README.md

In BradyAJohnston/simplePlates: Collection of simple functions for working with plate-based data.

simplePlates

A set of simple functions for working with plate-based data.

“omg this is the best thing ever i love simplePlates” - Somayra, 2020

Installation

devtools::install_github("bradyajohnston/simpleplates")

Example use cases.

make_plate()

For quickly generating sample and concentration data for a plate, to later match with observed data. The rows can be either letters or a numeric verctor (numbers must be > 0 and < 26).

make_plate(
  rows = LETTERS[1:3], 
  cols = 1:3, 
  sample = "foo"
)

##   wells cols rows sample
## 1    A1    1    A    foo
## 2    A2    2    A    foo
## 3    A3    3    A    foo
## 4    B1    1    B    foo
## 5    B2    2    B    foo
## 6    B3    3    B    foo
## 7    C1    1    C    foo
## 8    C2    2    C    foo
## 9    C3    3    C    foo

make_plate(
  rows = 1:3, 
  cols = 1:3, 
  sample = "foo"
)

##   wells cols rows sample
## 1    A1    1    A    foo
## 2    A2    2    A    foo
## 3    A3    3    A    foo
## 4    B1    1    B    foo
## 5    B2    2    B    foo
## 6    B3    3    B    foo
## 7    C1    1    C    foo
## 8    C2    2    C    foo
## 9    C3    3    C    foo

make_plate(
  rows = 1:3, 
  cols = 1:3, 
  sample = c("sampleA", "sampleB", "sampleC")
)

##   wells cols rows  sample
## 1    A1    1    A sampleA
## 2    A2    2    A sampleB
## 3    A3    3    A sampleC
## 4    B1    1    B sampleA
## 5    B2    2    B sampleB
## 6    B3    3    B sampleC
## 7    C1    1    C sampleA
## 8    C2    2    C sampleB
## 9    C3    3    C sampleC

make_plate(
  rows = 1:3, 
  cols = 1:3, 
  sample = rep(c("sampleA", "sampleB", "sampleC"), each = 3)
)

##   wells cols rows  sample
## 1    A1    1    A sampleA
## 2    A2    2    A sampleA
## 3    A3    3    A sampleA
## 4    B1    1    B sampleB
## 5    B2    2    B sampleB
## 6    B3    3    B sampleB
## 7    C1    1    C sampleC
## 8    C2    2    C sampleC
## 9    C3    3    C sampleC

make_plate() can also take concentration information, as well as perform dilution series`.

make_plate(
  rows = 1:3, 
  cols = 1:3, 
  sample = c("sampleA", "sampleB", "sampleC"), 
  conc = 500, 
  dil = 0.5, 
  direction = "vertical"
)

##   wells cols rows  sample conc
## 1    A1    1    A sampleA  500
## 2    A2    2    A sampleB  500
## 3    A3    3    A sampleC  500
## 4    B1    1    B sampleA  250
## 5    B2    2    B sampleB  250
## 6    B3    3    B sampleC  250
## 7    C1    1    C sampleA  125
## 8    C2    2    C sampleB  125
## 9    C3    3    C sampleC  125

make_plate(
  rows = 1:3, 
  cols = 1:3, 
  sample = rep(c("sampleA", "sampleB", "sampleC"), each = 3),
  conc = 500, 
  dil = 0.5, 
  direction = "horizontal"
)

##   wells cols rows  sample conc
## 1    A1    1    A sampleA  500
## 2    A2    2    A sampleA  250
## 3    A3    3    A sampleA  125
## 4    B1    1    B sampleB  500
## 5    B2    2    B sampleB  250
## 6    B3    3    B sampleB  125
## 7    C1    1    C sampleC  500
## 8    C2    2    C sampleC  250
## 9    C3    3    C sampleC  125

plate_map()

Cretes a visual representation of a plate’s contents.

df1 <- make_plate(
  rows = 1:8,
  cols = 1:12,
  sample = rep(c("sampleA", "sampleB", "sampleC"), each = 4),
  conc = 500,
  dil = 0.5,
  direction = "vertical"
)

library(ggplot2)

plate_map(df1, 
          cols = "cols", 
          rows = "rows", 
          colour = "sample") + 
  theme(legend.position = "bottom")

BradyAJohnston/simplePlates documentation built on Jan. 27, 2021, 5:57 p.m.