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StratPlot.R
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StratPlot.R
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## Super easy plotting of paleodata in R
## Ilja Kocken
## Student of Marine Sciences at Utrecht University
## First version: 2014-04-11
## Latest version: 2017-03-07
## Plot your age/depth data beautifully, with options for logaritmic axes, easy
## polygon- and bar plots plus options to add Geologic Time Scale information.
## necessary libraries for certain functions
library(astrochron) # for tuning stratigraphic series
library(png) # for working with png images
library(jpeg) # for working with jpg images
library(rasterImage) # for transposing images, might not work w/ Windows!
library(raster) # for working with raster images
StratPlot <- function(var, ...){
## S3-method for the main plotting function
## Args:
## var: the variable to plot: a dataframe, vector, matrix or list
## ...: other arguments
UseMethod("StratPlot", var)
}
StratPlot.default <- function(age, var, age.dir = "h", GTS = F,
pol = F, pol0 = NULL, pol.col = "#4682B4E6",
border = NA, bar = F, bar.col = "orange",
bar.lwd = 2, add = F, error = NULL,
error.type = "bars", error.col = "#BEBEBEE6",
error.lwd = 1, error.code = 3, gap.size = NULL,
abc = NULL, abc.adj = NULL, exaggerate = NULL,
ex.type = "l", ex.lty = 1, ex.col = "gray",
mar = "inherit",
xax = if (age.dir == "h") 1 else 3, yax = 2,
xlim = NULL, ylim = NULL, xlab = NULL,
ylab = NULL, xlab.line = 2, ylab.line = 2,
xlab.font = 1, ylab.font = 1, xlab.adj = NA,
ylab.adj = NA, xlab.align = c(0.5, NA),
ylab.align = c(0.5, NA),
xlab.ang = NULL, ylab.ang = NULL, xax.labs = NULL,
yax.labs = NULL, xlab.cex = 1, ylab.cex = 1,
xtck = NULL, ytck = NULL, xntck = 2, yntck = 2,
las = 1, log = "", bty = "n", type = "o", lty = 1,
pch = 16, verbose = TRUE, ...) {
## Creates a plot based on a depth/age vector and a variable vector
## Args:
## age: vector with age or depth information
## var:
## age.dir: direction of age "v", "ver", "vertical" or "h" "hor" "horizontal"
## GTS colour scale on age axis
## value of exaggeration line to add
## polygon to plot
## bar to plot
## mar: or "auto" or specified
## logical, add to plot or start new one
## vector of relative errors or matrix/df of absolute values to plot
## don't draw lines when agediff is larger
## add index letter topleft
## positions of minor tick marks
## number of minor tick marks between major marks
## default plot/log options
## default positions of axes (1:4)
## other graphical parameters
## age:
## var:
## age.dir = "h"
## GTS = F:
## pol = F:
## pol0 = NULL:
## pol.col = "#4682B4E6",
## border = NA:
## bar = F:
## bar.col = "orange",
## bar.lwd = 2:
## add = F:
## error = NULL:
## error.type = "bars":
## error.col = "#BEBEBEE6":
## error.lwd = 1:
## error.code = 3:
## gap.size = NULL:
## abc = NULL:
## abc.adj = NULL:
## exaggerate = NULL:
## ex.type = "l":
## ex.lty = 1:
## ex.col = "gray":
## mar = "inherit":
## xax = if (age.dir == "h") 1 else 3:
## yax = 2:
## xlim = NULL:
## ylim = NULL:
## xlab = NULL:
## ylab = NULL:
## xlab.line = 2:
## ylab.line = 2:
## xlab.font = 1:
## ylab.font = 1:
## xlab.adj = NA:
## ylab.adj = NA:
## xlab.align = c(0.5, NA):
## ylab.align = c(0.5, NA):
## xlab.ang = NULL:
## ylab.ang = NULL:
## xax.labs = NULL:
## yax.labs = NULL:
## xlab.cex = 1:
## ylab.cex = 1:
## xtck = NULL:
## ytck = NULL:
## xntck = 2:
## yntck = 2:
## las = 1:
## log = "":
## bty = "n":
## type = "o":
## lty = 1:
## pch = 16:
## verbose = TRUE:
## ...:
## Era = F, Period = T, Epoch = T, Age = F, GTSfrac = .05,
## TODO: add standard Geologic Time Scale to region near x or y axis
## xlab.pos = NULL, ylab.pos = NULL,
## check var and age
if (length(var) != length(age)) {
stop("Unequal length of var and age")
}
## insert gaps where needed
if (!is.null(gap.size)) {
too.large <- which(diff(age) > gap.size)
df <- InsertEmpty(data.frame(age, var), too.large)
age <- df$age
var <- df$var
}
## check age.dir
if (!age.dir %in% c("v", "ver", "vertical", "h", "hor", "horizontal")) {
