qplot_spStat: [+] Plot a summary statistic of spectroscopic data by group

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

[+] Plot a summary statistic of spectroscopic data by group

Description

Plot a summary of spectroscopic data in hyperSpec object by group. The summary statistic internally is generated by either function spStat or aggregate.

Usage

qplot_spStat(
  sp,
  by = stop("Argument 'by' is missing."),
  FUN = stop("Argument 'FUN' is missing."),
  Title = fCap(as.character(match.call()$FUN)),
  subTitle = NULL,
  All = FALSE,
  fixed.colors = All,
  All.color = "black",
  gr.color = c(hyGet_palette(sp), RColorBrewer::brewer.pal(8, "Dark2")),
  All.linetype = "dashed",
  gr.linetype = "solid",
  All.size = 1.1,
  gr.size = 0.8,
  legend.title = element_blank(),
  ...,
  add = FALSE
)

layer_spStat(
  sp,
  by = stop("Argument 'by' is missing."),
  FUN = stop("Argument 'FUN' is missing."),
  Title = fCap(as.character(match.call()$FUN)),
  subTitle = NULL,
  All = FALSE,
  ...,
  add = TRUE
)

Arguments

sp	Spectroscopic data (either a hyperSpec object or a matrix).
by	A grouping variable (either a vector or a variable name in sp).
FUN	A function that calculates one or several summary statistics.
Title	The main title of the plot.
subTitle	The second line of title, which will be smaller and and in italics.
All	Logical. If TRUE, plot additional curve for a statistic of all spectra (.ALL), not divided to groups.
fixed.colors	- Logical. If TRUE, color scheme where .ALL is plotted as a black line is be used.
All.color	A line color for .ALL.
gr.color	Line colors (a vector) for each level in by.
All.linetype	A line type for .ALL.
gr.linetype	Line types (a vector) for each level in by.
All.size	A line width for .ALL.
gr.size	Line widths (a vector) for each level in by.
legend.title	A title for legend. Default is no title.

Value

A ggplot object. More details in package ggplot2.

Author(s)

Vilmantas Gegzna

See Also

spStat

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_spRangeMedian(), qplot_spc(), rmExpr(), rm_stripes(), stat_chull()

Examples

qplot_spStat(chondro,"clusters",mean)
qplot_spStat(chondro,"clusters",mean,All=FALSE)
qplot_spStat(chondro,"clusters",mean_sd,All=FALSE) + facet_grid(.~clusters)

qplot_spStat(chondro,"clusters",median,All=FALSE, fixed.colors=FALSE)
qplot_spStat(chondro,"clusters",median, "My Title")


# Make facets with fewer ticks on the x axis:
qplot_spStat(chondro,"clusters",mean_pm_sd) +
     facet_grid(.~clusters) +
     nTick_x(2)


# Add as a layer:
qplot_spRange(chondro, "clusters") +
     layer_spStat(chondro,"clusters", mean, size = 1)

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