Incorporating experimental designs
Mike Blazanin
Source:vignettes/gc03_incorporate_designs.Rmd
gc03_incorporate_designs.RmdWhere are we so far?
- Introduction:
vignette("gc01_gcplyr") - Importing and reshaping data:
vignette("gc02_import_reshape") -
Incorporating experimental designs:
vignette("gc03_incorporate_designs") - Pre-processing and plotting your data:
vignette("gc04_preprocess_plot") - Processing your data:
vignette("gc05_process") - Analyzing your data:
vignette("gc06_analyze") - Dealing with noise:
vignette("gc07_noise") - Best practices and other tips:
vignette("gc08_conclusion") - Working with multiple plates:
vignette("gc09_multiple_plates") - Using make_design to generate experimental designs:
vignette("gc10_using_make_design")
So far, we’ve imported and transformed our measures data into
R. Now we’re going to address how to incorporate our
experimental design.
If you haven’t already, load the necessary packages.
library(gcplyr)
#> ##
#> ## gcplyr (Version 1.10.0, Build Date: 2024-07-09)
#> ## See http://github.com/mikeblazanin/gcplyr for additional documentation
#> ## Please cite software as:
#> ## Blazanin, Michael. gcplyr: an R package for microbial growth
#> ## curve data analysis. BMC Bioinformatics 25, 232 (2024).
#> ## https://doi.org/10.1186/s12859-024-05817-3
#> ##Including design elements
We often want to combine our data with information about the
experimental design. gcplyr enables incorporation of design
elements in two ways:
- Designs can be imported from files
- Designs can be generated in
Rusingmake_design
If you’re interested in generating your designs in R,
see vignette("gc10_using_make_design")
When reading design elements from files, gcplyr can read
block-shaped or tidy-shaped design files:
- If design files are block-shaped, they can be read with
import_blockdesigns - If design files are tidy-shaped, they can simply be read with
read_tidys
Importing block-shaped design files
To import block-shaped design files, use
import_blockdesigns, which will return a tidy-shaped
designs data frame (or list of data frames).
import_blockdesigns only requires a list of filenames
(or relative file paths) and will return a data.frame (or list of data
frames) in a tidy format that you can save in R.
A basic example
Let’s look at an example. First, we need to create an example file for the sake of this tutorial (normally you’d create this file in Excel)
make_example(vignette = 3, example = 1, dir = ".")
#> Files have been written
#> [1] "./mydesign.csv"Now let’s take a look at what the file looks like:
print_df(read.csv("mydesign.csv", header = FALSE, colClasses = "character"))
#> 1 2 3 4 5 6 7 8 9 10 11 12
#> A Tr1 Tr1 Tr1 Tr1 Tr1 Tr1 Tr2 Tr2 Tr2 Tr2 Tr2 Tr2
#> B Tr1 Tr1 Tr1 Tr1 Tr1 Tr1 Tr2 Tr2 Tr2 Tr2 Tr2 Tr2
#> C Tr1 Tr1 Tr1 Tr1 Tr1 Tr1 Tr2 Tr2 Tr2 Tr2 Tr2 Tr2
#> D Tr1 Tr1 Tr1 Tr1 Tr1 Tr1 Tr2 Tr2 Tr2 Tr2 Tr2 Tr2
#> E Tr1 Tr1 Tr1 Tr1 Tr1 Tr1 Tr2 Tr2 Tr2 Tr2 Tr2 Tr2
#> F Tr1 Tr1 Tr1 Tr1 Tr1 Tr1 Tr2 Tr2 Tr2 Tr2 Tr2 Tr2
#> G Tr1 Tr1 Tr1 Tr1 Tr1 Tr1 Tr2 Tr2 Tr2 Tr2 Tr2 Tr2
#> H Tr1 Tr1 Tr1 Tr1 Tr1 Tr1 Tr2 Tr2 Tr2 Tr2 Tr2 Tr2Here we can see that our design has Treatment 1 on the left-hand side
of the plate (wells in columns 1 through 6), and Treatment 2 on the
right-hand side of the plate (wells in columns 7 through 12). Let’s
import this design using import_blockdesigns, saving it
with the column name Treatment_numbers.
