I want to draw several (lets say - 5 for now) segments on my plot. I've tried segments() function but it draws only two segments out of 5 given coordinates. Here is the code :
begs <- c(34573131,35072050,35471145, 35746065,36504818)
ends <- c(34887083,35139735,35557793,35789178,36950091)
step <- 820000
plot(1, xlim = c(33900000,38000000), axes = F, xlab="Position")
axis(1, at = seq(33900000,38000000, by=step), labels=format(seq(33900000,38000000, by=step)/1e6, scientific=F, digits=3))
axis(4, at = seq(0,2,length.out = 5), labels = seq(0,2,length.out = 5) )
segments(x0 = begs, x1 = ends, y0 = c(0.1, 0.5 , 0.9 ,1.4, 1.9))
and the plot looks like that :
Your first call to plot() causes R to calculate the x and y range. Thus if your data in this first call is not representative of the range, you need to specify the range manually.
Concretely, add ylim=c(...) to your plot() call:
Try this:
min <- 33900000
max <- 38000000
plot(1, xlim = c(min, max), ylim=c(0, 2),
axes = FALSE, xlab="Position", ylab="", type="n")
axis(1, at = seq(min, max, by=step), labels=format(seq(min, max, by=step)/1e6,
scientific=F, digits=3))
axis(4, at = seq(0,2,length.out = 5), labels = seq(0,2,length.out = 5) )
segments(x0 = begs, x1 = ends, y0 = c(0.1, 0.5 , 0.9 ,1.4, 1.9))
Related
I compare two treatments A and B. The objective is to show that A is not inferior to B. The non inferiority margin delta =-2
After comparing Treatment A - Treatment B I have these results
Mean difference and 95% CI = -0.7 [-2.1, 0.8]
I would like to plot this either with a package or manually. I have no idea how to do it.
Welch Two Sample t-test
data: mydata$outcome[mydata$traitement == "Bras S"] and mydata$outcome[mydata$traitement == "B"]
t = 0.88938, df = 258.81, p-value = 0.3746
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
-2.133224 0.805804
sample estimates:
mean of x mean of y
8.390977 9.054688
I want to create this kind of plot:
You could abstract the relevant data from the t.test results and then plot in base R using segments and points to plot the data and abline to draw in the relevant vertical lines. Since there were no reproducible data, I made some up but the process is generally the same.
#sample data
set.seed(123)
tres <- t.test(runif(10), runif(10))
# get values to plot from t test results
ci <- tres$conf.int
ests <- tres$estimate[1] - tres$estimate[2]
# plot
plot(x = ci, ylim = c(0,2), xlim = c(-4, 4), type = "n", # blank plot
bty = "n", xlab = "Treatment A - Treatment B", ylab = "",
axes = FALSE)
points(x = ests, y = 1, pch = 20) # dot for point estimate
segments(x0 = ci[1], x1 = ci[2], y0 = 1) #CI line
abline(v = 0, lty = 2) # vertical line, dashed
abline(v = 2, lty = 1, col = "darkblue") # vertical line, solid, blue
axis(1, col = "darkblue") # add in x axis, blue
EDIT:
If you wanted to more accurately recreate your figure with the x axis in descending order and using your statement "Mean difference and 95% CI = -0.7 [-2.1, 0.8]", you can do the following manipulations to the above approach:
diff <- -0.7
ci <- c(-2.1, 0.8)
# plot
plot(1, xlim = c(-4, 4), type = "n",
bty = "n", xlab = "Treatment A - Treatment B", ylab = "",
axes = FALSE)
points(x = -diff, y = 1, pch = 20)
segments(x0 = -ci[2], x1 = -ci[1], y0 = 1)
abline(v = 0, lty = 2)
abline(v = 2, lty = 1, col = "darkblue")
axis(1, at = seq(-4,4,1), labels = seq(4, -4, -1), col = "darkblue")
I have created the following fanchart using the fanplot package. I'm trying to add axis ticks and labels to the y axis, however it's only giving me the decimals and not the full number. Looking for a solution to display the full number (e.g 4.59 and 4.61) on the y axis
I am also unsure of how to specify the breaks and number of decimal points for the labels on the y-axis using plot(). I know doing all of this in ggplot2 it would look something like this scale_y_continuous(breaks = seq(min(data.ts$Index),max(data.ts$Index),by=0.02)) . Any ideas on how to specify the breaks in the y axis as well as the number of decimal points using the base plot() feature in R?
