Map of the Integral (Interpolated) with Annotations

Integral map prepared from mIRage exported csv. First the dataset is imported by read.csv. In the early version of PTIR Studio there was a bug causing map beign flipped in Y direction. Depending on the software version please use function with or without sort. Band of interest is set as peak1 variable. Default integration range is 40 cm^-1 but it may be adjusted. Display interpolation is done with geom_raster and interpolate parameter set as TRUE. Additional layer of labels is done with annotate("text") command. Positions x and y, as well as label text is set manually in this example.

library(hyperSpec)
library(here)
f="RDX_mirrIR_finger_hyper4.csv"
path01<-here::here("DATA",f)
dataset01 <- read.csv(path01)
wavenumbers  <- read.csv(path01, header = FALSE, nrow = 1)
wavenumber<-as.vector(t(wavenumbers[3:length(wavenumbers)]))
spectra<-as.matrix(dataset01[,-c(1:2)])
d1<-as.data.frame(dataset01[,1])
#there is a bug in the export to csv in PTIR Studio 4.1
#causing map being flipped in Y direction
#line below there is a fix for this
#if this is corrected sort should be replaced by non sorted
d2<-as.data.frame(sort(dataset01[,2]))
#d2<-as.data.frame(dataset01[,2])
addata<-cbind(d1,d2)
colnames(addata)<-c("x","y")
addata1<-round(addata,digits=2)
hypspec1<-new("hyperSpec", wavelength = wavenumber,
              spc = spectra, data=addata1)

theme_new <- theme_set(theme_bw())
theme_new <- theme_update(axis.text = element_text(size = 14),
                          axis.title = element_text(size = 20,face = "bold"))
peak01<-1269
inten01<-apply(hypspec1[,,peak01-20~peak01+20], 1, mean)
long1<-as.long.df(inten01)
plot1<-ggplot(long1,aes(x, y)) +
  geom_raster(aes(fill=spc),interpolate = TRUE)+
  scale_fill_gradientn (colours = matlab.palette ())
plot1 +
  theme(axis.title       = element_blank(),
        panel.background = element_blank(),
        axis.text = element_text(size = 24))+
annotate("text", x = c(19466.5, 19467.5,19468.5, 19467.5, 19467.5),
         y = c(7767,7767,7767,7768,7766),
         label = c("l", "c", "r", "t", "b"), colour = "black", size=12)