stop("age.dir must be either 'v', 'ver', 'vertical' or 'h', 'hor, 'horizontal'")
} else {
age.dir <- substr(age.dir, 1, 1) # age.dir is converted to either 'v' or 'h'
}
if (!add) {
## mar (depends on xax and yax, which are not checked)
if (identical(mar, "auto")) {
mar <- c(if (1 %in% xax || 1 %in% yax) 5 else 2,
if (2 %in% xax || 2 %in% yax) 5 else 2,
if (3 %in% xax || 3 %in% yax) 5 else 2,
if (4 %in% xax || 4 %in% yax) 5 else 2) + .1
} else if (identical(mar, "inherit")) {
mar <- par(no.readonly = TRUE)$mar
}
## xlim, ylim
if (age.dir == "h") {
if (is.null(xlim)) xlim <- range(age, na.rm = TRUE)
if (is.null(ylim)) ylim <- range(var, na.rm = TRUE)
} else {
if (is.null(xlim)) xlim <- range(var, na.rm = TRUE)
if (is.null(ylim)) ylim <- rev(range(age, na.rm = TRUE))
}
## default xlab, ylab
if (age.dir == "h") {
if (is.null(xlab)) {
if (max(age, na.rm = T) < 100) {
if (verbose) message("Assuming age is given in Ma")
xlab <- "Age (Ma)"
} else {
if (verbose) message("Assuming age is given in ka")
xlab <- "Age (ka)"
}
}
if (is.null(ylab)) {
if (verbose) message("No ylab provided")
ylab <- ""
}
} else {
if (is.null(xlab)) {
if (verbose) message("No xlab provided")
xlab <- ""
}
if (is.null(ylab)) {
if (max(age, na.rm = T) < 100) {
if (verbose) message("Assuming age is given in Ma")
ylab <- "Age (Ma)"
} else {
if (verbose) message("Assuming age is given in ka")
ylab <- "Age (ka)"
}
}
}
## set up plotting margins
par(mar = mar, bty = bty)
## set up empty plot
plot(1, type = "n", xlim = xlim, ylim = ylim, log = log,
xlab = "", ylab = "", axes = FALSE, ...)
## axes added later
}
if (pol || bar) {
## baseline to draw polygon and bar to
if (is.null(pol0)) {
## logarithmic var axis -> draw polygon to minimum value
if ((age.dir == "h" && grepl("y", log)) ||
(age.dir == "v" && grepl("x", log))) {
pol0 <- min(var)
} else {
pol0 <- 0
}
}
}
## plot polygon
if (pol) {
if (anyNA(var) || anyNA(age)) {
if (verbose) message("NAs found in var/age, currently ignoring")
nona <- data.frame(var = var, age = age)
nona <- nona[complete.cases(nona), ]
x <- c(nona$age[1], nona$age, tail(nona$age, n = 1))
y <- c(pol0, nona$var, pol0)
## TODO: create polygons per non-NA region, like we do with errorregion
## enc <- rle(!is.na(var))
## endIdxs <- cumsum(enc$lengths)
## for (i in 1:length(enc$lengths)) {
## if (enc$values[i]) {
## endIdx <- endIdxs[i]
## startIdx <- endIdx - enc$lengths[i] + 1
## subvar <- var[startIdx:endIdx]
## subage <- age[startIdx:endIdx]
## x <- c(left, subvar, left)
## y <- c(subage[1], age, tail(age, n = 1))
## }
## }
} else {
## not sure if I want to use the current left or use:
## min(var, na.rm = TRUE) - .04 * diff(range(var, na.rm = TRUE))
x <- c(age[1], age, tail(age, n = 1))
y <- c(pol0, var, pol0)
}
polygon(x = if (age.dir == "h") x else y, y = if (age.dir == "h") y else x,
col = pol.col, border = border)
}
## plot exaggeration
if (!is.null(exaggerate)) {
points(if (age.dir == "h") age else var * exaggerate,
if (age.dir == "h") var * exaggerate else age,
type = ex.type, lty = ex.lty, col = ex.col)
}
## plot error bars/area
if (!is.null(error)) {
## if (length(error) > 0) { # plot errorstuff
if (!all(error.type %in% c("bars", "area"))) {
stop(paste0("Incorrect error.type '",
error.type,
"', specify error.type as 'bars' or 'area'"))
}
if ("bars" %in% error.type) {
ErrorBarsPlot(age, var, error, col = error.col, code = error.code,
age.dir = age.dir, lwd = error.lwd)
}
if ("area" %in% error.type) {
ErrorAreaPlot(age, var, error, col = error.col,
age.dir = age.dir)
}
## }
}
## plot bars (added after errors to overlap the possible areas)
if (bar) {
if (is.null(pol0)) pol0 <- 0
segments(x0 = if (age.dir == "h") age else rep(pol0, length(var)),
y0 = if (age.dir == "h") rep(pol0, length(var)) else age,
x1 = if (age.dir == "h") age else var,
y1 = if (age.dir == "h") var else age,
col = bar.col, lwd = bar.lwd)
}
## plot the actual record
points(x = if (age.dir == "h") age else var,
y = if (age.dir == "h") var else age, type = type,
pch = pch, lty = lty, ...)
