PvSTATEM (version 0.2.2)

plot_counts: Plot counts in a 96-well plate

Description

This function plots counts in a 96-well plate using a colour to represent the count ranges. There is a possibility of plotting exact counts in each well.

If the plot window is resized, it's best to re-run the function to adjust the scaling. Sometimes, when a legend is plotted, the whole layout may be shifted. It's best to stretch the window, and everything will be adjusted automatically.

Usage

plot_counts(
  plate,
  analyte_name,
  plot_counts = TRUE,
  plot_legend = FALSE,
  lower_threshold = 50,
  higher_threshold = 70
)

Value

A ggplot object

Arguments

plate

The plate object with the counts data

analyte_name

The name of the analyte

plot_counts

Logical indicating if the counts should be plotted

plot_legend

Logical indicating if the legend should be plotted

lower_threshold

The lower threshold for the counts, it separates green and yellow colours

higher_threshold

The higher threshold for the counts, it separates yellow and red colours

Examples

plate_filepath <- system.file("extdata", "CovidOISExPONTENT_CO.csv",
  package = "PvSTATEM", mustWork = TRUE
)
layout_filepath <- system.file("extdata", "CovidOISExPONTENT_CO_layout.xlsx",
  package = "PvSTATEM", mustWork = TRUE
)
plate <- read_luminex_data(plate_filepath, layout_filepath)
plot_counts(
  plate = plate, analyte_name = "OC43_NP_NA",
  plot_counts = TRUE, plot_legend = FALSE
)