PlotMetric {QuICSeedR} | R Documentation |
Create a customizable ggplot for metrics
Description
This is wrapper function to generate a ggplot object with default options for boxplot and jittered points. Additional ggplot2 functions can be applied to the plot.
Usage
PlotMetric(
calculation,
x = "content",
y = "RAF",
fill_var = NULL,
point = TRUE,
box = TRUE,
base_theme = theme_bw(),
...
)
Arguments
calculation |
A data frame containing the data to be plotted. Output of |
x |
Character string specifying the column name for the x-axis. Default is "content". |
y |
Character string specifying the column name for the y-axis. Default is "RAF". |
fill_var |
The name of the column to be used for fill color, or a vector of colors. If NULL, no fill color is applied. Default is NULL. |
point |
Logical. If TRUE (default), adds jittered points to the plot. |
box |
Logical. If TRUE (default), adds a boxplot to the plot. |
base_theme |
A ggplot2 theme object. Default is theme_bw(). |
... |
Additional ggplot2 functions to be applied to the plot. |
Value
A ggplot object.
Examples
# Define the path to the plate data file
plate_path <- system.file("extdata/20240716_p3",
file = '20240716_p3_plate.xlsx',
package = "QuICSeedR")
# Read the plate data
plate <- readxl::read_xlsx(plate_path)
# Define the path to the raw data file
raw_path <- system.file("extdata/20240716_p3",
file = '20240716_p3_raw.xlsx',
package = "QuICSeedR")
# Read the raw data
raw <- readxl::read_xlsx(raw_path)
# Get replicate data
replicate <- GetReplicate(plate)
# Ensure time displayed as decimal hours
plate_time = ConvertTime(raw)
#Get metadata and display the few rows
meta = CleanMeta(raw, plate, replicate)
#Clean data
cleanraw <- CleanRaw(meta, raw, plate_time)
#Get calculations using positive controls to normalize values.
calculation = GetCalculation(raw = cleanraw, meta, norm = TRUE, norm_ct = 'Pos')
#Default plot
PlotMetric(calculation)