Imagine the following simple plot with Plots
using Plots
plot([1,2,3,4,5], [1,2,3,4,5])
Output:
How can we change the origin to 0 in the plot above?
It is actually very simple, you can use the arguments xlims and ylims and pass 0 and Inf as the limits to force the axis to an origin of 0. Here is a reproducible example:
using Plots
plot([1,2,3,4,5], [1,2,3,4,5], xlims = [0,Inf], ylims = [0,Inf])
Output:
As you can see the origin has been changed!
Related
My problem is related to car package.
I create Kernal plot. However, since legend is too big, I would like to move legend outside the plot are, upper or lower?
Otherwise, I tried with cowplot::get_legend( ), but it did not work properly.
library(car)
mtcars$g <- as.factor(mtcars$vs)
densityPlot(mpg,mtcars$g,show.bw=T, kernel=depan,legend=list(location="topleft",title=NULL))
Probably the easiest thing is to not plot the legend using the densityPlot() function but rather add it separately using legend(). The following code is an example of how this can be done. The resulting figure look like this:
library(car)
mtcars$g <- as.factor(mtcars$vs)
par(mar=c(4,4,4,2))
# obtaining results from kernel density and saving results
# need saved values for bandwidth in legend
# also plots the kernel densities
d <- densityPlot(mtcars$mpg,mtcars$g
,show.bw=T
,kernel=depan
,legend=F # no default legend
,col = c('black','blue')
,lty=c(1,2))
# allows legend outside of plot area to be displayed
par(xpd=T)
# defining location based on the plot coordinates from par('usr')
legend(x=mean(par('usr')[c(1,2)]) # average of range of x-axis
,y=par('usr')[4]+0.015 # top of the y axis with additional shift
,legend = c(paste('0 (bw = ',round(d$`0`['bw'][[1]],4),')',sep='') # extract bw values from saved output and
,paste('1 (bw = ',round(d$`1`['bw'][[1]],4),')',sep='')) # formatting similar to default, except with rounding bw value
,ncol=1 # change to 2 if you want entries beside each other
,lty=c(1,2) # line types, same as above
,col=c('black','blue') # colors, same as above
,lwd=1
,xjust = 0.5 # centers legend at x coordinate
,yjust = 0.5 # centers legend at y coordinate
)
par(xpd=F)
I found some similar questions but the answers didn't solve my problem.
I try to plot a time series of to variables as a scatterplot and using the date to color the points. In this example, I created a simple dataset (see below) and I want to plot all data with timesteps in the 1960ties, 70ties, 80ties and 90ties with one colour respectively.
Using the standard plot command (plot(x,y,...)) it works the way it should, as I try using the ggplot library some strange happens, I guess I miss something. Has anyone an idea how to solve this and generate a correct plot?
Here is my code using the standard plot command with a colorbar
# generate data frame with test data
x <- seq(1,40)
y <- seq(1,40)
year <- c(rep(seq(1960,1969),2),seq(1970,1989,2),seq(1990,1999))
df <- data.frame(x,y,year)
# define interval and assing color to interval
myinterval <- seq(1959,1999,10)
mycolors <- rainbow(4)
colbreaks <- findInterval(df$year, vec = myinterval, left.open = T)
# basic plot
layout(array(1:2,c(1,2)),widths =c(5,1)) # divide the device area in two panels
par(oma=c(0,0,0,0), mar=c(3,3,3,3))
plot(x,y,pch=20,col = mycolors[colbreaks])
# add colorbar
ncols <- length(myinterval)-1
colbarlabs <- seq(1960,2000,10)
par(mar=c(5,0,5,5))
image(t(array(1:ncols, c(ncols,1))), col=mycolors, axes=F)
box()
axis(4, at=seq(0.5/(ncols-1)-1/(ncols-1),1+1/(ncols-1),1/(ncols-1)), labels=colbarlabs, cex.axis=1, las=1)
abline(h=seq(0.5/(ncols-1),1,1/(ncols-1)))
mtext("year",side=3,line=0.5,cex=1)
As I would like to use ggplot package, as I do for other plots, I tried this version with ggplot
# plot with ggplot
require(ggplot2)
ggplot(df, aes(x=x,y=y,color=year)) + geom_point() +
scale_colour_gradientn(colours= mycolors[colbreaks])
but it didn't work the way I thought it would. Obviously, there is something wrong with the color coding. Also, the colorbar looks strange. I also tried it with scale_color_manual and scale_color_gradient2 but I got more errors (Error in continuous_scale).
Any idea how to solve this and generate a plot according to the standard plot 3 including a colorbar.
I am using the following code to plot the ROC curve after having run the logistic regression.
fit1 <- glm(formula=GB160M3~Behvscore, data=eflscr,family="binomial", na.action = na.exclude)
prob1=predict(fit1, type=c("response"))
eflscr$prob1 = prob1
library(pROC)
g1 <- roc(GB160M3~prob1, data=eflscr, plot=TRUE, grid=TRUE, print.auc=TRUE)
The ROC curves plotted look like this (see link below)
The x-axis scale does not fill the who chart.
How can I change the x axis to report 1 - specifically?
