ggplot2: Releveling factors for sequentially added layers - r

I am writing a plotting method for class "foo". I would like this plot function to take multiple foo objects and plot them on the same graph.
The Code
#parabola function
parabolas <- function(x, parm) {
y <- parm[1]*(x^2)+parm[2]*x+parm[3]
return(y)
}
#make foo object
make_foo <- function(a, b, c) {
x <- runif(100, 0 , 20)
y <- parabolas(x = x, parm = c(a,b,c)) + rnorm(100, mean = 100 ,sd = 100)
foo <- list(data = data.frame(x = x, y = y), parameters = c(a,b,c))
class(foo) <- "foo"
return(foo)
}
#plot function
plot.foo <- function(x,
...,
labels) {
a <- ggplot(NULL, aes(x = x, y = y))
foo.list <- list(x, ...)
#browser()
#build plot
for(i in 1:length(foo.list)){
foo.obj <- foo.list[[i]]
foo.obj$data$lab <- factor(rep(labels[i], nrow(foo.obj$data)), levels = labels)
a <- a + geom_point(data = foo.obj$data, size = 5, alpha = .7, aes(color = lab))
a <- a + stat_function(data = foo.obj$data,
fun = parabolas,
args = list(parm = foo.obj$parameters), size = 1.2)
}
return(a)
}
The Problem
ggplot will relevel the factor levels of lab according to the alphabetical order of the factor labels. I do not know how to choose the factor level order for lab when adding these layers sequentially. I would like for the first element of labels to correspond to the first foo object plotted, and the second element to correspond to the second foo object, and so forth and so forth.
foo1 <- make_foo(2, 10, 3)
foo2 <- make_foo(-6, -3, 2000)
plot(foo1, foo2, labels = c("obj1","obj2"))
#label for foo1 is "obj1" and label for foo2 is "obj2"
plot(foo1, foo2, labels = c("obj3","obj2"))
#label for foo1 should be "obj3" and label for foo2 should be "obj2"
The motivation
The reason I structure the plot function like this as opposed to binding the data frames together and assigning the correct factor levels to lab is because in that particular case, facet_wrap and stat_function do not work well together. After applying multiple stat_function and using facet_wrap together, all curves will appear in each panel. This thread illustrates a similar problem.
Because I have these different layers limited to different data sets, facet_wrap will correctly facet each stat_function plot according to the data/parameters used to draw it.
plot(foo1, foo2, labels = c("z","a")) + facet_wrap(~lab, scales = "free")
#Shows facet_wrap works as intended but the labels for foo1 and foo2 are
#still not in the intended order

You can manually override the order of the color scale by setting the limits. Here is how:
plot.foo <- function(x,
...,
labels) {
a <- ggplot(NULL, aes(x = x, y = y))
foo.list <- list(x, ...)
#browser()
#build plot
for(i in 1:length(foo.list)){
foo.obj <- foo.list[[i]]
foo.obj$data$lab <- factor(rep(labels[i], nrow(foo.obj$data)), levels = labels)
a <- a + geom_point(data = foo.obj$data, size = 5, alpha = .7, aes(color = lab))
a <- a + stat_function(data = foo.obj$data,
fun = parabolas,
args = list(parm = foo.obj$parameters), size = 1.2)
}
### added line:
a <- a + scale_color_discrete(limits = labels)
###
return(a)
}

Related

Use a gradient fill under a facet wrap of density curves in ggplot in R?