my_design <- import_blockdesigns(files = "mydesign.csv",
block_names = "Treatment_numbers")
head(my_design, 20)
#> Well Treatment_numbers
#> 1 A1 Tr1
#> 2 A2 Tr1
#> 3 A3 Tr1
#> 4 A4 Tr1
#> 5 A5 Tr1
#> 6 A6 Tr1
#> 7 A7 Tr2
#> 8 A8 Tr2
#> 9 A9 Tr2
#> 10 A10 Tr2
#> 11 A11 Tr2
#> 12 A12 Tr2
#> 13 B1 Tr1
#> 14 B2 Tr1
#> 15 B3 Tr1
#> 16 B4 Tr1
#> 17 B5 Tr1
#> 18 B6 Tr1
#> 19 B7 Tr2
#> 20 B8 Tr2Importing multiple block-shaped design elements
What do you do if you have multiple designs? For instance, what if you have several strains each in several treatments? In that case, you have two options:
- Save each design component as a separate file, or in separate blocks within a file
- Save the design components pasted together in a single file
Regardless of which option you use, you can then import them all in
one go with import_blockdesigns.
Importing multiple block-shaped designs in separate files
First, let’s create both our example designs files. Again, just imagine that you’ve created these files in Excel.
make_example(vignette = 3, example = 1, dir = ".")
#> Files have been written
#> [1] "./mydesign.csv"
make_example(vignette = 3, example = 2, dir = ".")
#> Files have been written
#> [1] "./mydesign2.csv"Now let’s take a look at what these files looks like:
print_df(read.csv("mydesign.csv", header = FALSE, colClasses = "character"))
#> 1 2 3 4 5 6 7 8 9 10 11 12
#> A Tr1 Tr1 Tr1 Tr1 Tr1 Tr1 Tr2 Tr2 Tr2 Tr2 Tr2 Tr2
#> B Tr1 Tr1 Tr1 Tr1 Tr1 Tr1 Tr2 Tr2 Tr2 Tr2 Tr2 Tr2
#> C Tr1 Tr1 Tr1 Tr1 Tr1 Tr1 Tr2 Tr2 Tr2 Tr2 Tr2 Tr2
#> D Tr1 Tr1 Tr1 Tr1 Tr1 Tr1 Tr2 Tr2 Tr2 Tr2 Tr2 Tr2
#> E Tr1 Tr1 Tr1 Tr1 Tr1 Tr1 Tr2 Tr2 Tr2 Tr2 Tr2 Tr2
#> F Tr1 Tr1 Tr1 Tr1 Tr1 Tr1 Tr2 Tr2 Tr2 Tr2 Tr2 Tr2
#> G Tr1 Tr1 Tr1 Tr1 Tr1 Tr1 Tr2 Tr2 Tr2 Tr2 Tr2 Tr2
#> H Tr1 Tr1 Tr1 Tr1 Tr1 Tr1 Tr2 Tr2 Tr2 Tr2 Tr2 Tr2
print_df(read.csv("mydesign2.csv", header = FALSE, colClasses = "character"))
#> 1 2 3 4 5 6 7 8 9 10 11 12
#> A StrA StrA StrA StrA StrA StrA StrA StrA StrA StrA StrA StrA
#> B StrA StrA StrA StrA StrA StrA StrA StrA StrA StrA StrA StrA
#> C StrB StrB StrB StrB StrB StrB StrB StrB StrB StrB StrB StrB
#> D StrB StrB StrB StrB StrB StrB StrB StrB StrB StrB StrB StrB
#> E StrC StrC StrC StrC StrC StrC StrC StrC StrC StrC StrC StrC
#> F StrC StrC StrC StrC StrC StrC StrC StrC StrC StrC StrC StrC
#> G StrD StrD StrD StrD StrD StrD StrD StrD StrD StrD StrD StrD
#> H StrD StrD StrD StrD StrD StrD StrD StrD StrD StrD StrD StrDAs before, we have Treatment 1 on the left-hand side, and Treatment 2 on the right-hand side. In addition, we now also have Strain A in the first two rows, Strain B in the next two rows, and so on.
