Plot of the design matrix

Provides a graphical representation of the experimental design. It allows to visualize factors levels and check the design balance.

Usage

plotDesign(
  design = NULL,
  lmpDataList = NULL,
  x = NULL,
  y = NULL,
  rows = NULL,
  cols = NULL,
  title = "Plot of the design",
  theme = theme_bw()
)

Arguments

design

A data.frame representing the \(n \times k\) "freely encoded" experimental design. Can be NULL if lmpDataList is defined.

lmpDataList

If not NULL, a list with outcomes, design and formula, as outputted by data2LmpDataList.

x

By default, the first column of design ; otherwise if not NULL, a character string giving the column name of design to be used for the x-axis. The column needs to be a factor.

y

By default, the second column of design if present ; otherwise if not NULL, a character string giving the column name of design to be used for the y-axis.

rows

By default, the fourth column of design if present ; otherwise if not NULL, a character vector with one or several column name(s) of design to be used for faceting along the rows. The column needs to be a factor.

cols

By default, the third column of design if present ; otherwise if not NULL, a character vector with one or several column name(s) of design to be used for faceting along the columns. The column needs to be a factor.

title

Plot title.

theme

The ggplot2 theme, see ?ggtheme for more info.

Value

A ggplot2 plot of the design matrix.

Details

Either design or lmpDataList need to be defined. If both are given, the priority goes to design. The default behavior (parameters x, y, cols and rows are NULL) uses the first four columns of df. If at least one of these arguments is not NULL, the function will only use the non NULL parameters to be displayed.

Examples

### trout data
data(trout)

plotDesign(design = trout$design, x = "Day", y = "Treatment")


# equivalent to:
plotDesign(lmpDataList = trout, x = "Day", y = "Treatment")


### mtcars
data(mtcars)
library(tidyverse)
#> ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
#> ✔ dplyr     1.1.4     ✔ readr     2.1.5
#> ✔ forcats   1.0.0     ✔ stringr   1.5.1
#> ✔ ggplot2   3.5.1     ✔ tibble    3.2.1
#> ✔ lubridate 1.9.3     ✔ tidyr     1.3.1
#> ✔ purrr     1.0.2     
#> ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
#> ✖ lubridate::%within%() masks IRanges::%within%()
#> ✖ ggplot2::Position()   masks BiocGenerics::Position(), base::Position()
#> ✖ dplyr::collapse()     masks IRanges::collapse()
#> ✖ dplyr::combine()      masks Biobase::combine(), BiocGenerics::combine()
#> ✖ dplyr::count()        masks matrixStats::count()
#> ✖ dplyr::desc()         masks IRanges::desc()
#> ✖ tidyr::expand()       masks S4Vectors::expand()
#> ✖ dplyr::filter()       masks stats::filter()
#> ✖ dplyr::first()        masks S4Vectors::first()
#> ✖ dplyr::lag()          masks stats::lag()
#> ✖ purrr::reduce()       masks GenomicRanges::reduce(), IRanges::reduce()
#> ✖ dplyr::rename()       masks S4Vectors::rename()
#> ✖ lubridate::second()   masks S4Vectors::second()
#> ✖ lubridate::second<-() masks S4Vectors::second<-()
#> ✖ dplyr::slice()        masks IRanges::slice()
#> ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors
df <- mtcars %>%
  dplyr::select(cyl, vs, am, gear, carb) %>%
  as.data.frame() %>%
  dplyr::mutate(across(everything(), as.factor))

# Default behavior: display the 4 first factors in the design
plotDesign(design = df)


# 2 factors
plotDesign(
  design = df, x = "cyl", y = "vs",
  cols = NULL, rows = NULL
)

# 3 factors
plotDesign(
  design = df, x = "cyl", y = "vs",
  cols = NULL, rows = c("am")
)

# 4 factors
plotDesign(
  design = df, x = "cyl", y = "vs",
  cols = c("gear"), rows = c("am")
)

# 5 factors
plotDesign(
  design = df, x = "cyl", y = "vs",
  cols = c("gear"), rows = c("am", "carb")
)


plotDesign(
  design = df, x = "cyl", y = "vs",
  cols = c("vs"), rows = c("am", "carb")
)


### UCH
data("UCH")
plotDesign(design = UCH$design, x = "Hippurate", y = "Citrate", rows = "Day")