## add axes
if (!add) {
## loop so that I can specify both 1 and 2 for example.
for (i in xax) {
AddAxis(i, lim = xlim, ntck = xntck, las = las, labels = xax.labs)
AddAxLab(xlab, i, line = xlab.line, adj = xlab.adj, font = xlab.font,
ang = xlab.ang, lab.adj = xlab.align, cex = xlab.cex)
}
for (i in yax) {
AddAxis(i, lim = ylim, ntck = yntck, las = las, labels = yax.labs)
AddAxLab(ylab, i, line = ylab.line, adj = ylab.adj, font = ylab.font,
ang = ylab.ang, lab.adj = ylab.align, cex = ylab.cex)
}
if (GTS) {
AddGTS(age.dir = age.dir, Era = F, Period = T, Epoch = T, Age = F, frac = GTSfrac)
}
}
## add corner ABC
if (!is.null(abc)) {
if (is.null(abc.adj)) {
abc.adj <- 0.04 * abs(diff(par("usr")[1:2]))
}
AddABC(abc, abc.adj)
}
}
ErrorBarsPlot <- function(age, var = NULL, error, col = "#BEBEBEE6", code = 3,
lwd = 1, length = 0.05, angle = 90, age.dir = "h") {
## add error bars to a plot
## Args:
## age: a vector of age/depth values
## var: a vector of the variable of interest
## error: a vector/matrix/dataframe of error values
## col: the colour of the error bars
## code: the code of the 'arrows' argument, 3 is caps
## lwd: the line width of the error bars
## length: the length of the whiskers of the error bars
## angle: the angle of the arrows to be drawn, default 90 degrees
## age.dir: the direction that age is plotted in, "h" or "v"
## data frame or matrix with two columns
if (is.data.frame(error) || is.matrix(error) && ncol(error) == 2) {
## Error handling
if (!(nrow(error) == 1 || nrow(error) == length(var)))
warning("Number of rows in error not equal to var length, recycling")
if (age.dir == "h")
arrows(age, error[, 1], age, error[, 2], col = col, length = length,
angle = angle, code = code, lwd = lwd)
else if (age.dir == "v")
arrows(error[, 1], age, error[, 2], age, col = col, length = length,
angle = angle, code = code, lwd = lwd)
} else { # single (vector of) error value(s)
if (!(length(error) == length(var) || length(error) == 1))
warning("Length of error not equal to var length, recycling")
if (age.dir == "h") {
arrows(x0 = age, y0 = var - error, x1 = age, y1 = var + error,
col = col, length = length, angle = angle, code = code,
lwd = lwd)
}
else if (age.dir == "v") {
arrows(x0 = var - error, y0 = age, x1 = var + error, y1 = age,
col = col, length = length, angle = angle, code = code,
lwd = lwd)
}
}
}
ErrorAreaPlot <- function(age, var = NULL, error, col = "#BEBEBE4D",
age.dir = "h", ...) {
## add an error area to a plot
## Args:
## age: a vector of age/depth values
## var: a vector of the variable of interest
## error: a vector/matrix/dataframe of error values
## col: the colour of the error bars
## age.dir: the direction that age is plotted in, "h" or "v"
## ...: other arguments for the polygon function
## Error handling
if (!is.numeric(error) && is.null(var))
stop("Provide either dataframe/matrix of low and high error values or vector of relative error values.")