Let’s now import both designs using import_blockdesigns,
saving them to columns named Treatment_numbers and
Strain_letters.
my_design <-
import_blockdesigns(files = c("mydesign.csv", "mydesign2.csv"),
block_names = c("Treatment_numbers", "Strain_letters"))
#> Inferred 'into' column names as: Treatment_numbers, Strain_letters
head(my_design, 20)
#> Well Treatment_numbers Strain_letters
#> 1 A1 Tr1 StrA
#> 2 A2 Tr1 StrA
#> 3 A3 Tr1 StrA
#> 4 A4 Tr1 StrA
#> 5 A5 Tr1 StrA
#> 6 A6 Tr1 StrA
#> 7 A7 Tr2 StrA
#> 8 A8 Tr2 StrA
#> 9 A9 Tr2 StrA
#> 10 A10 Tr2 StrA
#> 11 A11 Tr2 StrA
#> 12 A12 Tr2 StrA
#> 13 B1 Tr1 StrA
#> 14 B2 Tr1 StrA
#> 15 B3 Tr1 StrA
#> 16 B4 Tr1 StrA
#> 17 B5 Tr1 StrA
#> 18 B6 Tr1 StrA
#> 19 B7 Tr2 StrA
#> 20 B8 Tr2 StrAImporting multiple separated block-shaped designs in one file
If you have your blocks separated but saved in the same file, you simply specify the location of each block within the file:
make_example(vignette = 3, example = 3, dir = ".")
#> Files have been written
#> [1] "./mydesign_sep.csv"
#Print what the file looks like
print_df(read.csv("mydesign_sep.csv", header = FALSE, colClasses = "character"))
#> 1 2 3 4 5 6 7 8 9 10 11 12
#> A Tr1 Tr1 Tr1 Tr1 Tr1 Tr1 Tr2 Tr2 Tr2 Tr2 Tr2 Tr2
#> B Tr1 Tr1 Tr1 Tr1 Tr1 Tr1 Tr2 Tr2 Tr2 Tr2 Tr2 Tr2
#> C Tr1 Tr1 Tr1 Tr1 Tr1 Tr1 Tr2 Tr2 Tr2 Tr2 Tr2 Tr2
#> D Tr1 Tr1 Tr1 Tr1 Tr1 Tr1 Tr2 Tr2 Tr2 Tr2 Tr2 Tr2
#> E Tr1 Tr1 Tr1 Tr1 Tr1 Tr1 Tr2 Tr2 Tr2 Tr2 Tr2 Tr2
#> F Tr1 Tr1 Tr1 Tr1 Tr1 Tr1 Tr2 Tr2 Tr2 Tr2 Tr2 Tr2
#> G Tr1 Tr1 Tr1 Tr1 Tr1 Tr1 Tr2 Tr2 Tr2 Tr2 Tr2 Tr2
#> H Tr1 Tr1 Tr1 Tr1 Tr1 Tr1 Tr2 Tr2 Tr2 Tr2 Tr2 Tr2
#>
#> 1 2 3 4 5 6 7 8 9 10 11 12
#> A StrA StrA StrA StrA StrA StrA StrA StrA StrA StrA StrA StrA
#> B StrA StrA StrA StrA StrA StrA StrA StrA StrA StrA StrA StrA
#> C StrB StrB StrB StrB StrB StrB StrB StrB StrB StrB StrB StrB
#> D StrB StrB StrB StrB StrB StrB StrB StrB StrB StrB StrB StrB
#> E StrC StrC StrC StrC StrC StrC StrC StrC StrC StrC StrC StrC
#> F StrC StrC StrC StrC StrC StrC StrC StrC StrC StrC StrC StrC
#> G StrD StrD StrD StrD StrD StrD StrD StrD StrD StrD StrD StrD
#> H StrD StrD StrD StrD StrD StrD StrD StrD StrD StrD StrD StrD
#Read in the designs
my_design <-
import_blockdesigns(files = c("mydesign_sep.csv"),
block_names = c("Treatment_numbers", "Strain_letters"),
startrow = c(1, 11), endrow = c(9, 19))
#> Inferred 'into' column names as: Treatment_numbers, Strain_letters
head(my_design, 20)
#> Well Treatment_numbers Strain_letters
#> 1 A1 Tr1 StrA
#> 2 A2 Tr1 StrA
#> 3 A3 Tr1 StrA
#> 4 A4 Tr1 StrA
#> 5 A5 Tr1 StrA
#> 6 A6 Tr1 StrA
#> 7 A7 Tr2 StrA
#> 8 A8 Tr2 StrA
#> 9 A9 Tr2 StrA
#> 10 A10 Tr2 StrA
#> 11 A11 Tr2 StrA
#> 12 A12 Tr2 StrA
#> 13 B1 Tr1 StrA
#> 14 B2 Tr1 StrA
#> 15 B3 Tr1 StrA
#> 16 B4 Tr1 StrA
#> 17 B5 Tr1 StrA
#> 18 B6 Tr1 StrA
#> 19 B7 Tr2 StrA
#> 20 B8 Tr2 StrAImporting multiple pasted block-shaped designs
Alternative to saving your designs separated, often it may be easiest to save all the design information into a single block, separating the distinct components of the design with some character.
