I'm generating a simple line plot in R, however it adds another unwanted straight horizontal line to my plot that I don't want. And it happens in all of my line plots. I have tried google, however it only gives me instructions on how to add an extra line and not why this is happening. I am using RStudio 0.98.1028 on Mac OS X Yosemite.
plot(data2$interval,data2$steps,main="Plot of Average Activity",
xlab = "Interval", type="l", ylab="Average steps taken")
I guess the problem is with your data. You might have rows at the end of the data frame that "return" to the origin. Here you have a reproducible example:
data2 <- data.frame(interval = 1:200, steps = rnorm(200, 50, 20))
data2[1,2] <- 0
data2[200,2] <- 0
data2[201, ] <- c(0, 0)
plot(data2$interval,data2$steps,main="Plot of Average Activity",
xlab = "Interval", type="l", ylab="Average steps taken")
please vote if the answer is fine with you :)
Related
Hopefully this is a quick fix. I am trying to make boxplots of nutrient river concentrations using R code written by the person previously in my position (and I am not so experienced with R, but we use it only for this). The issue is that the output boxplot axis have multiple overlapping text, some of which seems to come from another part of the code which I thought did not dictate axis labels. The original code is shown below (the working directory is already set and csv files imported and I know that works), and the resulting boxplot is in 1.
Edit: Code below
png(filename="./TP & TN Plotting/Plots/TN Concentration/Historical TN Concentrations Zoomed to Medians.png",
width=10,
height=4,
unit="in",
res=600)
par(mar=c(5,5,3,1),
cex=.75)
tnhistconc<-(boxplot(Conc_ppb[Year!=2009 & Year !=2010]~Year[Year!=2009 & Year !=2010],
data=TNhist))
boxplot(Conc_ppb[Year!=2009 & Year !=2010]~Year[Year!=2009 & Year !=2010],
data=TNhist,
ylim=c(0,3000),
xaxt="n"),
at=c(1:3,5:8,10:(length(tnhistconc$n)+2)))
axis.break(axis=1,breakpos=c(4),style="slash")
axis.break(axis=1,breakpos=c(9),style="slash")
text(c(1:3,5:8,10:(length(tnhistconc$n)+2)),
-50,
paste("n=",
tnhistconc$n),
cex=0.8)
title(ylab="TN Concentration (ppb)",
xlab="Year")
title(main=paste("Historical (1998 - 2000), (2005 - 2008) + UMass (2012 -
",max(TNhist$Year),") TN Concentration"))
dev.off()
I made the edit of adding ,xlab="",ylab="" after xlab="Year" towards the bottom, since this fixed this issue in other similar sections of boxplot code (except it seems I needed to add it to a different part of those sections, see 2 - also tried it after xaxt ="n" as in 2 and got the same result). It fixes the overlapping text issue, but the axis labels are still not what I want them to be ("Year", and "TN Concentration (ppb)), and this is shown in 3.
So, does anyone potentially know of a simple fix that might get rid of these unwanted labels and replace them with the correct ones? Am I missing something basic? The same original code seemed to work fine in the past before I was doing this (for 2018 data), and the spreadsheets the data is being imported from are the same, same setup and everything. Many thanks in advance!
Edit: I have a sample dataset which is just the last 2 years of data. See here: https://docs.google.com/spreadsheets/d/10oo9w-IzXkLWdY10A9gHYhDH67MeSibBpc2q67L6o88/edit?usp=sharing
Original code result
How this code fixed other similar issues
Partially fixed result based on edit
I don't know if it is a typo but you have an extra parenthesis after xatx = "n".
