]]
## [1] 2
##
## [[2]]
## [1] 4
##
## [[3]]
## [1] 6
```

One useful variant is `map2()`

which takes two lists and applies a two-argument
function to the first elements of both lists, second elements and so on. This
can be used to pass additional variables into the function.

```
# list of random values from different distributions
x <- list(
rpois(100, lambda = 5),
rpois(100, lambda = 5),
rgamma(100, shape = 5),
rgamma(100, shape = 5)
)
# list of additional parameters
y <- list(
"mean",
"median",
"mean",
"median"
)
# function that takes values and a mode argument
centrality <- function(x, mode = c("mean", "median")) {
mode <- match.arg(mode)
if (mode == "mean") {
mean = mean(x)
} else if (mode == "median") {
median = median(x)
}
}
# using map2 to apply function to two lists
map2(x, y, centrality)
```

```
## [[1]]
## [1] 4.7
##
## [[2]]
## [1] 5
##
## [[3]]
## [1] 5.139844
##
## [[4]]
## [1] 4.572513
```

The fundamental `benchmark_tbl()`

is derived from the `tibble`

object which
acts mostly indentical to a regular `data.frame`

. Therefore it is compatible
with the `dplyr`

set of table manipulation functions.

```
library(dplyr)
# list of data
datasets <- list(
set1 = rnorm(500, mean = 2, sd = 1),
set2 = rnorm(500, mean = 1, sd = 2)
)
# list of functions
add_noise <- list(
none = identity,
add_bias = function(x) { x + 1 }
)
res <- apply_methods(datasets, add_noise)
class(res)
```

`## [1] "benchmark_tbl" "tbl_df" "tbl" "data.frame"`

`res`

```
## # A tibble: 4 × 3
## data add_noise result
## <fct> <fct> <list>
## 1 set1 none <dbl [500]>
## 2 set1 add_bias <dbl [500]>
## 3 set2 none <dbl [500]>
## 4 set2 add_bias <dbl [500]>
```

From our results we can filter the rows or manipulat the columns with regular
`dplyr`

operations.

```
# filtering rows to only data from set 1
res %>%
filter(data == "set1")
```

```
## # A tibble: 2 × 3
## data add_noise result
## <fct> <fct> <list>
## 1 set1 none <dbl [500]>
## 2 set1 add_bias <dbl [500]>
```

```
# filtering rows to only add_bias method
res %>%
filter(add_noise == "add_bias")
```

```
## # A tibble: 2 × 3
## data add_noise result
## <fct> <fct> <list>
## 1 set1 add_bias <dbl [500]>
## 2 set2 add_bias <dbl [500]>
```

```
# mutating data column to prepend "data" to data set names
res %>%
mutate(data = paste0("data", data))
```

```
## # A tibble: 4 × 3
## data add_noise result
## <chr> <fct> <list>
## 1 dataset1 none <dbl [500]>
## 2 dataset1 add_bias <dbl [500]>
## 3 dataset2 none <dbl [500]>
## 4 dataset2 add_bias <dbl [500]>
```

We often want to plot two or more metrics against each other, for this purpose it is most useful to have each metric in its own column. The default CellBench model does not appear to support this, but it can be done quite easily using `spread()`

from the `tidyr`

package.

```
metric <- list(
mean = mean,
median = median
)
# simply applying the metrics results in a single column
res %>%
apply_methods(metric)
```

```
## # A tibble: 8 × 4
## data add_noise metric result
## <fct> <fct> <fct> <dbl>
## 1 set1 none mean 2.07
## 2 set1 none median 2.04
## 3 set1 add_bias mean 3.07
## 4 set1 add_bias median 3.04
## 5 set2 none mean 1.08
## 6 set2 none median 1.24
## 7 set2 add_bias mean 2.08
## 8 set2 add_bias median 2.24
```

```
# spread metrics across columns
res %>%
apply_methods(metric) %>%
spread(metric, result)
```

```
## # A tibble: 4 × 4
## data add_noise mean median
## <fct> <fct> <dbl> <dbl>
## 1 set1 none 2.07 2.04
## 2 set1 add_bias 3.07 3.04
## 3 set2 none 1.08 1.24
## 4 set2 add_bias 2.08 2.24
```

Tibble results are easy to use with ggplot2. For a more extensive introduction to ggplot2 see R for Data Science: Chapter 3. Here we will plot results of our pipelines in a single plot, because the result column is a list-column, it needs to be unnested to produce a “flat” table, see `?tidyr::unnest`

for more explanation on unnesting. For convenience, we also use `pipeline_collapse()`

from CellBench to concatenate the method names at each stop to produce a single character string representing a pipeline.

```
library(tidyr)
library(ggplot2)
# I prefer my own theme for ggplot2, following theme code is optional
theme_set(theme_bw() + theme(
plot.title = element_text(face = "plain", size = rel(20/12),
hjust = 1/2, margin = margin(t = 10, b = 20)),
axis.text = element_text(size = rel(14/12)),
strip.text.x = element_text(size = rel(16/12)),
axis.title = element_text(size = rel(16/12))
))
scale_colour_discrete <- function(...) scale_colour_brewer(..., palette="Set1")
scale_fill_discrete <- function(...) scale_fill_brewer(... , palette="Set1")
```

```
# pipeline collapse constructs a single string from the pipeline steps,
# unnest expands the list-column of results, transforming the result
# into a flat table.
collapsed_res <- pipeline_collapse(res) %>%
unnest()
```

```
## Warning: `cols` is now required when using `unnest()`.
## ℹ Please use `cols = c(result)`.
```

```
ggplot(collapsed_res, aes(x = pipeline, y = result)) +
geom_boxplot()
```

We can “facet” the above plot by sectioning off related graphics. This general idea covered in the facet section of the previously linked text. This also demonstrates the benefits of having the data in a tibble format.

```
# remember that we have to unnest the data before it's appropriate
# for plotting
ggplot(unnest(res), aes(x = add_noise, y = result)) +
geom_boxplot() +
facet_grid(~data)
```

```
## Warning: `cols` is now required when using `unnest()`.
## ℹ Please use `cols = c(result)`.
```