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

In baynec2/phgrofit: Extracting Physiological Data From Kinetic OD600 and pH Curves

dendrospect Copyright (c) 2019. Kaleido Biosciences. All Rights Reserved

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)

baynec2/phgrofit documentation built on March 24, 2024, 7:10 a.m.