Maybe you can try something like that:
png(filename="./TP & TN Plotting/Plots/TN Concentration/Historical TN Concentrations Zoomed to Medians.png",
width=10, height=4, unit="in", res=600)
par(mar=c(5,5,3,1), cex=.75)
tnhistconc<-(boxplot(Conc_ppb[Year!=2009 & Year !=2010]~Year[Year!=2009 & Year !=2010], data=TNhist))
boxplot(Conc_ppb[Year!=2009 & Year !=2010]~Year[Year!=2009 & Year !=2010],
data=TNhist,
ylim=c(0,3000),
xaxt="n", ylab = "", xlab = "",
at=c(1:3,5:8,10:(length(tnhistconc$n)+2)))
axis.break(axis=1,breakpos=c(4),style="slash")
axis.break(axis=1,breakpos=c(9),style="slash")
text(c(1:3,5:8,10:(length(tnhistconc$n)+2)),
-50,
paste("n=",
tnhistconc$n),
cex=0.8)
title(ylab="TN Concentration (ppb)",
xlab="Year",
main=paste("Historical (1998 - 2000), (2005 - 2008) + UMass (2012 -
",max(TNhist$Year),") TN Concentration"))
dev.off()
xatx will remove the x axis (that will control by axis.break. xlab and ylab will remove x and y axis title and they will be set later by title.
Hopefully, it will works
EDIT: Using ggplot2
Your dataframe is actually in a longer format making it easily ready to be plot using ggplot2 in few lines. Here your dataset is named df:
library(ggplot2)
ggplot(df, aes(x = as.factor(Year), y = Conc_ppb))+
geom_boxplot()+
labs(x = "Year", y = "TN Concentration (ppb)",
title = paste("Historical (1998 - 2000), (2005 - 2008) + UMass (2012 -
",max(df$Year),") TN Concentration"))
How to create multiple boxplot with value shown in R ?
Now I'm using this code
boxplot(Data_frame[ ,2] ~ Data_frame[ ,3], )
I tried to use this
boxplot(Data_frame[ ,2] ~ Data_frame[ ,3], )
text(y=fivenum(Data_frame$x), labels =fivenum(Data_frame$x), x=1.25)
But only first boxplot have value. How to show value in all boxplot in one graph.
Thank you so much!
As far as I understand your question (it is not clear how the fivenum summary should be displayed) here is one solution. It presents the summary using the top axis.
x <- data.frame(
Time = c(1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,3,3,3,3,3,3,3,3),
Value = c(5,10,15,20,30,50,70,80,100,5,7,9,11,15,17,19,17,19,100,200,300,400,500,700,1000,200))
boxplot(x$Value ~ x$Time)
fivenums <- aggregate(x$Value, by=list(Time=x$Time), FUN=fivenum)
labels <- apply(fivenums[,-1], 1, function(x) paste(x[-1], collapse = ", "))
axis(3, at=fivenums[,1],labels=labels, las=1, col.axis="red")
Of course you can additionally play with the font size or rotation for this summary. Moreover you can break the line in one place, so the label will have smaller width.
Edit
In order to get what have you posted in the comment below you can add
text(x = 3 + 0.5, y = fivenums[3,-1], labels=fivenums[3,-1])
and you will get
however it won't be readable for other boxplots.
I´m recently trying to analyse my data and want to make the graphs a little nicer but I´m failing at this.
So I have a data set with 144 sites and 5 environmental variables. It´s basically about the substrate composition around an island and the fish abundance. On this island there is supposed to be a difference in the substrate composition between the north and the southside. Right now I am doing a pca and with the biplot function it works quite fine, but I would like to change the plot a bit.
I need one where the sites are just points and not numbered, arrows point to the different variable and the sites are colored according to their location (north or southside). So I tried everything i could find.
Most examples where with the dune data and suggested something like this:
library(vegan)
library(biplot)
data(dune)
mod <- rda(dune, scale = TRUE)
biplot(mod, scaling = 3, type = c("text", "points"))
So according to this I would just need to say text and points and R would label the variables and just make points for the sites. When i do this, however I get the Error:
Error in plot.default(x, type = "n", xlim = xlim, ylim = ylim, col = col[1L], :
formal argument "type" matched by multiple actual arguments
No idea how to get around this.