## error is a dataframe/matrix with 2 columns for negative and positive
## absolute error values
if (is.data.frame(error) || is.matrix(error) && ncol(error) == 2) {
## TODO: support for NA values in age when specifying strict errorvalues
if (nrow(error) != length(var))
warning("Number of rows in error not equal to var length, recycling")
x <- c(age, rev(age))
y <- c(error[, 1], rev(error[, 2]))
} else {
if (anyNA(var) | anyNA(age)) {
enc <- rle(!is.na(var)) # calculate amount of non-NA polygons
endIdxs <- cumsum(enc$lengths) # lengths of polygons
for (i in seq_along(enc$lengths)){ # for each polygon
if (enc$values[i]){ # for non-na regions
endIdx <- endIdxs[i]
startIdx <- endIdx - enc$lengths[i] + 1
subdat <- var[startIdx:endIdx]
subsd <- error[startIdx:endIdx]
subage <- age[startIdx:endIdx]
x <- c(subdat - subsd, rev(subdat + subsd))
y <- c(subage, rev(subage))
}
}
} else {
x <- c(age, rev(age))
y <- c(var - error, rev(var + error))
}
}
polygon(x = if (age.dir == "h") x else y, y = if (age.dir == "h") y else x,
col = col, border = NA, ...)
}
StratPlot.data.frame <- function(var, # dataframe
age = NULL, # optional vector
age.dir = "h", # "v", "ver", "vertical" or "h" "hor" "horizontal"
pol = F, bar = F, # polygon/bar
gap.size = NULL, # lines not drawn for timesteps > gap.size
oneplot = F, # logical, if TRUE plot all variables in the same plot
genframe = T, # show plots in same window
add = F, error = NULL, # vector of errors to plot (note: relative values!)
stacked = F, # logical, calculate cumulative sum for vars, currently doesn't work.
..., xax = if (age.dir == "h") 1 else 3, # default position of x-axis
log = "",
yax = 2, # default position of yaxis
las = 1, # default direction of axis labels
mar = "auto", # generated based on xax and yax
ylab = NULL, xlab = NULL, xlim = NULL,
ylim = NULL,
xntck = 2, yntck = 2,
bty = "n", col = "black",
lwd = 1, lty = 1, type = "o", pch = 16,
error.type = "bars", pol0 = NULL,
error.col = "#BEBEBEE6", pol.col = "#4682BEE6",
ex.col = "#325C87", bar.col = "#325C87",
border = NULL, legend = NULL) {
## Takes a dataframe of one or multiple variable(s) to create a (set of) plot(s)
## subset numeric columns
## var <- var[, sapply(var, is.numeric)]
## TODO: do this as option?
## check var and age
if (!is.null(age)){
if (length(age) != nrow(var)) {
stop("Length of age is unequal to nrow(var)")
}
## TODO add gapmaker support!
if (verbose) message("Assuming only variables in dataframe")
} else { # only var is provided
## find column that has age/depth
depth.col <- grep("depth", names(var), ignore.case = TRUE)
if (length(depth.col) > 1) warning("multiple depth columns found, using first")
age.col <- grep("age|time", names(var), ignore.case = TRUE)
if (length(age.col) > 1) warning("multiple age columns found, using first")
## depth.col found but age.col isn't
if (length(depth.col) >= 1 && length(age.col) == 0) {
## extract age/depth from var
age <- var[, depth.col[1]]
var <- var[, -depth.col[1]]
## overwrite agelab if default
if (age.dir == "h") {
if (is.null(xlab)) {
xlab <- "Depth (mbsf)"
}
} else if (age.dir == "v") {
if (is.null(ylab)) {
ylab <- "Depth (mbsf)"
}
}
## age.col found but depth.col isn't
} else if (length(depth.col) == 0 && length(age.col) >= 1) {
## extract age/depth from var
age <- var[, age.col[1]]
var <- var[, -age.col[1]]
## both age.col and depth.col found, using age.col
} else if (length(depth.col) > 0 && length(age.col) > 0) {
## TODO: interactive selection of desired age
## extract age/depth from var
age <- var[, age.col[1]] # for now we just use age if both are available
## omit depth and age
var <- var[, - c(depth.col[1], age.col[1])]
} else { # no depth.col, no age.col found: use first column
## extract age/depth from var
age <- var[, 1]
var <- var[, -1]
if (verbose) message("Assuming age or depth in first column of var")
}
}
## number of variables after extraction of age
if (is.vector(var)) {
nvar <- 1
} else {
nvar <- ncol(var)
}
## parsing of x- and ylab
if (age.dir == "h") {