Similar questions have been asked before in other forms. Some can be found here and here. However, I cant seem to adapt them when using a facet wrap displaying multiple density plots.
I tried adapting the other examples, but failed... I also tried using the ggpattern package, but when there is a large amount of data, it takes several minutes on my machine to create a plot.
I am trying to create a gradient under the density curve... but with the gradient pointing down. Something like in the example image below:
Some example data to work with:
library(ggplot2)
set.seed(321)
# create data
varNames <- c("x1", "x2", "x3")
df <- data.frame(
var = sample(varNames, 100, replace = T),
val = runif(100)
)
# create plot
ggplot(df, aes(x = val)) +
geom_density(aes(colour = var, fill = var)) +
facet_wrap(~var) +
theme_bw() +
theme(legend.position = "none")
You can use teunbrand's function, but you will need to apply it to each facet. Here simply looping over it with lapply
library(tidyverse)
library(polyclip)
#> polyclip 1.10-0 built from Clipper C++ version 6.4.0
## This is teunbrands function copied without any change!!
## from https://stackoverflow.com/a/64695516/7941188
fade_polygon <- function(x, y, n = 100) {
poly <- data.frame(x = x, y = y)
# Create bounding-box edges
yseq <- seq(min(poly$y), max(poly$y), length.out = n)
xlim <- range(poly$x) + c(-1, 1)
# Pair y-edges
grad <- cbind(head(yseq, -1), tail(yseq, -1))
# Add vertical ID
grad <- cbind(grad, seq_len(nrow(grad)))
# Slice up the polygon
grad <- apply(grad, 1, function(range) {
# Create bounding box
bbox <- data.frame(x = c(xlim, rev(xlim)),
y = c(range[1], range[1:2], range[2]))
# Do actual slicing
slice <- polyclip::polyclip(poly, bbox)
# Format as data.frame
for (i in seq_along(slice)) {
slice[[i]] <- data.frame(
x = slice[[i]]$x,
y = slice[[i]]$y,
value = range[3],
id = c(1, rep(0, length(slice[[i]]$x) - 1))
)
}
slice <- do.call(rbind, slice)
})
# Combine slices
grad <- do.call(rbind, grad)
# Create IDs
grad$id <- cumsum(grad$id)
return(grad)
}
## now here starts the change, loop over your variables. I'm creating the data frame directly instead of keeping the density object
dens <- lapply(split(df, df$var), function(x) {
dens <- density(x$val)
data.frame(x = dens$x, y = dens$y)
}
)
## we need this one for the plot, but still need the list
dens_df <- bind_rows(dens, .id = "var")
grad <- bind_rows(lapply(dens, function(x) fade_polygon(x$x, x$y)), .id = "var")
ggplot(grad, aes(x, y)) +
geom_line(data = dens_df) +
geom_polygon(aes(alpha = value, group = id),
fill = "blue") +
facet_wrap(~var) +
scale_alpha_continuous(range = c(0, 1))
Created on 2021-12-05 by the reprex package (v2.0.1)

Standalone legend in ggpairs

How can I include a legend inside one of the empty panels of the following matrix plot?
I have color coded different regression lines in the plots. I need a legend based on color.
I believe this answer comes closest to answer my question, yet I do not know how exactly to modify my code to get a legend based on color for different regression lines.
As for the background of the code, I am trying to study different robust and non-robust regression methods applied to multivariate data with and without outliers.
library(ggplot2)
library(GGally)
library(MASS)
library(robustbase)
## Just create data -- you can safely SKIP this function.
##
## Take in number of input variables (k), vector of ranges of k inputs
## ranges = c(min1, max1, min2, max2, ...) (must have 2k elements),
## parameters to create data (must be consistent with the number of
## input variables plus one), parameters are vector of linear
## coefficients (b) and random seed (seed), number of observations
## (n), vector of outliers (outliers)
##
## Return uncontaminated dataframe and contaminated dataframe
create_data <- function(k, ranges, b, seed = 6, n,
outliers = NULL) {
x <- NULL # x: matrix of input variables
for (i in 1:k) {
set.seed(seed^i)
## x <- cbind(x, runif(n, ranges[2*i-1], ranges[2*i]))
x <- cbind(x, rnorm(n, ranges[2*i-1], ranges[2*i]))
}
set.seed(seed - 2)
x_aug = cbind(rep(1, n), x)
y <- x_aug %*% b
y_mean = mean(y)
e <- rnorm(n, 0, 0.20 * y_mean) # rnorm x
y <- y + e
df <- data.frame(x = x, y = y)
len <- length(outliers)
n_rows <- len %/% (k+1)
if (!is.null(outliers)) {
outliers <- matrix(outliers, n_rows, k+1, byrow = TRUE)
df_contamin <- data.frame(x = rbind(x, outliers[,1:k]), y = c(y, outliers[,k+1]))
} else {
df_contamin <- df
}
dat <- list(df, df_contamin)
}
# plot different regression models (some are robust) for two types of
# data (one is contaminated with outliers)
plot_models <- function(data, mapping, data2) {
cb_palette <- c("#999999", "#E69F00", "#56B4E9", "#009E73", "#F0E442", "#0072B2", "#D55E00", "#CC79A7")
## 1.grey, 2.light orange, 3.light blue, 4.green, 5.yellow, 6.blue, 7.red, 8.purple
plt <- ggplot(data = data, mapping = mapping) +
geom_point() +
theme_bw() +
geom_smooth(method = lm, formula = y ~ x, data = data2, color = cb_palette[3], se = FALSE) +
geom_smooth(method = lm, formula = y ~ x, color = cb_palette[7], se = FALSE) +
geom_smooth(method = rlm, formula = y ~ x, color = cb_palette[4], se = FALSE) +
geom_smooth(method = lmrob, formula = y ~ x, color = cb_palette[1], se = FALSE)
plt
}
# trim the upper and right panels of plots
trim_gg <- function(gg) {
n <- gg$nrow
gg$nrow <- gg$ncol <- n-1
v <- 1:n^2
gg$plots <- gg$plots[v > n & v%%n != 0]
gg$xAxisLabels <- gg$xAxisLabels[-n]
gg$yAxisLabels <- gg$yAxisLabels[-1]
gg
}
dat <- create_data(3, c(1, 10, 1, 10, 1, 10), c(5, 8, 6, 7), 6, 20, c(30, 30, 50, 400))
df <- dat[[1]]
df_contamin <- dat[[2]]
## Note that plot_models is called here
g <- ggpairs(df_contamin, columns = 1:4, lower = list(continuous = wrap(plot_models, data2 = df)), diag = list(continuous = "blankDiag"), upper = list(continuous = "blank")) #, legend = lgd)
gr <- trim_gg(g)
print(gr)
Created on 2019-10-09 by the reprex package (v0.3.0)
Sorry for the long code, but most probably only the plot_models function and the line where ggpairs is called need to be modified.
I want to get a legend in the blank upper half of the plots. It may be done by somehow tweaking the plot_models function, setting the mapping in ggpairs to color using ggplot2::aes_string, and using getPlot and putPlot of the GGally package. But I can't wrap my head around how to do it exactly.

