ggplate (version 0.1.5)

plate_plot: Plate Layout Plot

Description

Plots a culture plate or microplate in the desired format. Both continuous as well as discrete values can be displayed with colours and labels.

Usage

plate_plot(
  data,
  position,
  value,
  label,
  plate_size = 96,
  plate_type = "square",
  colour,
  limits,
  title,
  title_size,
  show_legend = TRUE,
  legend_n_row,
  label_size,
  silent = TRUE,
  scale
)

Value

A plate layout plot.

Arguments

data

a data frame that contains at least a column with plate position information and a column with values or labels.

position

a character column in the data data frame that contains plate positions. These should be in the format: row = letter, column = number. So for example A1, D12 etc.

value

a character or numeric column in the data data frame that contains values that should be plotted as colours on the plate layout. Can be the same column as label.

label

a character or numeric column in the data data frame that contains values that should be plotted as labels on the plate layout. Can be the same column as value.

plate_size

a numeric value that specifies the plate size (number of wells) used for the plot. Possible values are: 6, 12, 24, 48, 96, 384 and 1536.

plate_type

a character value that specifies the well type. Possible values are "round" and "square". The default is "square".

colour

optional, a character vector that contains colours used for the plot. If the value argument is discrete the colours are used as provided. If it is continuous a gradient is created using the colours.

limits

optional, a numeric vector of length two providing new limits for a colour gradient. Use NA to refer to the existing minimum or maximum. If this argument is not supplied the existing minimum and maximum of the values provided to the value argument are used for the start and end point of the colour gradient.

title

optional, a character value that contains the plot title.

title_size

optional, a numeric value that determines the text size of the title. The size is also affected by the scale argument.

show_legend

a logical value that specifies if the plot legend is shown. Default is TRUE.

legend_n_row

optional, a numeric value that specifies the number of rows of legends. If no value is provided, the automatic ggplot default is used.

label_size

optional, a numeric value that determines the text size of the well labels. The size is also affected by the scale argument.

silent

a logical value that specifies if the function should report the size of the plotting area and the adjusted scale parameter. Default is TRUE meaning it will not return any message. The plot was optimized for a device size of: width = 5.572917 in and height = 3.177083 in, which was determined using the function par("fin"). This means if the device has these dimensions the scaling factor is 1.

scale

a numeric value that scales point sizes and labels of the plot. If not provided, the plot uses the device size to find the optimal scaling factor for the output, however, this might be slightly off (e.g. due to number of labels) and can be manually adjusted with this argument.

Examples

library(dplyr)
library(tidyr)
library(stringr)

# Load example data
data("data_continuous_96")
data("data_continuous_384")
data("data_discrete_6")
data("data_discrete_24")

# Create a 96-well plot with round wells
plate_plot(
  data = data_continuous_96,
  position = well,
  value = Value,
  label = Value,
  plate_size = 96,
  plate_type = "round"
)

# Create a 384-well plot with square wells
# Define a custom lower limit
# Define a custom colour scheme
# Define a custom title with a custom size
plate_plot(
  data = data_continuous_384,
  position = well,
  value = Value,
  label = Value,
  plate_size = 384,
  colour = c("#000004FF", "#51127CFF", "#B63679FF", "#FB8861FF", "#FCFDBFFF"),
  limits = c(0, NA),
  title = "Custom Title",
  title_size = 20
)

# Create a 24-well plot
# Show a 6 row legend
# Scale the plot to 1.2
plate_plot(
  data = data_discrete_24,
  position = well,
  value = Condition,
  plate_size = 24,
  plate_type = "round",
  scale = 1.2,
  legend_n_row = 6
)

# Create a 6-well plot
# Define a custom colour scheme
# Adjust label_size to fit text
# Let the plot return width, height and scale
plate_plot(
  data = data_discrete_6,
  position = well,
  value = Condition,
  label = Condition,
  plate_size = 6,
  plate_type = "round",
  colour = c("#3a1c71", "#d76d77", "#ffaf7b"),
  label_size = 4,
  show_legend = FALSE,
  silent = FALSE
)