Here is a reproductible of my dataset data.ts
structure(c(4.6049904235401, 4.60711076016453, 4.60980084146652,
4.61025389170935, 4.60544515681515, 4.60889021700954, 4.60983993107244,
4.61091608826696, 4.61138799159174, 4.61294431148318, 4.61167545843765,
4.61208284263432, 4.61421991328081, 4.61530485425155, 4.61471465043043,
4.6155992084451, 4.61195799200607, 4.61178486640435, 4.61037927954796,
4.60744590947049, 4.59979957741728, 4.59948551500254, 4.60078678080182,
4.60556092645471, 4.60934962087565, 4.60981147563749, 4.61060477704678,
4.61158365084251, 4.60963435263623, 4.61018215733317, 4.61209710959768,
4.61231368335184, 4.61071363571141, 4.61019496497916, 4.60948652606191,
4.61068813487859, 4.6084092003352, 4.60972706132393, 4.60866915174087,
4.61192565195909, 4.60878767339377, 4.61341471281265, 4.61015272152397,
4.6093479714315, 4.60750965935653, 4.60768790690338, 4.60676463096309,
4.60746490411374, 4.60885670935448, 4.60686846708382, 4.60688947889575,
4.60867708110485, 4.60448791268212, 4.60387348166032, 4.60569806689426,
4.6069320880709, 4.6087143894128, 4.61059688801283, 4.61065399116698,
4.61071421014339), .Tsp = c(2004, 2018.75, 4), class = "ts")
and here is a reproductible of the code I'm using
# # Install and Load Packages
## pacman::p_load(forecast,fanplot,tidyverse,tsbox,lubridate,readxl)
# Create an ARIMA Model using the auto.arima function
model <- auto.arima(data.ts)
# Simulate forecasts for 4 quarters (1 year) ahead
forecasts <- simulate(model, n=4)
# Create a data frame with the parameters needed for the uncertainty forecast
table <- ts_df(forecasts) %>%
rename(mode=value) %>%
mutate(time0 = rep(2019,4)) %>%
mutate(uncertainty = sd(mode)) %>%
mutate(skew = rep(0,4))
y0 <- 2019
k <- nrow(table)
# Set Percentiles
p <- seq(0.05, 0.95, 0.05)
p <- c(0.01, p, 0.99)
# Simulate a qsplitnorm distribution
fsval <- matrix(NA, nrow = length(p), ncol = k)
for (i in 1:k)
fsval[, i] <- qsplitnorm(p, mode = table$mode[i],
sd = table$uncertainty[i],
skew = table$skew[i])
# Create Plot
plot(data.ts, type = "l", col = "#75002B", lwd = 4,
xlim = c(y0 - 2,y0 + 0.75), ylim = range(fsval, data.ts),
xaxt = "n", yaxt = "n", ylab = "",xlab='',
main = '')
title(ylab = 'Log AFSI',main = 'Four-Quarter Ahead Forecast Fan - AFSI',
xlab = 'Date')
rect(y0 - 0.25, par("usr")[3] - 1, y0 + 2, par("usr")[4] + 1,
border = "gray90", col = "gray90")
fan(data = fsval, data.type = "values", probs = p,
start = y0, frequency = 4,
anchor = data.ts[time(data.ts) == y0 - .25],
fan.col = colorRampPalette(c("#75002B", "pink")),
ln = NULL, rlab = NULL)
# Add axis labels and ticks
axis(1, at = y0-2:y0 + 2, tcl = 0.5)
axis(1, at = seq(y0-2, y0 + 2, 0.25), labels = FALSE, tcl = 0.25)
abline(v = y0 - 0.25, lty = 1)
abline(v = y0 + 0.75, lty = 2)
axis(2, at = range(fsval, data.ts), las = 2, tcl = 0.5)
range(blah) will only return two values (the minimum and maximum). The at parameter of axis() requires a sequence of points at which you require axis labels. Hence, these are the only two y values you have on your plot. Take a look at using pretty(blah) or seq(min(blah), max(blah), length.out = 10).
The suggestions of #Feakster are worth looking at, but the problem here is that the y-axis margin isn't wide enough. You could do either of two things. You could round the labels so they fit within the margins, for example you could replace this
axis(2, at = range(fsval, data.ts), las = 2, tcl = 0.5)
with this
axis(2, at = range(fsval, data.ts),
labels = sprintf("%.3f", range(fsval, data.ts)), las = 2, tcl = 0.5)
Or, alternatively you could increase the y-axis margin before you make the plot by specifying:
par(mar=c(5,5,4,2)+.1)
plot(data.ts, type = "l", col = "#75002B", lwd = 4,
xlim = c(y0 - 2,y0 + 0.75), ylim = range(fsval, data.ts),
xaxt = "n", yaxt = "n", ylab = "",xlab='',
main = '')
Then everything below that should work. The mar element of par sets the number of lines printed in the margin of each axis. The default is c(5,4,4,2).