So next strategy I found, is to make a plot manually like this:
require("vegan")
data(dune, dune.env)
mod <- rda(dune, scale = TRUE)
scl <- 3 ## scaling == 3
colvec <- c("red2", "green4", "mediumblue")
plot(mod, type = "n", scaling = scl)
with(dune.env, points(mod, display = "sites", col = colvec[Use],
scaling = scl, pch = 21, bg = colvec[Use]))
text(mod,display="species", scaling = scl, cex = 0.8, col = "darkcyan")
with(dune.env, legend("bottomright", legend = levels(Use), bty = "n",
col = colvec, pch = 21, pt.bg = colvec))
This works fine so far as well, I get different colors and points, but now the arrows are missing. So I found that this should be corrected easy, if i just put "display="bp"" in the text line. But this doesn´t work either. Everytime I put "bp" R says:
Error in match.arg(display) :
argument "display" is missing, with no default
So I´m kind of desperate now. I looked through all the answers here and I don´t understand why display="bp" and type=c("text","points") is not working for me.
If anyone has an idea i would be super grateful.
https://www.dropbox.com/sh/y8xzq0bs6mus727/AADmasrXxUp6JTTHN5Gr9eufa?dl=0
This is the link to my dropbox folder. It contains my R-script and the csv files. The one named environmentalvariables_Kon1 also contains the data about north and southside.
So yeah...if anyone could help me. That would be awesome. I really don´t know what to do anymore.
Best regards,
Nancy
You can add arrows with arrows(). See the code for vegan:::biplot.rda to see how it works in the original function.
With your plot, add
g <- scores(mod, display = "species")
len <- 1
arrows(0, 0, len * g[, 1], len * g[, 2], length = 0.05, col = "darkcyan")
You might want to adjust the value of len to make the arrows longer
pretty new to R studio and R in general, I have a 3d scattered plot using the library scatterplot3d
The snip of code I have as follows:
s3d <- scatterplot3d(averageTime$Score, averageTime$Status, averageTime$Time, pch=16, highlight.3d=TRUE, type="h", main="3D Scatterplot", ylab="status", xlab= "Score", zlab="Time")
Right now the y axis comes out as 0-5 but I want to fill in custom text to replace it so as opposed to 0 I want the text "NA", 1 I would want "Covered"ect
Ive already tried applying the previous question seen here but to no avail: R: Replace X-axis with own values
please let me know if there is an easier application. Thank you
the answer is:
scatterplot3d(1:10, 1:10, 1:10, y.ticklabs=c("NA", "Covered", "Blah", "blub", "hmpf", "etc."))
According to the docs, microbenchmark:::autoplot "Uses ggplot2 to produce a more legible graph of microbenchmark timings."
Cool! Let's try the example code:
library("ggplot2")
tm <- microbenchmark(rchisq(100, 0),
rchisq(100, 1),
rchisq(100, 2),
rchisq(100, 3),
rchisq(100, 5), times=1000L)
autoplot(tm)
I don't see anything about the...squishy undulations in the documentation, but my best guess from this answer by the function creator is that this is like a smoothed series of boxplots of the time taken to run, with the upper and lower quartiles connected over the body of the shape. Maybe? These plots look too interesting not to find out what is going on here.
What is this a plot of?
The short answer is a violin plot:
It is a box plot with a rotated kernel density plot on each side.
The longer more interesting(?) answer. When you call the autoplot function, you are actually calling
## class(ts) is microbenchmark
autoplot.microbenchmark
We can then inspect the actual function call via
R> getS3method("autoplot", "microbenchmark")
function (object, ..., log = TRUE, y_max = 1.05 * max(object$time))
{
y_min <- 0
object$ntime <- convert_to_unit(object$time, "t")
plt <- ggplot(object, ggplot2::aes_string(x = "expr", y = "ntime"))
## Another ~6 lines or so after this
The key line is + stat_ydensity(). Looking at ?stat_ydensity you
come to the help page on violin plots.