By default pROC sets asp = 1 to ensure the plot is square and both sensitivity and specificity are on the same scale. You can set it to NA or NULL to free the axis and fill the chart, but your ROC curve will be misshaped.
plot(g1, asp = NA)
Using par(pty="s") as suggested by Joe is probably a better approach
This is purely a labeling problem: note that the x axis goes decreasing from 1 to 0, which is exactly the same as plotting 1-specificity on an increasing axis. You can set the legacy.axes argument to TRUE to change the behavior if the default one bothers you.
plot(g1, legacy.axes = TRUE)
A good shortcut to getting a square plot is to run the following before plotting:
par(pty="s")
This forces the shape of the plot region to be square. Set the plotting region back to maximal by simply resetting the graphics device and clearing the plot.
dev.off()
As pointed out by #Calimo, there is the legacy.axes argument to reverse the x-axis and the label is also changed automatically. You can run ?plot.roc to see all the pROC plotting options.
Example
# Get ROC object
data(aSAH)
roc1 <- roc(aSAH$outcome, aSAH$s100b)
# Plot
par(pty="s")
plot(roc1, grid = TRUE, legacy.axes = TRUE)
# Reset graphics device and clear plot
dev.off()
Say I want to create an ordinary xyplot without explicitly specifying axis limits, then how are axis limits calculated?
The following line of code produces a simple scatter plot. However, axis limits do not exactly range from 1 to 10, but are slightly expanded to the left and right and top and bottom sides (roughly by 0.5).
library(lattice)
xyplot(1:10 ~ 1:10, cex = 1.5, pch = 20, col = "black",
xlab = "x", ylab = "y")
Is there any way to determine the factor by which the axes were expanded on each site, e.g. using trellis.par.get? I already tried the following after executing the above-mentioned xyplot command:
library(grid)
downViewport(trellis.vpname(name = "figure"))
current.panel.limits()
$xlim
[1] 0 1
$ylim
[1] 0 1
Unfortunately, the panel limits are returned as normalized parent coordinates, which makes it impossible to obtain the "real" limits. Any suggestions would be highly appreciated!
Update:
Using base-R plot, the data range (and consequently the axis limits) is by default extended by 4% on each side, see ?par. But this factor doesn't seem to apply to 'trellis' objects. So what I am looking for is an analogue to the 'xaxs' (and 'yaxs') argument implemented in par.
Axis limits for xyplot are calculated in the extend.limits function. This function isn't exported from the lattice package, so to see it, type lattice:::extend.limits. Concerning a numeric vector, this function is passed the range of values from the corresponding data (c(1, 10) in this example). The final limits are calculated according to the following equation:
lim + prop * d * c(-1, 1)
lim are the limits of the data, in this case c(1, 10)
prop is lattice.getOption("axis.padding")$numeric, which by default is 0.07
d is diff(as.numeric(lim)), in this case 9
The result in this case is c(0.37, 10.63)
In case you're interested, the call stack from xyplot to extend.limits is
xyplot
xyplot.formula
limits.and.aspect
limitsFromLimitList
extend.limits
Using R and polygon I'm trying to shade the area under the line of a plot from the line to the x-axis and I'm not sure what I am doing wrong here.
The shading is using some point in the middle of the y range to shade from, not 0, the x-axis.
The data set ratioresults is a zoo object but I don't think that's the issue since I tried coercing the y values to as.numeric and as.vector and got the same results.
Code:
plot(index(ratioresults),ratioresults$ratio, type="o", col="red")
polygon(c(1,index(ratioresults),11),c(0, ratioresults$ratio, 0) , col='red')
What's index(ratioresults)? For a simple zoo object I see:
> index(x)
[1] "2003-02-01" "2003-02-03" "2003-02-07" "2003-02-09" "2003-02-14"
which is a vector of Date objects. You are trying to prepend/append values of 1 and 11 to this vector. Its not going to work.
Here's a reproducible example:
x=zoo(matrix(runif(11),ncol=1),as.Date("2012-08-01") + 0:10)
colnames(x)="ratio"
plot(index(x),x$ratio,type="o",col="red",ylim=c(0,1))
polygon(index(x)[c(1,1:11,11)],c(0,x$ratio,0),col="red")
Differences from yours:
I call my thing x.
I set ylim on the plot - I don't know how your plot managed to start at 0 on the Y axis.
I complete the polygon using the x-values of the first and 11th (last) point, rather than 1 and 11 themselves.
#With an example dataset: please provide one when you need help!
ratioresults<-as.zoo(runif(10,0,1))
plot(index(ratioresults),ratioresults, type="o", col="red",
xaxs="i",yaxs="i", ylim=c(0,2))
polygon(c(index(ratioresults),rev(index(ratioresults))),
c(as.vector(ratioresults),rep(0,length(ratioresults))),col="red")
The issue with your question is that the x-axis is not a line defined by a given y value by default, so one way to fill under a curve to the x-axis using polygon would be to define a y values for the x-axis using ylim (here I chose 0). Whatever value you choose you will want to specify that the plot stop exactly at the value using yaxs="i".
You also have to construct your polygon with the value you chose for you x-axis.