plotTH: Plot thresholds

In snwikaij/GRASS: GRadient AnalySiS for ecologists

Description

Plots the thresholds returned from the cusTH function. This plot is created with ggplot2.

Usage

plotTH(x, AUC = TRUE, devCI = 0.05, xlab = "Gradient", psize = 0, range = TRUE, display = "none", log = FALSE)

Arguments

x	The unchanged data frame returned from the cusTH function
AUC	An argument that can be used to select the displayed taxa based on the the AUC (see AUC.test for detailed description). Default is TRUE.
devCI	The minimal distance the LCI(a) and HCI(a) need to have from a random effect (0.5). Default is 0.05.
xlab	The label of the x-axis. Default is "Gradient".
psize	A numeric value which can be used to scale the size of the points. Default is 0.
range	An argument that can be used to display the min and max range in the plot. Default is TRUE.
display	An argument that can be used to display the LCI and HCI of the positive and negative threshold of assembly in the plot. By default this is "none", but can display "both", only positive "pos" and only negative "neg".
log	An argument that can be used to set the x-axis to Log scale. Default is FALSE.

Details

The points represent the locations of the thresholds. The horizontal lines the LCI(t) and HCI(t). The colour of the points indicates the response score (direction). Black indicates a negative response and white indicates a positive response.

Author(s)

Willem Kaijser

References

Wickham, H., 2009. ggplot2: Elegant Graphics for Data Analysis. Springer-Verlag New York.

Examples

## Not run: 
#Using the provided data-set named "hco3"
results <- cusTH(hco3$Sample, hco3$Taxon, hco3$Variable, hco3$Abundance)

#Plot the results
plotTH(results)
## End(Not run)

snwikaij/GRASS documentation built on July 29, 2020, 1:54 p.m.