hyperSpec Plotting Examples with ggplot2

2020-03-17

Load packages

library(hyperSpec)
library(spHelper)
library(plotly)

qplotspc

data(chondro, package = "hyperSpec")
#> Warning in data(chondro, package = "hyperSpec"): data set 'chondro' not found
qplotspc(chondro)

qplotspc(paracetamol, c(2800 ~ max, min ~ 1800)) +
    scale_x_reverse(breaks = seq(0, 3200, 400)) 

# +
#     theme(strip.text = element_blank(),
#           strip.background = element_blank())

qplotspc(hyperSpec::aggregate(chondro, chondro$clusters, mean),
        mapping = aes(x = .wavelength,
                      y = spc,
                      colour = clusters)) +
    facet_grid(clusters ~ .)

qplotspc(hyperSpec::aggregate(chondro, chondro$clusters, mean_pm_sd),
        mapping = aes(x = .wavelength,
                      y = spc,
                      colour = clusters,
                      group = .rownames)) +
facet_grid(clusters ~ .)

qplotc

qplotc(flu)
#> Warning in qplotc(flu): Intensity at first wavelengh only is used.
#> Warning: Using `as.character()` on a quosure is deprecated as of rlang 0.3.0.
#> Please use `as_label()` or `as_name()` instead.
#> This warning is displayed once per session.

qplotc(flu[,,440])

qplotc(flu) + geom_smooth(method = "lm",  size = .5)
#> Warning in qplotc(flu): Intensity at first wavelengh only is used.
#> `geom_smooth()` using formula 'y ~ x'

qplotmap

qplotmap(chondro)

qplotmap(chondro) + scale_fill_gradientn(colours = alois.palette())

## works also with discrete x or y axis:
qplotmap(chondro,
         mapping = aes(x = x, y = y, fill = spc))

qplotmixmap

qplotmap with colour mixing for multivariate overlay

chondro <- chondro - spc.fit.poly.below(chondro)
chondro <- sweep(chondro, 1, apply(chondro, 1, mean), "/")
chondro <- sweep(chondro, 2, apply(chondro, 2, quantile, 0.05), "-")

qplotmixmap(chondro[,,c(940, 1002, 1440)],
             purecol = c(colg = "red",
                         Phe = "green",
                         Lipid = "blue"))
#> Warning: Removed 300 rows containing missing values (geom_point).