To demonstrate this, first let’s create our example designs file. Again, just imagine that you’ve created this file in Excel.
make_example(vignette = 3, example = 4, dir = ".")
#> Files have been written
#> [1] "./mydesign_pasted.csv"Now let’s take a look at what the file looks like:
print_df(read.csv("mydesign_pasted.csv", header = FALSE, colClasses = "character")[, 1:10])
#> 1 2 3 4 5 6 7 8 9
#> A Tr1_StrA Tr1_StrA Tr1_StrA Tr1_StrA Tr1_StrA Tr1_StrA Tr2_StrA Tr2_StrA Tr2_StrA
#> B Tr1_StrA Tr1_StrA Tr1_StrA Tr1_StrA Tr1_StrA Tr1_StrA Tr2_StrA Tr2_StrA Tr2_StrA
#> C Tr1_StrB Tr1_StrB Tr1_StrB Tr1_StrB Tr1_StrB Tr1_StrB Tr2_StrB Tr2_StrB Tr2_StrB
#> D Tr1_StrB Tr1_StrB Tr1_StrB Tr1_StrB Tr1_StrB Tr1_StrB Tr2_StrB Tr2_StrB Tr2_StrB
#> E Tr1_StrC Tr1_StrC Tr1_StrC Tr1_StrC Tr1_StrC Tr1_StrC Tr2_StrC Tr2_StrC Tr2_StrC
#> F Tr1_StrC Tr1_StrC Tr1_StrC Tr1_StrC Tr1_StrC Tr1_StrC Tr2_StrC Tr2_StrC Tr2_StrC
#> G Tr1_StrD Tr1_StrD Tr1_StrD Tr1_StrD Tr1_StrD Tr1_StrD Tr2_StrD Tr2_StrD Tr2_StrD
#> H Tr1_StrD Tr1_StrD Tr1_StrD Tr1_StrD Tr1_StrD Tr1_StrD Tr2_StrD Tr2_StrD Tr2_StrDAs before, we have Treatment 1 on the left-hand side, and Treatment 2 on the right-hand side, with Strain A in the first two rows, Strain B in the next two rows, and so on. However, this information is now pasted together, with “_” as the separating string (you can use any string as a separator).
To import this design with import_blockdesigns, we
simply need to specify the sep string, as well as the
output column names. Since the designs have been pasted together, the
column names will result from splitting the designs apart. The easiest
way to specify these split column names is to use the into
argument passed to separate_tidy [if into is
not specified, import_blockdesigns will attempt to split
the block_names (either specified or inferred) with
sep to generate the output column names].
my_design <-
import_blockdesigns(files = "mydesign_pasted.csv",
into = c("Treatment_numbers", "Strain_letters"),
sep = "_")
head(my_design, 20)
#> Well Treatment_numbers Strain_letters
#> 1 A1 Tr1 StrA
#> 2 A2 Tr1 StrA
#> 3 A3 Tr1 StrA
#> 4 A4 Tr1 StrA
#> 5 A5 Tr1 StrA
#> 6 A6 Tr1 StrA
#> 7 A7 Tr2 StrA
#> 8 A8 Tr2 StrA
#> 9 A9 Tr2 StrA
#> 10 A10 Tr2 StrA
#> 11 A11 Tr2 StrA
#> 12 A12 Tr2 StrA
#> 13 B1 Tr1 StrA
#> 14 B2 Tr1 StrA
#> 15 B3 Tr1 StrA
#> 16 B4 Tr1 StrA
#> 17 B5 Tr1 StrA
#> 18 B6 Tr1 StrA
#> 19 B7 Tr2 StrA
#> 20 B8 Tr2 StrAImporting tidy-shaped design files
You can import tidy-shaped designs with read_tidys.
read_tidys only requires a filename (or vector of
filenames, or relative file paths) and will return a
data.frame (or list of data.frames) that you can save in
R.
