dendrospect: dendrospect Copyright (c) 2019. Kaleido Biosciences. All...

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

Description

Allows the user to easily see what the average kinetic profile corresponding with a given cluster is. Note that data should be scaled before using this function.

Usage

dendrospect(phgrofit_data, phgropro_data, colored_bar_label = NULL, k = 8)

Arguments

phgrofit_data	This is the data originating from phgrofit or one of it's modifying functions such as scale_phgrofit or avg_phgrofit.
phgropro_data	This is the data originating from phgropro or one of it's modifying functions such as avg_phgropro. It must contain the same Sample.IDs as phgrofit data.
colored_bar_label	This is the character name of a column that the user would like to include as colored bar below the dendogram.
k	The number of clusters.

Value

A ggplot2 object containing a colored dendrogram w ith a colored bar label and the corresponding kinetic OD600 and pH data.

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)

## processing phgrofit data by averaging and scaling
## Not run:  phgrofit_data = avg_phgrofti(phgrofit_output,c("Community","Compound")) %>%
scale_phgrofit()
## End(Not run)
### plotting heatmap with colored labels for community and mouse over information about the compounds.
## Not run: plot = PCA(phgrofit_data,"Community")
plot
## End(Not run)

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