if (!is.null(ylab)) {
## TODO: parse ylab in similar manner as xlab, with proper expression check
if (is.character(ylab) && length(ylab) > 1 && length(ylab) != nvar){
stop("Incorrect length of ylab")
}
if (class(ylab) == "formula"){
if (length(ylab == 1)) {
ylab <- as.expression(ylab)
} else {
lapply(ylab, as.expression)
}
}
} else {
if (verbose) message("Using varnames as ylabs")
ylab <- names(var)
}
if (length(ylab) > 1 && length(ylab) == nvar) {
ylabs <- ylab
}
} else { # age.dir = v
if (!is.null(xlab)) {
if (length(xlab) > 1 && length(xlab) != nvar){
stop("Incorrect length of xlab")
}
if (class(xlab) == "formula"){
if (length(xlab == 1)) {
xlab <- as.expression(xlab)
} else {
xlabs <- lapply(xlab, as.expression)
}
}
} else {
if (verbose) message("Using varnames as xlabs")
xlabs <- names(var)
}
if (length(xlab) > 1 && length(xlab) == nvar) {
xlabs <- xlab
}
}
## specific plotting variables can also be defined for all variables in var
if (length(type) > 1) {
if (length(type) == nvar) {
types <- type
} else stop("Incorrect length of type")
}
if (length(pch) > 1) {
if (length(pch) == nvar) {
pchs <- pch
} else stop("Incorrect length of pch")
}
if (length(col) > 1) {
if (length(col) == nvar) {
cols <- col
} else stop("Incorrect length of col")
} else cols <- NULL
if (length(lty) > 1) {
if (length(lty) == nvar) {
ltys <- lty
} else stop("Incorrect length of lty")
}
if (length(lwd) > 1) {
if (length(lwd) == nvar) {
lwds <- lwd
} else stop("Incorrect length of lwd")
}
if (length(pol) > 1) {
if (length(pol) == nvar) {
pols <- pol
} else stop("Incorrect length of pol")
}
if (length(pol.col) > 1) {
if (length(pol.col) == nvar) {
pol.cols <- pol.col
} else stop("Incorrect length of pol.col")
}
if (length(bar) > 1) {
if (length(bar) == nvar) {
bars <- bar
} else stop("Incorrect length of bar")
}
if (length(bar.col) > 1) {
if (length(bar.col) == nvar) {
bar.cols <- bar.col
} else stop("Incorrect length of bar.col")
}
if (length(ex.col) > 1) {
if (length(ex.col) == nvar) {
ex.cols <- ex.col
} else stop("Incorrect length of ex.col")
}
if (is.list(ylim)){
if (length(ylim) == nvar) {
ylims <- ylim
} else stop("Incorrect length of ylim")
}
## TODO: also do this for bty?, error.type, error.col, pol0 and border?
if (length(log) > 1) {
if (length(log) == nvar) {
logs <- log
} else stop("Incorrect length of log")
}
## set up the plotting region
## last is to check if it wasn't a df with only 2 columns
if (!oneplot && genframe && is.data.frame(var)) {
if (age.dir == "h") {
par(mfrow = c(nvar, 1))
} else {
par(mfrow = c(1, nvar))
}
}
## call StratPlot.numeric, multiple times if necessary
for (i in seq_len(nvar)) {
StratPlot(if (nvar == 1) {
var
} else if (stacked) {
if (i == 1) var[, 1]
else rowSums(var[, 1:i])
} else { var[, i] }, age = age, age.dir = age.dir,
gap.size = gap.size,
pol = if (exists("pols")) pols[i] else pol, ## pol = pol[i],
bar = if (exists("bars")) bars[i] else bar,
add = if (is.null(add)) { if ((oneplot || stacked) && i != 1) TRUE else FALSE } else { add },
error = error, xax = xax, yax = yax, mar = mar, ## TODO: change exists check for something else b/c it currently uses the global space
ylab = if (exists("ylabs")) ylabs[i] else ylab,
xlab = if (exists("xlabs")) xlabs[i] else xlab, xntck = xntck,
yntck = yntck,
xlim = if (oneplot && age == "v") range(var, na.rm = TRUE) else xlim,
ylim = if (oneplot && age == "h") range(var, na.rm = TRUE) else if (exists("ylims")) ylims[[i]] else ylim,
bty = bty, lty = if (exists("ltys")) ltys[i] else lty,
col = if (!is.null(cols)) cols[i] else col,
lwd = if (exists("lwds")) lwds[i] else lwd,
type = if (exists("types")) types[i] else type,
pch = if (exists("pchs")) pchs[i] else pch,
log = if (exists("logs")) logs[i] else log,
error.type = error.type, error.col = error.col, pol0 = pol0,
pol.col = if (exists("pol.cols")) pol.cols[i] else pol.col,
bar.col = if (exists("bar.cols")) bar.cols[i] else bar.col,
ex.col = if (exists("ex.cols")) ex.cols[i] else ex.col,
border = border, ...)
