I made a plot using plot() using RStudio.
x = X$pos
y = X$anc
z = data.frame(x,y)
#cut in segments
my_segments = c(52660, 106784, 151429, 192098, 233666,
273857, 307933, 343048, 373099, 408960,
441545, 472813, 497822, 518561, 537471,
556747, 571683, 591232, 599519, 616567,
625727, 633744)
my_cuts = cut(x,my_segments, labels = FALSE)
my_cuts[is.na(my_cuts)] = 0
This is the code:
#create subset of segments
z_alt = z
z_alt[my_cuts %% 2 == 0,] = NA
#plot green, then alternating segments in blue
plot(z, type="p", cex = 0.3,pch = 16,
col="black",
lwd=0.2,
frame.plot = F,
xaxt = 'n', # removes x labels,
ylim = c(0.3, 0.7),
las = 2,
xlim = c(0, 633744),
cex.lab=1.5, # size of axis labels
ann = FALSE, # remove axis titles
mgp = c(3, 0.7, 0))
lines(z_alt,col="red", lwd=0.2)
# adjust y axis label size
par(cex.axis= 1.2, tck=-0.03)
If you see, some black dots are separated, but other black dots have red connecting lines. Does anyone know how to remove these annoying lines?. I just want black and red dots. Many thanks
there is no need to call the points in a second function. you can try to directly set the color in the plot function using a color vector.
# create some data as you have not provided some
set.seed(123)
df <- data.frame(x=1:100,y=runif(100))
# some sgment breaks
my_segments <- c(0,10,20,50,60)
gr <- cut(df$x, my_segments,labels = FALSE, right = T)
gr[is.na(gr)] <- 0
# create color vector with 1 == black, and 2 == red
df$color <- ifelse(gr %% 2 == 0, 1, 2)
# and the plot
plot(df$x, df$y, col = df$color, pch = 16)
The problem here is that you are using lines to add your z_alt. As the name of the function suggests, you will be adding lines. Use points instead.
z <- runif(20,0,1)
z_alt <- runif(20,0.8,1.2)
plot(z, type="p", col="black", pch = 16, lwd=0.2, ylim = c(0,1.4))
points(z_alt, col = "red", pch = 16, lwd = 0.2)
Related
I am doing quarterly analysis, for which I want to plot a graph. To maintain continuity on x axis I have turned quarters into factors. But then when I am using plot function and trying to color it red, the col argument is not working.
An example:
quarterly_analysis <- data.frame(Quarter = as.factor(c(2020.1,2020.2,2020.3,2020.4,2021.1,2021.2,2021.3,2021.4)),
AvgDefault = as.numeric(c(0.24,0.27,0.17,0.35,0.32,0.42,0.38,0.40)))
plot(quarterly_analysis, col="red")
But I am getting the graph in black color as shown below:
Converting it to a factor is not ideal to plot unless you have multiple values for each factor - it tries to plot a box plot-style plot. For example, with 10 observations in the same factor, the col = "red" color shows up as the fill:
set.seed(123)
fact_example <- data.frame(factvar = as.factor(rep(LETTERS[1:3], 10)),
numvar = runif(30))
plot(fact_example$factvar, fact_example$numvar,
col = "red")
With only one observation for each factor, this is not ideal because it is just showing you the line that the box plot would make.