List of plots generated in ggplot2 using scale_color_gradientn have wrong coloring

I'm attempting to use library(scales) and scale_color_gradientn() to create a custom mapping of colors to a continuous variable, in an attempt to limit the effect of outliers on the coloring of my plot. This works for a single plot, but does not work when I use a loop to generate several plots and store them in a list.
Here is a minimal working example:
library(ggplot2)
library(scales)
data1 <- as.data.frame(cbind(x = rnorm(100),
y = rnorm(100),
v1 = rnorm(100, mean = 2, sd = 1),
v2 = rnorm(100, mean = -2, sd = 1)))
#add outliers
data1[1,"v1"] <- 200
data1[2,"v1"] <- -200
data1[1,"v2"] <- 50
data1[2,"v2"] <- -50
#define color palette
cols <- colorRampPalette(c("#3540FF","black","#FF3535"))(n = 100)
#simple color scale
col2 <- scale_color_gradient2(low = "#3540FF",
mid = "black",
high = "#FF3535"
)
#outlier-adjusted color scale
{
aa <- min(data1$v1)
bb <- quantile(data1$v1, 0.05)
cc <- quantile(data1$v1, 0.95)
dd <- max(data1$v1)
coln <- scale_color_gradientn(colors = cols[c(1,5,95,100)],
values = rescale(c(aa,bb,cc,dd),
limits = c(aa,dd))
)
}
Plots:
1. Plot with simple scales - outliers cause scales to stretch out.
ggplot(data1, aes(x = x, y = y, color = v1))+
geom_point()+
col2
2. Plot with outlier-adjusted scales - correct color scaling.
ggplot(data1, aes(x = x, y = y, color = v1))+
geom_point()+
coln
3. The scales for v1 do not work for v2 as the data is different.
ggplot(data1, aes(x = x, y = y, color = v2))+
geom_point()+
coln
#loop to produce list of plots each with own scale
{
plots <- list()
k <- 1
for (i in c("v1","v2")){
aa <- min(data1[,i])
bb <- quantile(data1[,i],0.05)
cc <- quantile(data1[,i], 0.95)
dd <- max(data1[,i])
colm <- scale_color_gradientn(colors = cols[c(1,5,95,100)],
values = rescale(c(aa,bb,cc,dd),
limits = c(aa,dd)))
plots[[k]] <- ggplot(data1, aes_string(x = "x",
y = "y",
color = i
))+
geom_point()+
colm
k <- k + 1
}
}
4. First plot has the wrong scales.
plots[[1]]
5. Second plot has the correct scales.
plots[[2]]
So I'm guessing this has something to do with the scale_color_gradientn() function being called when the plotting takes place, rather than within the loop.
If anyone can help with this, it'd be much appreciated. In base R I would bin the continuous data and assigning hex colors into a vector used for fill color, but I'm unsure how I can apply this within ggplot.
You need to use a closure (function with associated environment):
{
plots <- list()
k <- 1
for (i in c("v1", "v2")){
colm <- function() {
aa <- min(data1[, i])
bb <- quantile(data1[, i], 0.05)
cc <- quantile(data1[, i], 0.95)
dd <- max(data1[, i])
scale_color_gradientn(colors = cols[c(1, 5, 95, 100)],
values = rescale(c(aa, bb, cc, dd),
limits = c(aa, dd)))
}
plots[[k]] <- ggplot(data1, aes_string(x = "x",
y = "y",
color = i)) +
geom_point() +
colm()
k <- k + 1
}
}
plots[[1]]
plots[[2]]

Transform color scale to probability-transformed color distribution with scale_fill_gradientn()