I am looking for advice for plotting 2 similar wave forms with different y axes scales (one is mmHg and another is m/s) in the same plot. However, I would like to stagger the plots with respect to each other.
For example, using the below:
set.seed(123)
y <- sin(2*pi*x)
g <- sin(2*pi*x)+ rnorm(200, sd=0.1)
plot(y,type="l",
ann = F,
axes = F)
axis(side = 2)
par(new = T)
plot(g,type="l",
ann = F,
axes = F)
axis(side = 4)
Gives:
I would like to achieve something like this (see link below):
How to achieve this?
Here's a slightly cheaty solution:
x <- seq(from = 1, to = 3, by = 0.01)
y <- sin(2*pi*x)
set.seed(123)
g <- sin(2*pi*x)+ rnorm(length(x), sd=0.1)
stagger <- 2
glabels <- c(-1, 0, 1)
plot(c(min(y),max(y)+stagger) ~ c(1,length(y)), type="n", axes=FALSE, ann=FALSE)
lines(y)
axis(side = 2, at = min(y):max(y))
par(new = T)
lines(g+stagger)
axis(side = 4, at = glabels + stagger, labels = glabels)
Results in:
There's probably a better way to generate the positions and labels for the y-axis for g.
I want to plot a confusion matrix, but, I don't want to just use a heatmap, because I think they give poor numerical resolution. Instead, I want to also plot the frequency in the middle of the square. For instance, I like the output of this:
library(mlearning);
data("Glass", package = "mlbench")
Glass$Type <- as.factor(paste("Glass", Glass$Type))
summary(glassLvq <- mlLvq(Type ~ ., data = Glass));
(glassConf <- confusion(predict(glassLvq, Glass, type = "class"), Glass$Type))
plot(glassConf) # Image by default
However, 1.) I don't understand that the "01, 02, etc" means along each axis. How can we get rid of that?
2.) I would like 'Predicted' to be as the label of the 'y' dimension, and 'Actual' to be as the label for the 'x' dimension
3.) I would like to replace absolute counts by frequency / probability.
Alternatively, is there another package that will do this?
In essence, I want this in R:
http://www.mathworks.com/help/releases/R2013b/nnet/gs/gettingstarted_nprtool_07.gif
OR:
http://c431376.r76.cf2.rackcdn.com/8805/fnhum-05-00189-HTML/image_m/fnhum-05-00189-g009.jpg
The mlearning package seems quite inflexible with plotting confusion matrices.
Starting with your glassConf object, you probably want to do something like this:
prior(glassConf) <- 100
# The above rescales the confusion matrix such that columns sum to 100.
opar <- par(mar=c(5.1, 6.1, 2, 2))
x <- x.orig <- unclass(glassConf)
x <- log(x + 0.5) * 2.33
x[x < 0] <- NA
x[x > 10] <- 10
diag(x) <- -diag(x)
image(1:ncol(x), 1:ncol(x),
-(x[, nrow(x):1]), xlab='Actual', ylab='',
col=colorRampPalette(c(hsv(h = 0, s = 0.9, v = 0.9, alpha = 1),
hsv(h = 0, s = 0, v = 0.9, alpha = 1),
hsv(h = 2/6, s = 0.9, v = 0.9, alpha = 1)))(41),
xaxt='n', yaxt='n', zlim=c(-10, 10))
axis(1, at=1:ncol(x), labels=colnames(x), cex.axis=0.8)
axis(2, at=ncol(x):1, labels=colnames(x), las=1, cex.axis=0.8)
title(ylab='Predicted', line=4.5)
abline(h = 0:ncol(x) + 0.5, col = 'gray')
abline(v = 0:ncol(x) + 0.5, col = 'gray')
text(1:6, rep(6:1, each=6),
labels = sub('^0$', '', round(c(x.orig), 0)))
box(lwd=2)
par(opar) # reset par
The above code uses bits and pieces of the confusionImage function called by plot.confusion.
Here is a function for plotting confusion matrices I developed from jbaums excellent answer.
It is similar, but looks a bit nicer (IMO), and does not transpose the confusion matrix you feed it, which might be helpful.
