PCA: PCA: Easily making a PCA plot with phgrofit data Copyright...

In Kaleido-Biosciences/phgrofit: Extracting Physiological Data From Kinetic OD600 and pH Curves

Description

Intended to allow the user to easily generate PCA plots from phgrofit data. Note that the values should first be scaled before using this function. This can be acomplished with scale_phgrofit()

Usage

PCA(phgrofit_data, group = "Sample.ID", mouse_over = "Compound")

Arguments

phgrofit_data	This is the output origniating from phgrofit or one of it's modifying functions such as scale_phgrofit or avg_phgrofit.
group	This is the name of the column that you would like to color the ordination by. A 95 percent confidence interval for this group will be assigned.
mouse_over	Category for which you would like data on mouse over on the plot.

Value

a ggplot2 object containing the 95 percent confidence interval for the group specified.

Examples

### phgropro processing
## Not run: phgropro_output = phgropro(biotek_export = filepath.txt,metadata = metadata.csv,Plate_Type = 96)

### phgrofit processing
## Not run: phgrofit_output = phgrofit(phgropro_output)

## scaling phgrofit data
## Not run:  phgrofit_data = scale_phgrofit(phgrofit_output)

### printing PCA plot with colored confidence intervals for community
## Not run: community_PCA = PCA(phgrofit_data,"Community")
print(community_PCA)
## End(Not run)

Kaleido-Biosciences/phgrofit documentation built on Feb. 8, 2022, 5:16 a.m.