}
if (!is.null(legend)) {
legend("topright", legend = legend, col = if (exists("cols")) cols else col,
lty = if (exists("ltys")) ltys else lty,
lwd = if (exists("lwds")) lwds else lwd,
pch = if (exists("pchs")) pchs else pch)
}
}
StratPlot.list <- function(ls, ...) {
## apply the stratplotter to all the elements of a list
## Args:
## ls: the list who's elements are to be plotted
## ...: other arguments
lapply(ls, StratPlot, ...)
}
SubsetRange <- function(dat, min, max, column = "depth") {
## subset dataframe to range of age/depth
## Args:
## dat: the dataframe to be subsetted
## min: the minimum value to subset by
## max: the maxiumum value to subset by
## column: the column name to subset by
return(dat[dat[, column] > min & dat[, column] < max, ])
}
GapMaker <- function(df, gap.size = .5, column = "age") {
## insert empty rows between values that differ more than gap.size
## Args:
## df: the data frame
## gap.size: the size of the gaps
## column: the column name to base gaps on
too.large <- which(diff(df[, column]) > gap.size)
df <- InsertEmpty(df, too.large)
return(df)
}
InsertEmpty <- function(df, afterrow) {
## insert empty rows in a dataframe after afterrow
## Args:
## df: the dataframe
## afterrow: empty row is inserted after this row
## create indices for the data order
df$id <- seq_len(nrow(df))
df[max(df$id) + seq_along(afterrow), ] <- NA
df$id[is.na(df$id)] <- afterrow + .5
df <- df[order(df$id), ]
df <- df[ , !names(df) %in% "id"]
return(df)
}
AddAxis <- function(ax = 1, labels = NULL, lim = NULL, ntck = NULL,
tck = NULL, las = 1, ...) {
## adds a pretty axis, with minor ticks and pretty log options
## Args:
## ax:
## labels:
## lim:
## ntck:
## tck:
## las:
## ...:
if (is.null(ntck)) {
ntck <- 2
}
if (ax %in% c(1, 3)) { # bottom or top x-axis
log <- par("xlog")
if (is.null(lim) && log) {
lim <- c(1e-100, 1e100) # just use a mega range...
}
} else if (ax %in% c(2, 4)) { # left or right y-axis
log <- par("ylog")
if (is.null(lim) && log) {
lim <- c(1e-100, 1e100)
}
} else stop("ax must be 1: bottom, 2: left, 3: top or 4: right")
## if the axis is on a logarithmic scale
if (log) {
## the log10 range of powers that need something done
pow <- c(
if (lim[1] == 0) -100
else if (lim[1] > 0) floor(log10(lim[1]))
else - floor(log10(-lim[1])),
if (lim[2] == 0) -100
else if (lim[2] > 0) ceiling(log10(lim[2]))
else -ceiling(log10(-lim[2])))
if (is.null(tck))
tck <- c(1:10 %o% 10^((pow)[1]:(pow)[2]))
## log axis with nicer 10^pow labels for all the ax
if (is.null(labels))
labels <- sapply((pow)[1]:(pow)[2], # or -xpow[1]?
function(i) {
as.expression(bquote(10^ .(i)))})
axis(ax, at = 10^(pow[1]:pow[2]), labels = labels, las = las, ...)
} else { # non-log axis
## default axis
axis(ax, las = las, labels = labels, ...)