I am trying to visualize heavily tailed raster data, and I would like a non-linear mapping of colors to the range of the values. There are a couple of similar questions, but they don't really solve my specific problem (see links below).
library(ggplot2)
library(scales)
set.seed(42)
dat <- data.frame(
x = floor(runif(10000, min=1, max=100)),
y = floor(runif(10000, min=2, max=1000)),
z = rlnorm(10000, 1, 1) )
# colors for the colour scale:
col.pal <- colorRampPalette(c("#00007F", "blue", "#007FFF", "cyan", "#7FFF7F", "yellow", "#FF7F00", "red", "#7F0000"))
fill.colors <- col.pal(64)
This is how the data look like if not transformed in some way:
ggplot(dat, aes(x = x, y = y, fill = z)) +
geom_tile(width=2, height=30) +
scale_fill_gradientn(colours=fill.colors)
My question is sort of a follow-up question related to
this one or this one , and the solution given here actually yields exactly the plot I want, except for the legend:
qn <- rescale(quantile(dat$z, probs=seq(0, 1, length.out=length(fill.colors))))
ggplot(dat, aes(x = x, y = y, fill = z)) +
geom_tile(width=2, height=30) +
scale_fill_gradientn(colours=fill.colors, values = qn)
Now I want the colour scale in the legend to represent the non-linear distribution of the values (now only the red part of the scale is visible), i.e. the legend should as well be based on quantiles. Is there a way to accomplish this?
I thought the trans argument within the colour scale might do the trick, as suggested here , but that throws an error, I think because qnorm(pnorm(dat$z)) results in some infinite values (I don't completely understand the function though..).
norm_trans <- function(){
trans_new('norm', function(x) pnorm(x), function(x) qnorm(x))
}
ggplot(dat, aes(x = x, y = y, fill = z)) +
geom_tile(width=2, height=30) +
scale_fill_gradientn(colours=fill.colors, trans = 'norm')
> Error in seq.default(from = best$lmin, to = best$lmax, by = best$lstep) : 'from' must be of length 1
So, does anybody know how to have a quantile-based colour distribution in the plot and in the legend?
This code will make manual breaks with a pnorm transformation. Is this what you are after?
ggplot(dat, aes(x = x, y = y, fill = z)) +
geom_tile(width=2, height=30) +
scale_fill_gradientn(colours=fill.colors,
trans = 'norm',
breaks = quantile(dat$z, probs = c(0, 0.25, 1))
)
I believe you have been looking for a quantile transform. Unfortunately there is none in scales, but it is not to hard to build one yourself (on the fly):
make_quantile_trans <- function(x, format = scales::label_number()) {
name <- paste0("quantiles_of_", deparse1(substitute(x)))
xs <- sort(x)
N <- length(xs)
transform <- function(x) findInterval(x, xs)/N # find the last element that is smaller
inverse <- function(q) xs[1+floor(q*(N-1))]
scales::trans_new(
name = name,
transform = transform,
inverse = inverse,
breaks = function(x, n = 5) inverse(scales::extended_breaks()(transform(x), n)),
minor_breaks = function(x, n = 5) inverse(scales::regular_minor_breaks()(transform(x), n)),
format = format,
domain = xs[c(1, N)]
)
}
ggplot(dat, aes(x = x, y = y, fill = z)) +
geom_tile(width=2, height=30) +
scale_fill_gradientn(colours=fill.colors, trans = make_quantile_trans(dat$z))
Created on 2021-11-12 by the reprex package (v2.0.1)

Using geom_text in a for loop with ggplot2

I want to display a list of text labels on a ggplot graph with the geom_text() function.
The positions of those labels are stored in a list.
When using the code below, only the second label appears.
x <- seq(0, 10, by = 0.1)
y <- sin(x)
df <- data.frame(x, y)
g <- ggplot(data = df, aes(x, y)) + geom_line()
pos.x <- list(5, 6)
pos.y <- list(0, 0.5)
for (i in 1:2) {
g <- g + geom_text(aes(x = pos.x[[i]], y = pos.y[[i]], label = paste("Test", i)))
}
print(g)
Any idea what is wrong with this code?
I agree with #user2728808 answer as a good solution, but here is what was wrong with your code.
Removing the aes from your geom_text will solve the problem. aes should be used for mapping variables from the data argument to aesthetics. Using it any differently, either by using $ or supplying single values can give unexpected results.
Code
for (i in 1:2) {
g <- g + geom_text(x = pos.x[[i]], y = pos.y[[i]], label = paste("Test", i))
}
I'm not exactly sure how geom_text can be used within a for-loop, but you can achieve the desired result by defining the text labels in advance and using annotate instead. See the code below.
library(ggplot2)
x <- seq(0, 10, by = 0.1)
y <- sin(x)
df <- data.frame(x, y)
pos.x <- c(5, 6)
pos.y <- c(0, 0.5)
titles <- paste("Test",1:2)
ggplot(data = df, aes(x, y)) + geom_line() +
annotate("text", x = pos.x, y = pos.y, label = titles)

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