You could use border = "red:
plot(quarterly_analysis$Quarter,
quarterly_analysis$AvgDefault, border="red")
Or if you want more flexibility, you can plot it numerically and do a little tweaking for more control (i.e., can change the pch, or make it a line graph):
# make numeric x values to plot
x_vals <- as.numeric(substr(quarterly_analysis$Quarter,1,4)) + rep(seq(0, 1, length.out = 4))
par(mfrow=c(1,3))
plot(x_vals,
quarterly_analysis$AvgDefault, col="red",
pch = 7, main = "Square Symbol", axes = FALSE)
axis(1, at = x_vals,
labels = quarterly_analysis$Quarter)
axis(2)
plot(x_vals,
quarterly_analysis$AvgDefault, col="red",
type = "l", main = "Line graph", axes = FALSE)
axis(1, at = x_vals,
labels = quarterly_analysis$Quarter)
axis(2)
plot(x_vals,
quarterly_analysis$AvgDefault, col="red",
type = "b", pch = 7, main = "Both", axes = FALSE)
axis(1, at = x_vals,
labels = quarterly_analysis$Quarter)
axis(2)
Data
set.seed(123)
quarterly_analysis <- data.frame(Quarter = as.factor(paste0(2019:2022,
rep(c(".1", ".2", ".3", ".4"),
each = 4))),
AvgDefault = runif(16))
quarterly_analysis <- quarterly_analysis[order(quarterly_analysis$Quarter),]
QUESTION: I am building a triplot for the results of my distance-based RDA in R, library(vegan). I can get a triplot to build, but can't figure out how to make the colours of my sites different based on their location. Code below.
#running the db-RDA
spe.rda.signif=capscale(species~canopy+gmpatch+site+year+Condition(pair), data=env, dist="bray")
#extract % explained by first 2 axes
perc <- round(100*(summary(spe.rda.signif)$cont$importance[2, 1:2]), 2)
#extract scores (coordinates in RDA space)
sc_si <- scores(spe.rda.signif, display="sites", choices=c(1,2), scaling=1)
sc_sp <- scores(spe.rda.signif, display="species", choices=c(1,2), scaling=1)
sc_bp <- scores(spe.rda.signif, display="bp", choices=c(1, 2), scaling=1)
#These are my location or site names that I want to use to define the colours of my points
site_names <-env$site
site_names
#set up blank plot with scaling, axes, and labels
plot(spe.rda.signif,
scaling = 1,
type = "none",
frame = FALSE,
xlim = c(-1,1),
ylim = c(-1,1),
main = "Triplot db-RDA - scaling 1",
xlab = paste0("db-RDA1 (", perc[1], "%)"),
ylab = paste0("db-RDA2 (", perc[2], "%)")
)
#add points for site scores - these are the ones that I want to be two different colours based on the labels in the original data, i.e., env$site or site_names defined above. I have copied the current state of the graph
points(sc_si,
pch = 21, # set shape (here, circle with a fill colour)
col = "black", # outline colour
bg = "steelblue", # fill colour
cex = 1.2) # size
Current graph
I am able to add species names and arrows for environmental predictors, but am just stuck on how to change the colour of the site points to reflect their location (I have two locations defined in my original data). I can get them labelled with text, but that is messy.
Any help appreciated!
I have tried separating shape or colour of point by site_name, but no luck.