## find stepsize used in default axis
if (is.null(tck))
stepsize <- abs(diff(axTicks(ax)[1:2])) / ntck
## add ntck ticks between
tck <- seq(from = min(axTicks(ax)) - stepsize * ntck,
to = max(axTicks(ax)) + stepsize * ntck,
by = stepsize)
}
## minor x-axis tick marks
axis(ax, at = tck, labels = FALSE, tcl = -.2)
}
## if (grepl("x", log) || las == 1) 3
## else 2
AddAxLab <- function (lab = "", side = 1, line = 2, adj = NA,
lab.adj = c(0.5, NA), cex = 1, ang = NULL, pos = NULL,
font = 1, x = NULL, y = NULL, ...) {
## add axis labels
## Args:
## lab:
## side:
## line:
## adj:
## lab.adj:
## cex:
## ang:
## pos:
## font:
## x:
## y:
## ...:
## no angle, and no specific x and y position for the label just use mtext
if (is.null(ang) || (!is.null(x) && !is.null(y))) {
mtext(lab, side = side, line = line, adj = adj, pos = pos,
font = font, cex = cex, ...)
} else {
if (side %in% c(1, 3)) { # default horizontal axis:
## parse x from adj
if (is.null(x)) {
if (is.na(adj)) {
x <- mean(par("usr")[1:2])
} else {
x <- par("usr")[1] + diff(par("usr")[1:2]) * adj
}
}
## parse y from line
if (is.null(y)) {
if (side == 1) {
y <- par("usr")[3] - diff(par("usr")[3:4])/28 * line
} else if (side == 3) {
y <- par("usr")[4] + diff(par("usr")[3:4])/28 * line
}
}
} else if (side %in% c(2, 4)) { # vertical axis
## parse y from adj
if (is.null(y)) {
if (is.na(adj)) {
y <- mean(par("usr")[3:4])
} else {
y <- par("usr")[3] + diff(par("usr")[3:4]) * adj
}
}
## parse x from line
if (is.null(x)) {
if (side == 2) {
x <- par("usr")[1] - diff(par("usr")[1:2])/28 * line/2
} else if (side == 4) {
x <- par("usr")[2] + diff(par("usr")[1:2])/28 * line/2
}
}
}
text(x, y, labels = lab, font = font, srt = ang, pos = pos, xpd = TRUE,
adj = lab.adj, cex = cex, ...)
}
}
AddABC <- function(char = "A", xadj = 0.04 * abs(diff(par("usr")[1:2])),
yadj = 0.04 * abs(diff(par("usr")[3:4])), cex = 2) {
## add large a/b/c in top left corner of current plot
## TODO: also work for log axes
xpos <- par("usr")[1] + xadj
ypos <- par("usr")[4] + yadj
mtext(char, 3, at = xpos, cex = cex)
## text(xpos, ypos, char, cex = cex, xpd = NA)
}
AddGTS <- function(age, xleft = NULL, xright = NULL, frac = 0.05,
agelim = range(age), age.dir = "h",
type = NULL,
Eon = T, Era = T, Period = T, Epoch = T, Age = T,
Chron = T,
horizontal.text = NULL, relwidth = NULL, cex.text = NULL,
verbose = T) {
## Add Geologic Time Scale information to a plot
## check types
if (is.null(type)) {
type <- c(Eon, Era, Period, Epoch, Age, Chron)
}
## subset types to plot
alltypes = c("Eon", "Era", "Period", "Epoch", "Age", "Chron")
types <- alltypes[type]
if (verbose) cat("\nplotting types:", types)
## read GTS table with color and age info
## todo: make this sharable
if (sum(types %in% alltypes[1:5]) > 0) {
GTS <- read.csv("~/Dropbox/StratPlot/GTS_colours.csv", stringsAsFactors = F)
GTS$hex <- rgb(GTS$R, GTS$G, GTS$B, maxColorValue = 255)
GTS$mean <- (GTS$end - GTS$start) / 2 + GTS$start
## order the type factor
GTS$type <- factor(GTS$type, alltypes[1:5], ordered = T)
}
## read chron table
if (sum(types %in% alltypes[6]) > 0) {
Chron <- read.csv("~/Dropbox/StratPlot/Chronages.csv", stringsAsFactors = F)
Chron$name <- Chron$Pol
Chron$hex <- "#000000"
Chron$hex[grepl("r", Chron$Pol)] <- "#FFFFFF"
Chron$start <- c(22, Chron$GTS2012[-nrow(Chron)])
Chron$end <- Chron$GTS2012
Chron$mean <- (Chron$end - Chron$start) / 2 + Chron$start
}
## default xleft/xright
if (is.null(xleft)) {
if (age.dir == "h") {
xleft <- par("usr")[3]
} else {
xleft <- par("usr")[1]
}
}
if (verbose) cat(" from ", xleft)
if (is.null(xright)) {
if (age.dir == "h") {
fullright <- par("usr")[4]
} else {