### Function for plotting confusion matrices
confMatPlot = function(confMat, titleMy, shouldPlot = T) {
#' Function for plotting confusion matrice
#'
#' #param confMat: confusion matrix with counts, ie integers.
#' Fractions won't work
#' #param titleMy: String containing plot title
#' #return Nothing: It only plots
## Prepare data
x.orig = confMat; rm(confMat) # Lazy conversion to function internal variable name
n = nrow(x.orig) # conf mat is square by definition, so nrow(x) == ncol(x)
opar <- par(mar = c(5.1, 8, 3, 2))
x <- x.orig
x <- log(x + 0.5) # x<1 -> x<0 , x>=1 -> x>0
x[x < 0] <- NA
diag(x) <- -diag(x) # change sign to give diagonal different color
## Plot confusion matrix
image(1:n, 1:n, # grid of coloured boxes
# matrix giving color values for the boxes
# t() and [,ncol(x):1] since image puts [1,1] in bottom left by default
-t(x)[, n:1],
# ylab added later to avoid overlap with tick labels
xlab = 'Actual', ylab = '',
col = colorRampPalette(c("darkorange3", "white", "steelblue"),
bias = 1.65)(100),
xaxt = 'n', yaxt = 'n'
)
# Plot counts
text(rep(1:n, each = n), rep(n:1, times = n),
labels = sub('^0$', '', round(c(x.orig), 0)))
# Axis ticks but no lables
axis(1, at = 1:n, labels = rep("", n), cex.axis = 0.8)
axis(2, at = n:1, labels = rep("", n), cex.axis = 0.8)
# Tilted axis lables
text(cex = 0.8, x = (1:n), y = -0.1, colnames(x), xpd = T, srt = 30, adj = 1)
text(cex = 0.8, y = (n:1), x = +0.1, colnames(x), xpd = T, srt = 30, adj = 1)
title(main = titleMy)
title(ylab = 'Predicted', line = 6)
# Grid and box
abline(h = 0:n + 0.5, col = 'gray')
abline(v = 0:n + 0.5, col = 'gray')
box(lwd = 1, col = 'gray')
par(opar)
}
Example of output:
I have the following data
test<-data.frame(group=1:10, var.a=rnorm(n=10,mean=500,sd=20), var.b=runif(10))
I would like a barplot with 2 y axis (one for var.a, one for var.2). Each group (x axis, 1:10) should have 2 bars next to each other, one for var.a and one for var.b.
I cannot use one y-axis because of the difference morder of magnitude of var.a and var.b
Is this possible with base R?
Thank you
To use the graphics package in R, one could create new variables as the values in var.a and var.b converted into proportions of the maximum values in the respective variable:
test <- data.frame(group = 1:10, var.a = rnorm(n = 10, mean = 500, sd = 20),
var.b = runif(10))
funProp <- function(testCol) {
test[, testCol]/max(test[, testCol])
}
test$var.a.prop <- funProp("var.a")
test$var.b.prop <- funProp("var.b")
Then draw the plot using barplot() without the axes:
barplot(t(as.matrix(test[, c("var.a.prop", "var.b.prop")])), beside = TRUE,
yaxt = "n", names.arg = test$group)
Then add the axes on the left and the right using the original value ranges for the labels (the labels argument) and the proportional value ranges to place the labels on the axes (the at argument) (this part is not pretty, but it gets the job done):
axis(2, at = seq(0, max(test$var.a.prop), length.out = 10),
labels = round(seq(0, max(test$var.a), length.out = 10)))
axis(4, at = seq(0, max(test$var.b.prop), length.out = 10),
labels = round(seq(0, max(test$var.b), length.out = 10), 2))
(Sorry for the lack of an image)
EDIT:
To get the axes a bit prettyer,
myLeftAxisLabs <- pretty(seq(0, max(test$var.a), length.out = 10))
myRightAxisLabs <- pretty(seq(0, max(test$var.b), length.out = 10))
myLeftAxisAt <- myLeftAxisLabs/max(test$var.a)
myRightAxisAt <- myRightAxisLabs/max(test$var.b)
barplot(t(as.matrix(test[, c("var.a.prop", "var.b.prop")])),
beside = TRUE, yaxt = "n", names.arg = test$group,
ylim=c(0, max(c(myLeftAxisAt, myRightAxisAt))))
axis(2, at = myLeftAxisAt, labels = myLeftAxisLabs)
axis(4, at = myRightAxisAt, labels = myRightAxisLabs)