# install new packages (once)
# install.packages('planar',repos='http://cran.r-project.org') planar is
# similar to Splac
library(ggplot2) # load a package
# ggplot2 is for plotting
getwd() # where is the current working dir
## [1] "/Users/auguieba/Documents/r/github/tutorial"
setwd("/Users/auguieba/Documents/r/github/tutorial/") # set the location
# list all files with a pattern in the current wd
list.files(pattern = "txt")
## [1] "1_radius_0-01_medium_1_coating_1-52_thickness_0_gold_Mie_2012-04-21.txt"
## [2] "2_radius_0-02_medium_1_coating_1-52_thickness_0_gold_Mie_2012-04-21.txt"
## [3] "3_radius_0-03_medium_1_coating_1-52_thickness_0_gold_Mie_2012-04-21.txt"
## [4] "4_radius_0-04_medium_1_coating_1-52_thickness_0_gold_Mie_2012-04-21.txt"
## [5] "5_radius_0-05_medium_1_coating_1-52_thickness_0_gold_Mie_2012-04-21.txt"
## [6] "6_radius_0-06_medium_1_coating_1-52_thickness_0_gold_Mie_2012-04-21.txt"
## [7] "7_radius_0-07_medium_1_coating_1-52_thickness_0_gold_Mie_2012-04-21.txt"
## [8] "8_radius_0-08_medium_1_coating_1-52_thickness_0_gold_Mie_2012-04-21.txt"
## [9] "9_radius_0-09_medium_1_coating_1-52_thickness_0_gold_Mie_2012-04-21.txt"
fname <- "9_radius_0-09_medium_1_coating_1-52_thickness_0_gold_Mie_2012-04-21.txt"
d <- read.table(fname, header = TRUE)
Basic functions to check the data
str(d) # structure
## 'data.frame': 801 obs. of 4 variables:
## $ wavelength: num 0.4 0.401 0.402 0.403 0.404 0.405 0.406 0.407 0.408 0.409 ...
## $ extinction: num 0.0831 0.0831 0.0831 0.0831 0.0831 ...
## $ scattering: num 0.0434 0.0434 0.0435 0.0435 0.0435 ...
## $ absorption: num 0.0396 0.0396 0.0396 0.0396 0.0396 ...
names(d) # names
## [1] "wavelength" "extinction" "scattering" "absorption"
summary(d)
## wavelength extinction scattering absorption
## Min. :0.4 Min. :0.00545 Min. :0.00476 Min. :0.00069
## 1st Qu.:0.6 1st Qu.:0.01225 1st Qu.:0.01132 1st Qu.:0.00093
## Median :0.8 Median :0.03645 Median :0.03476 Median :0.00169
## Mean :0.8 Mean :0.05126 Mean :0.04097 Mean :0.01029
## 3rd Qu.:1.0 3rd Qu.:0.08639 3rd Qu.:0.06083 3rd Qu.:0.01243
## Max. :1.2 Max. :0.12667 Max. :0.11066 Max. :0.04324
head(d)
## wavelength extinction scattering absorption
## 1 0.400 0.08306 0.04342 0.03964
## 2 0.401 0.08306 0.04344 0.03962
## 3 0.402 0.08307 0.04346 0.03961
## 4 0.403 0.08308 0.04347 0.03960
## 5 0.404 0.08308 0.04349 0.03959
## 6 0.405 0.08309 0.04350 0.03958
plot(d[, 1], d[, 2]) # basic plot
data.frameplot(d[, 1], d[, 2], type = "l", col = "red", lty = "dashed", lwd = 3,
xlab = expression(Wavelength/mu * m), ylab = "Cross-section", main = "Mie theory for a gold sphere")
# ?plot to see help on plot function and all options, also ?par
# adding lines to it
lines(d[, 1], d[, 3], col = "blue")
# ... or points
d2 <- d[seq(1, nrow(d), by = 10), ]
points(d2[, 1], d2[, 4], col = "green")
matplot(d[, 1] * 1000, d[, 2:4], type = "l", col = 1:3, lty = "solid",
xlab = "Wavelength / nm", ylab = "Cross-section")
legend("topright", c("Extinction", "Scattering", "Absorption"), lty = 1,
col = 1:3)
ggplot(data = d, mapping = aes(x = wavelength, y = extinction)) +
geom_path()
Often, you need to reshape the data from wide to long format,
library(reshape2)
m <- melt(d, id.var = "wavelength")
str(d)
## 'data.frame': 801 obs. of 4 variables:
## $ wavelength: num 0.4 0.401 0.402 0.403 0.404 0.405 0.406 0.407 0.408 0.409 ...
## $ extinction: num 0.0831 0.0831 0.0831 0.0831 0.0831 ...
## $ scattering: num 0.0434 0.0434 0.0435 0.0435 0.0435 ...
## $ absorption: num 0.0396 0.0396 0.0396 0.0396 0.0396 ...
str(m)
## 'data.frame': 2403 obs. of 3 variables:
## $ wavelength: num 0.4 0.401 0.402 0.403 0.404 0.405 0.406 0.407 0.408 0.409 ...
## $ variable : Factor w/ 3 levels "extinction","scattering",..: 1 1 1 1 1 1 1 1 1 1 ...
## $ value : num 0.0831 0.0831 0.0831 0.0831 0.0831 ...
p <- ggplot(data = m, mapping = aes(x = wavelength * 1000, y = value)) +
geom_path(mapping = aes(colour = variable))
p
p + facet_grid(variable ~ .) + labs(x = "Wavelength / nm", y = "Cross-section",
colour = "Type") + theme_bw()
l <- list.files(patt = "txt") # list files
ld <- llply(l, read.table, head = TRUE) # read each file and store in a list
names(ld) <- paste("file", seq_along(ld)) # give unique names
m <- melt(ld, id.var = "wavelength")
str(m)
## 'data.frame': 21627 obs. of 4 variables:
## $ wavelength: num 0.4 0.401 0.402 0.403 0.404 0.405 0.406 0.407 0.408 0.409 ...
## $ variable : Factor w/ 3 levels "extinction","scattering",..: 1 1 1 1 1 1 1 1 1 1 ...
## $ value : num 0.000107 0.000107 0.000106 0.000106 0.000106 ...
## $ L1 : chr "file 1" "file 1" "file 1" "file 1" ...
These data can be plotted,
ggplot(data = m, mapping = aes(x = wavelength * 1000, y = value)) +
facet_wrap(~L1, ncol = 3, scales = "free") + geom_path(mapping = aes(colour = variable)) +
labs(x = "Wavelength / nm", y = "Cross-section", colour = "Type") + theme_bw() +
opts(strip.background = theme_blank())