If you only have a few groups (in your case, two), you could make the group a factor (within the plot call). In R, factors are represented as an integer "behind the scenes" - you can represent up to 8 colors in base R using a simple integer:
set.seed(123)
df <- data.frame(xvals = runif(100),
yvals = runif(100),
group = sample(c("A", "B"), 100, replace = TRUE))
plot(df[1:2], pch = 21, bg = as.factor(df$group),
bty = "n", xlim = c(-1, 2), ylim = c(-1, 2))
legend("topright", unique(df$group), pch = 21,
pt.bg = unique(as.factor(df$group)), bty = "n")
If you have more than 8 groups, or if you would like to define your own colors, you can simply create a vector of colors the length of your groups and still use the same factor method, though with a few slight tweaks:
# data with 10 groups
set.seed(123)
df <- data.frame(xvals = runif(100),
yvals = runif(100),
group = sample(LETTERS[1:10], 100, replace = TRUE))
# 10 group colors
ccols <- c("red", "orange", "blue", "steelblue", "maroon",
"purple", "green", "lightgreen", "salmon", "yellow")
plot(df[1:2], pch = 21, bg = ccols[as.factor(df$group)],
bty = "n", xlim = c(-1, 2), ylim = c(-1, 2))
legend("topright", unique(df$group), pch = 21,
pt.bg = ccols[unique(as.factor(df$group))], bty = "n")
For pch just a slight tweak to wrap it in as.numeric:
pchh <- c(21, 22)
ccols <- c("slateblue", "maroon")
plot(df[1:2], pch = pchh[as.numeric(as.factor(df$group))], bg = ccols[as.factor(df$group)],
bty = "n", xlim = c(-1, 2), ylim = c(-1, 2))
legend("topright", unique(df$group),
pch = pchh[unique(as.numeric(as.factor(df$group)))],
pt.bg = ccols[unique(as.factor(df$group))], bty = "n")
I have a problem where I have data with (x,y) coordinates that I want to plot in the x-y plane. Furthermore, I have some box constraints such that -7 < x < 7 and -5 < y < 5 need to be drawn and checked. All points that fall outside of this box constraint I would like to color red. To do this I have the following code in R:
library(rgl)
x <- 7
y <- 5
data.x <- rnorm(10,0,5)
data.y <- rnorm(10,0,5)
plot(data.x, data.y, xlim = c(min(-x,data.x),max(x,data.x)),
ylim = c(min(-y,data.y),max(y,data.y)), pch = 19)
rect(-x, -y, x, y, col = "lightgrey")
idx <- abs(data.x) > x | abs(data.y) > y
points(data.x[idx], data.y[idx], col = "red", pch = 19)
points(data.x[!idx], data.y[!idx], col = "deepskyblue", pch = 19)
Now, where I am stuck, is on how to plot this type of data picture when I have a third group of data and a third constraint. I.e.,
### How to generalize when I have a third axis and constraint, i.e., a 3D cube
z <- 4
data.z <- rnorm(10, 0, 5)
So essentially I want to plot a box constraint as a cube in the x-y-z plane, and to color the points that fall outside the box constraint red again.
Also, I should say I understand there are functions for plottig 3d scatter plots in R, however, what I am struggling with is how to draw the 3D cube that defines the constraints.
The difficulty with a 3D plot such as this is being able to interpret the "depth" of the points in the image. An animated 3D image might be helpful here:
library(plot3D)
x <- 7
y <- 5
z <- 6
set.seed(123)
data.x <- rnorm(10, 0, 5)
data.y <- rnorm(10, 0, 5)
data.z <- rnorm(10, 0, 5)
in_out <- abs(data.x) > x | abs(data.y) > y | abs(data.z) > z
for(i in seq(0, 358, 2)) {
png(paste0("box", sprintf("%03d", i), ".png"))
box3D(-x, -y, -z, x, y, z, col = NA, border = "gray50", theta = i, phi = 15,
xlim = c(-10, 10), ylim = c(-10, 10), zlim = c(-10, 10),
axes = TRUE, ticktype = "detailed")
points3D(data.x, data.y, data.z, colvar = in_out, pch = 16, cex = 3,
add = TRUE, colkey = FALSE, col = c("lightblue", "red"))
dev.off()
}
library(magick)
list.files(pattern = 'box\\d+\\.png', full.names = TRUE) %>%
image_read() %>%
image_join() %>%
image_animate(fps=50) %>%
image_write("box.gif")
box.gif
I've inherited this R code that plots a simple line graph. However, it does it so that the y axis values are plotted downwards below 0 (plots it in the 4th quadrant with 0 at the top and +3600 at the bottom). I want to plot the data right-side up (1st quadrant) so the y axis data goes from 0 up to +3600 at the top like a typical grade-school plot.
I've tried ylim = rev(y) but it returns an error...
