eempf_residuals_plot: Plot samples by means of whole sample, each single component...

In staRdom: PARAFAC Analysis of EEMs from DOM

Plot samples by means of whole sample, each single component and residuum

Description

A raster of plots is created. Each column shows one sample. The top n rows show the n components from the model according their occurance in the certain samples. The second last row shows the residual, not covered by any component in the model and the last row shows the whole sample.

Usage

eempf_residuals_plot(
  pfmodel,
  eem_list,
  res_data = NULL,
  spp = 5,
  select = NULL,
  residuals_only = FALSE,
  cores = parallel::detectCores(logical = FALSE),
  contour = FALSE,
  colpal = "default"
)

Arguments

pfmodel	object of class parafac containing the generated model
eem_list	object of class eemlist with all the samples that should be plotted
res_data	optional, data of sample residuals related to the model, output from eempf_residuals
spp	optional, samples per plot
select	optional, character vector of samples you want to plot
residuals_only	plot only residuals
cores	number of cores to use for parallel processing
contour	logical, states whether contours should be plotted
colpal	"default" to use the viridis colour palette, "rainbow" to use a subset of the rainbow palette, any custom vector of colors or a colour palette. A gradient will be produced from this vector. Larger vectors (e.g. 50 elements) can produce smoother gradients.

Details

eem_list may contain samples not used for modelling. Calculation is done by A_missing. This especially interesting if outliers are excluded prior modelling and should be evaluated again afterwards. Usually, residuals contain negative values, while these is the exception in samples and PARAFAC components. Therefore, we decided to use a similar colour palette as in the other plot functions but adding a purple tone for negative values.

Value

several ggplot objects

Examples

data(eem_list)
data(pf_models)

eem_list <- eem_extract(eem_list, 1:10)

eem_list <- eem_rem_scat(eem_list, rep(TRUE, 4), c(15,10,16,12))

eempf_residuals_plot(pf4[[1]], eem_list, cores = 2)

# use other colour schemes:
# eempf_residuals_plot(pf4[[1]], eem_list, colpal = c("blue",heat.colors(50)))
# plots <- eempf_residuals_plot(pf4[[1]], eem_list)
# lapply(plots, function(pl){
#   pl +
#     scale_fill_viridis_c() +
#     scale_colour_viridis_c()
# })

staRdom documentation built on July 9, 2023, 5:57 p.m.