qplot_spRange: [!] Plot range of spectroscopic data intensities

In GegznaV/spHelper: Extension of Package `hyperSpec` and Various Convenience Functions

[!] Plot range of spectroscopic data intensities

Description

Plot range of y axis values (usually intensities) of spectroscopic data between selected percentilles.
Function qplot_spRange() returns whole ggplot and function layer_spRange() returns a layer which can be added to a ggplot.

Usage

check_palette(palette, Groups)

qplot_spRange(
  sp,
  by = NULL,
  percent = NULL,
  probs = NULL,
  palette = hyGet_palette(sp),
  ...,
  alpha = 0.2,
  add = FALSE,
  name_if_by_is_NULL = "All Data"
)

layer_spRange(sp, by = NULL, percent = NULL, probs = NULL, ..., alpha = 0.2)

gg_spRange(sp, by = NULL, percent = NULL, probs = NULL, ..., alpha = 0.2)

Arguments

sp	hyperSpec object.
by	A vector (factor variable) with indicated groups for each case: either variable name inside the object sp, or a vector of length nrow(sp).
percent	Numeric value between 0 and 100 that indicates percentage of samples nearest to median be plotted as a ribbon.
probs	verctor of size 2 with values between 0 and 1 that indicates probabilities at which percentiles should be plotted.
...	further arguments to geom_ribon.
alpha	(numeric from 0 to 1) transperency.
add	(logical) add plot to an existing ggplot object?

Value

A ggplot object. More details in package ggplot2.

Author(s)

Vilmantas Gegzna

See Also

Other spHelper plots: layer_spRangeMean(), plot_colors(), plot_hyPalette(), plot_spCompare(), plot_spDiff(), plot_spDistribution(), qplot_confusion(), qplot_crosstab(), qplot_infoDim(), qplot_kAmp(), qplot_kSp(), qplot_prediction(), qplot_spRangeCenter(), qplot_spRangeMedian(), qplot_spStat(), qplot_spc(), rmExpr(), rm_stripes(), stat_chull()

Examples

library(spHelper)
library(spPlot)

qplot_spRange(Spectra2)
qplot_spRange(Spectra2, "gr")

# Both lines below gives identical plots with different default titles:
qplot_spRange(Spectra2, "gr", percent = 50)
qplot_spRange(Spectra2, "gr", probs = c(.25, .75))

## Not run: 
\donttest{
Error is expected, if added to existing ggplot:
     ggplot() + qplot_spRange(Spectra2, "gr")
}
## End(Not run)

# This sis solved by setting parameter `add` to `TRUE`:
     ggplot() + qplot_spRange(Spectra2, "gr", add = TRUE)

     qplot_spStat(Spectra2, "gr", mean) +
         layer_spRange(Spectra2)

     ggplotly_tidy()

GegznaV/spHelper documentation built on April 16, 2023, 1:42 p.m.