I've also tried flipping the seq() command but no luck there.
list.vlevel = numeric(9) # placeholder
plot(
rep(0, length(list.vlevel)),
seq(1, length(list.vlevel)),
type = "n",
xlim = biaslim,
axes = F,
main = paste(list.var.bias[vv], list.score.bias[vv]),
xlab = "",
ylab = ""
)
abline(h = seq(1, length(list.vlevel)),
lty = 3,
col = 8)
axis(2,
labels = list.vlevel,
at = seq(length(list.vlevel), 1, -1),
las = 1)
axis(1)
box()
legend(
x = min(biasarray.var.runhour),
y = length(list.vlevel),
legend = expname,
lty = 3,
lwd = 3,
col = expcol
)
for (exp in seq(length(expname), 1, -1)) {
lines(
biasarray.var.runhour[exp, ],
seq(length(list.vlevel), 1, -1),
col = expcol[exp],
lwd = 3,
lty = 3
)
}
abline(v = 0, lty = 3)
The plot should end up in the first quadrant with yaxis values increasing from 0 upwards to +###.
The axis(2, ...) line draws the y axis. You can see that is the labels follow a descending sequence: seq(length(list.vlevel), 1, -1). seq(1, length(list.vlevel))
Similarly, inside lines(), probably you need to make the same change from seq(length(list.vlevel), 1, -1) to ``seq(1, length(list.vlevel))`
That's as much as we can tell with the info you've provided - can't run any of yoru code without values for all the constants you use, e.g., biasarray.var.runhour, list.var.bias, vv, etc.
I am having a 3D plot in which the points are colored acording to some extra vector. My problem is to add a color gradient legend. This is my code:
x = matrix(NA,100,6)
#x value
x[,1] = runif(100, 0, 10)
#y value
x[,2] = runif(100, 0, 10)
#z value
x[,3] = x[,1]+x[,2]
#additional value
x[,4] = runif(100, 0, 1)
#find out in which interval each additional value is
intervals = seq(0,1,1/10)
x[,5] = findInterval(x[,4], intervals)
colours = topo.colors(length(intervals))
x[,6] = colours[x[,5]]
library(rgl)
plot3d(as.numeric(x[,1]),as.numeric(x.stab.in[,2]), as.numeric(x[,3]),
type="p", col=x[,6], size=2, xlab = "x(t)", ylab = "y(t)",
zlab = "z(t)")
decorate3d(xlab = "x", ylab = "y", zlab = "z")
legend3d("topright", legend = intervals, pch = 16, col = colours, cex=1, inset=c(0.02))
grid3d(c("x", "y+", "z"),col = "gray")
The plot looks like this
but I want the legend in a gradient form. That means I don't want separate points for each color but one box in which the colors fade into each other.
Here is a possible solution if you are okay with using scatterplot3d package instead of rgl. It is basically same but non-interactive. Here is your code modified to produce your expected result.
x = matrix(NA,100,6)
#x value
x[,1] = runif(100, 0, 10)
#y value
x[,2] = runif(100, 0, 10)
#z value
x[,3] = x[,1]+x[,2]
#additional value
x[,4] = runif(100, 0, 1)
#find out in which interval each additional value is
intervals = seq(0,1,1/10)
x[,5] = findInterval(x[,4], intervals)
#produce gradient of colors
#you can define different colors (two or more)
gradient <- colorRampPalette(colors = c("yellow", "green", "blue"))
colours <- gradient(length(intervals))
x[,6] = colours[x[,5]]
library(scatterplot3d)
png('3d.png', width = 600, height = 400)
layout(matrix(1:2, ncol=2), width = c(3, 1), height = c(1, 1))
scatterplot3d(as.numeric(x[,1]),as.numeric(x[,2]), as.numeric(x[,3]), type = 'p',
cex.symbols = 1.25, color=x[,6], pch = 16, xlab = "x(t)", ylab = "y(t)", zlab = "z(t)")
plot(x = rep(1, 100), y = seq_along(x[,6]),
pch = 15, cex = 2.5,
col = gradient(length(x[,6])),
ann = F, axes = F, xlim = c(1, 2))
axis(side = 2, at = seq(1, nrow(x), length.out = 11),
labels = 1:11,
line = 0.15)
dev.off()
This will plot the following graph
Here is another solution if you want to plot a gradient on an interactive 3d plot, such as if you needed to animate the plot into a movie.