fullright <- par("usr")[2]
}
xright <- xleft + frac * (diff(c(xleft, fullright)))
}
if (verbose) cat(" to ", xright, "\n")
if (is.null(relwidth)) {
## default relwidths
relwidth <- c(0.08, 0.08, 0.1, 0.3, 0.44, 0.44)
## subset/make relative to selected types
relwidth <- relwidth[type] / sum(relwidth[type])
}
if (is.null(horizontal.text)) {
if (age.dir == "h") horizontal.text <- c(F, F, F, F, F, F)[type]
else horizontal.text <- c(F, F, F, T, T, T)[type]
}
if (is.null(cex.text)) {
cex.text <- c(1, 1, 1, .8, .7, 0.7)[type]
}
## this subfunction plots one gts bar
PlotGTS <- function(xleft, xright, gts, ad, td = T, cex.t, textpos = NULL) {
## add rectangles with appropriate colour
rect(if (ad == "h") gts$start else xleft,
if (ad == "h") xleft else gts$start,
if (ad == "h") gts$end else xright,
if (ad == "h") xright else gts$end,
col = gts$hex, border = Darken(gts$hex))
## add name in centre
## TODO: if the centre is outside of the plot margins, add it to
## the closest plot area
## TODO: xright if Chron
text(if (ad == "h") gts$mean else mean(c(xleft, xright)),
if (ad == "h") mean(c(xleft, xright)) else gts$mean,
labels = gts$name,
srt = if (td) 0 else 90,
cex = cex.t, pos = textpos)
}
nbars <- sum(type)
totwidth <- diff(c(xleft, xright))
## loop over type, so one loop is one bar of age info
for (bar in seq_len(nbars)) {
xright <- xleft + relwidth[bar] * totwidth
PlotGTS(xleft, xright,
if (types[bar] != "Chron") GTS[GTS$type == types[bar], ]
else Chron,
ad = age.dir, td = horizontal.text[bar], cex.t = cex.text[bar],
textpos = if (types[bar] != "Chron") NULL else NULL)
## TODO: fix text position for chron to right of xright with pos = 4.
xleft <- xright
}
}
## TODO: create addChron function that does the same as AddGTS but with
## normal/reversed magnetostrat + names
Darken <- function(color = col, factor=1.4){
## darken a colour
## Args:
## color: the colour input
## factor: the factor by which to darken
## Returns: the darkened colour
col <- col2rgb(color)
col <- col/factor
col <- rgb(t(col), maxColorValue=255)
col
}
Lighten <- function(color = col, factor=1.4){
## lighten a colour
## Args:
## color: the colour input
## factor: the factor by which to lighten
## Returns: the lightened colour
col <- col2rgb(color)
col <- col*factor
col <- rgb(t(as.matrix(apply(col, 1, function(x) if (x > 255) 255 else x))), maxColorValue=255)
col
}
## adds a linear model with confidence levels to the plot
plotLM <- function(x = NULL, y = NULL, confidence = 0.90,
col = "red", lty = 2, lwd = 1) {
## linmod = NULL,
## if (is.null(linmod) && (is.null(x) && is.null(y))) stop("Specify x and y or linmod")
## if (is.null(linmod)) linmod <- lm(y ~ x)
linmod <- lm(y ~ x)
## TODO: doesn't work with only linmod because of variable names in newdata
## plot(a,y,xlim=c(20,90),ylim=c(0,80))
abline(linmod, col="red")
newx <- seq(par("usr")[1], par("usr")[2], length.out = 100)
prd<-predict(linmod,
newdata = data.frame(x = newx),
interval = c("confidence"),
level = confidence, type="response")
lines(newx,prd[,2],col = col, lty = lty, lwd = lwd)
lines(newx,prd[,3],col = col, lty = lty, lwd = lwd)
}
## plots the R2 value of a linear model in a corner
plotLMinfo <- function(linmod, pos = "topleft", formula.offset = 1, digits = 4) {
r2 <- bquote(R^2~"="~.(format(summary(linmod)$adj.r.squared,
digits = digits)))
form <- bquote("y ="~.(format(summary(linmod)$coefficients[2],
digits = digits))~
"x +"~.(format(summary(linmod)$coefficients[1],
digits = digits)))
lgdinfo <- legend(pos, bty="n", legend = form, trace = T)
legend(lgdinfo$rect$left, lgdinfo$rect$top + formula.offset,
bty="n", legend = r2, trace = T)
}