[!] Plot Median and range of spectroscopic data intensities

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.

qplot_spRangeMedian(
  sp,
  by = NULL,
  percent = NULL,
  probs = NULL,
  palette = hyGet_palette(sp),
  ...,
  lwd_median = 1,
  legend_title = by,
  alpha = 0.2,
  add = FALSE,
  name_if_by_is_NULL = "All Data"
)

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.

legend_title

(character|NULL) The title for legend.

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.

See also

Other spHelper plots: check_palette(), 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_spStat(), qplot_spc(), rmExpr(), rm_stripes(), stat_chull()

Author

Vilmantas Gegzna

Examples

library(spHelper)
library(spPlot)

qplot_spRangeMedian(Spectra2)

qplot_spRangeMedian(Spectra2, "gr")


# Both lines below gives identical plots with different default titles:
qplot_spRangeMedian(Spectra2, "gr", percent = 50)

qplot_spRangeMedian(Spectra2, "gr", probs = c(.25, .75))



ggplotly_tidy()
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