require(car)
require(rgl)
require(RColorBrewer)
require(mgcv)
require(magick) #Only for creating the animation of the plot as a gif
#Creating mock dataset
Example_Data <- data.frame(Axis1 = rnorm(100),
Axis2 = rnorm(100),
Axis3 = rnorm(100))
Example_Data$Value <- Example_Data$Axis1+Example_Data$Axis2
#Defining function that takes a vector of numeric values and converts them to
#a spectrum of rgb colors to help color my scatter3d plot
get_colors <- function(values){
v <- (values - min(values))/diff(range(values))
x <- colorRamp(rev(brewer.pal(11, "Spectral")))(v)
rgb(x[,1], x[,2], x[,3], maxColorValue = 255)
}
#Writing function that takes a vector of numeric values and a title and creates
#a gradient legend based on those values and the title and suitable for addition
#to a scatter3d plot via a call to bgplot3d()
#Note, I didn't have time to make this automatically adjust text position/size for different size
#plot windows, so values may need to be adjusted manually depending on the size of the plot window.
gradient_legend_3d <- function(values, title){
min_val <- min(values)
max_val <- max(values)
x <- colorRamp(brewer.pal(11, "Spectral"))((0:20)/20)
colors <- rgb(x[,1], x[,2], x[,3], maxColorValue = 255)
legend_image <- as.raster(matrix(colors, ncol=1))
plot(c(0,1),c(0,1),type = 'n', axes = F,xlab = '', ylab = '', main = '') #Generates a blank plot
text(x=0.92, y = seq(0.5, 1,l=5), labels = signif(seq(min_val, max_val,l=5), 2), cex = 1.5) #Creates the numeric labels on the scale
text(x = 0.85, y = 1, labels = title, adj = 1, srt = 90, cex = 1.5) #Determines where the title is placed
rasterImage(legend_image, 0.87, 0.5, 0.9,1) #Values can be modified here to alter where and how wide/tall the gradient is drawn in the plotting area
}
#Creating scatter3d plot
scatter3d(x = Example_Data$Axis1, y = Example_Data$Axis2, z = Example_Data$Axis3, xlab = "Axis1", ylab = "Axis2", zlab = "Axis3", surface = F, grid = F, ellipsoid = F, fogtype = "none", point.col = get_colors(Example_Data$Value))
#Changing size of plotting window and orientation to optimize for addition of static legend
#This may not work on another machine, so the window may need to be adjusted manually
par3d(windowRect = c(0,23,1536,824))
par3d(userMatrix = matrix(c(-0.98181450, -0.02413967, 0.18830180, 0, -0.03652956, 0.99736959, -0.06260729, 0, -0.18629514, -0.06834736, -0.98011345, 0, 0, 0, 0, 1), nrow = 4, ncol = 4, byrow = T))
#Adding legend
bgplot3d(gradient_legend_3d(Example_Data$Value, "Point Value"))
#Animating plot and saving as gif
movie3d(spin3d(axis = c(0,1,0), rpm = 5), duration = 12, dir = getwd(), fps = 5, convert = FALSE, clean = FALSE)
frames <- NULL
for(j in 0:60){
if(j == 1){
frames <- image_read(sprintf("%s%03d.png", "movie", j))
} else {
frames <- c(frames, image_read(sprintf("%s%03d.png", "movie", j)))
}
}
animation <- image_animate(frames, fps = 10, optimize = TRUE)
image_write(animation, path = "Example.gif")
for(j in 0:60){
unlink(sprintf("%s%03d.png", "movie", j))
}
See link to view 3d plot generated by this code:
gif of 3d plot with gradient color scale