Once these design elements have been read into the R
environment, they are ready to merge.
Merging growth curve data with designs
Once we have both our design and data in R and
tidy-shaped, we can merge them using merge_dfs.
To demonstrate this, we’ll use the data in the
example_widedata_noiseless dataset that is included with
gcplyr, and which was the source for our previous examples
with import_blockmeasures and read_wides.
In the example_widedata_noiseless dataset, we have 48
different bacterial strains. The left side of the plate has all 48
strains in a single well each, and the right side of the plate also has
all 48 strains in a single well each:
| Row names | Column 1 | … | Column 6 | Column 7 | … | Column 12 |
|---|---|---|---|---|---|---|
| Row A | Strain #1 | … | Strain #6 | Strain #1 | … | Strain #6 |
| Row B | Strain #7 | … | Strain #12 | Strain #7 | … | Strain #12 |
| … | … | … | … | … | … | … |
| Row G | Strain #37 | … | Strain #42 | Strain #37 | … | Strain #42 |
| Row H | Strain #43 | … | Strain #48 | Strain #43 | … | Strain #48 |
Then, on the right hand side of the plate a phage was also inoculated (while the left hand side remained bacteria-only):
| Row names | Column 1 | … | Column 6 | Column 7 | … | Column 12 |
|---|---|---|---|---|---|---|
| Row A | No Phage | … | No Phage | Phage Added | … | Phage Added |
| Row B | No Phage | … | No Phage | Phage Added | … | Phage Added |
| … | … | … | … | … | … | … |
| Row G | No Phage | … | No Phage | Phage Added | … | Phage Added |
| Row H | No Phage | … | No Phage | Phage Added | … | Phage Added |
Let’s transform the example_widedata_noiseless to
tidy-shaped.
example_tidydata <- trans_wide_to_tidy(example_widedata_noiseless,
id_cols = "Time")gcplyr also includes the design for this data for easy
use:
example_design <- example_design_tidy
head(example_design_tidy)
#> Well Bacteria_strain Phage
#> 1 A1 Strain 1 No Phage
#> 2 A2 Strain 2 No Phage
#> 3 A3 Strain 3 No Phage
#> 4 A4 Strain 4 No Phage
#> 5 A5 Strain 5 No Phage
#> 6 A6 Strain 6 No PhageNow that we have our data and designs tidy-shaped, we merge the two
using merge_dfs, saving the result to
ex_dat_mrg, short for example_data_merged.
merge_dfs merges using columns with the same name between
the two data.frames.
ex_dat_mrg <- merge_dfs(example_tidydata, example_design)
#> Joining with `by = join_by(Well)`
head(ex_dat_mrg)
#> Time Well Measurements Bacteria_strain Phage
#> 1 0 A1 0.002 Strain 1 No Phage
#> 2 0 B1 0.002 Strain 7 No Phage
#> 3 0 C1 0.002 Strain 13 No Phage
#> 4 0 D1 0.002 Strain 19 No Phage
#> 5 0 E1 0.002 Strain 25 No Phage
#> 6 0 F1 0.002 Strain 31 No PhageWhat’s next?
Now that you’ve merged your data and designs, you can pre-process and plot your data
- Introduction:
vignette("gc01_gcplyr") - Importing and reshaping data:
vignette("gc02_import_reshape") - Incorporating experimental designs:
vignette("gc03_incorporate_designs") - Pre-processing and plotting your data:
vignette("gc04_preprocess_plot") - Processing your data:
vignette("gc05_process") - Analyzing your data:
vignette("gc06_analyze") - Dealing with noise:
vignette("gc07_noise") - Best practices and other tips:
vignette("gc08_conclusion") - Working with multiple plates:
vignette("gc09_multiple_plates") - Using make_design to generate experimental designs:
vignette("gc10_using_make_design")