I have generated this plot in R with some strange numbers format in the x-axis:
enter image description here
I want to have in the x-axis the numbers in the format (ax) as 2^6, 6^6, 10^6. this would simplify the x-axis to get data in all points. Please do you have any suggestions?
Here my code :
data=read.csv("my_file.csv",row.names = 1)
plot(genes~Prot,cex=1.5,data, function(x) 10^x, xlab="Proteome
size(codons)",ylim=c(0,30), ylab="Genes in pathway")
abline(lm(prot~genes,data),lty=2, lwd=3,col="black")
Use xaxt = 'n' as an argument to plot to turn off the x-axis labelling. Then use the Axis function to set tick marks and label as required.
# Generating some data
power <- seq(1, 6, length.out = 20)
Prot = 10^power
genes <- runif(20, min = 5, max = 30)
# plotting
plot(x= Prot, y= genes, cex=1.5, xlab="Proteome size(codons)", ylab="Genes in pathway", xaxt = 'n', log = 'xy')
Axis(at = c(2^6, 6^6, 10^6), side = 1, labels = c('2^6', '6^6', '10^6'), las = 1)
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),]
I am trying to plot a chunk size in relation to run time with the different chunk sizes on the x-axis being 1000, 10000, 100000, and 1000000. However, when I create the plot using the plot() and axis commands.
plot(chunk, totTime, main="Runtime with Different Chunks", xaxt = "n",ylim = c(4,5),ylab="Runtime (sec)", xlab = "Size of Chunk", type="l")
axis(side = 1, c(1000,10000,100000,1000000))
I get a plot that looks like this.
I've tried axp in plot() and at in the axis function but it still has the same spacing. So, I wonder if there was a way to change how the graph spaces the data in the plot so the graph will look cleaner.
Try converting to the log scale but labeling your x-axis according to the set values you want (here, xvalues). This will put equal spacing between orders of magnitude:
# Sample data
totTime <- c(4.4, 4.01, 4.01, 4.8)
chunk <- c(1000, 10000, 100000, 1000000)
# Values desired on the x-asis
xvalues <- c(1000, 10000, 100000, 1000000)
# Plot
plot(
log(chunk), # note the log scale
totTime,
main = "Runtime with Different Chunks",
xaxt = "n",
ylim = c(4, 5),
ylab = "Runtime (sec)",
xlab = "Size of Chunk",
type = "l"
)
axis(side = 1,
at = log(xvalues), # note the log scale
label = xvalues)
Output:
I want to create a figure where for various reasons I need to specify the axis labels myself. But when I specify my labels (some have one digit, some two digits) R suppresses every other two-digit label because it decides there isn't enough room to show them all, but it leaves all of the one-digit labels, leaving the axis looking lopsided.
Is there a way to suppress labels consistently across the whole axis, based on whether any of them need to be skipped? Note: I have a lot of plots with varying scales, so I was looking for something I could use for all of them - I don't want to render all the labels for every plot, or to skip every other label in every plot. Suppressing labels will be desirable for some plots and not for others. I just want to skip every other label consistently, if that's what R chooses to do for the particular plot.
(Here is an example figure of what I mean. What I want is for the "6%" label to also be suppressed in the x axis.)
Example code:
library(labeling)
df <- data.frame("estimate" = c(9.81, 14.29, 12.94),
"lower" = c(4.54, 6.25, 5.12),
"upper" = c(12.85, 20.12, 15.84))
ticks <- extended(min(df$lower), max(df$upper), m = 5, only.loose = TRUE,
Q=c(2, 5, 10))
png("examplePlot.png", width = 1200, height = 900, pointsize = 10, res = 300)
bars <- barplot(df$estimate, horiz = TRUE, col = "white", border = NA,
xlim = c(min(ticks), max(ticks)), xaxt = "n", main = "Example")
arrows(df$lower, bars, df$upper, bars, code = 3, angle = 90, length = 0.03)
points(df$estimate, bars, pch = 20)
tickLabels <- paste(ticks, "%", sep = "")
axis(1, at=ticks, labels = tickLabels, cex.axis=1)
axis(2, at = bars, labels = c("c", "b", "a"), lwd = 0, las = 2)
dev.off()
This depends on the size of the plot, so you'll have to plot each label separately:
axis(1, lwd.ticks = 1, labels = FALSE, at = ticks) # plot line and ticks
i <- seq(1,length(ticks),2) # which labels to plot
for(ii in i)
axis(1, at = ticks[ii], labels = tickLabels[ii], cex.axis = 1, lwd = 0)
I know there are strong opinions about mixing plot types in the same figures, especially if there are two y axes involved. However, this is a situation in which I have no alternative - I need to create a figure using R that follows a standard format - a histogram on one axis (case counts), and a superimposed line graph showing an unrelated rate on an independent axis.
The best I have been able to do is stacked ggplot2 facets, but this is not as easy to interpret for the purposes of this analysis as the combined figure. The people reviewing this output will need it in the format they are used to.
I'm attaching an example below.
Any ideas?
For etiquette purposes, sample data below:
y1<-sample(0:1000,20,rep=TRUE)
y2<-sample(0:100,20,rep=TRUE)
x<-1981:2000
I feel your pain - have had to recreate plots before. even did it in SAS once
if it's a once off, I'm be tempted to go old-school. something like this:
# Generate some data
someData <- data.frame(Year = 1987:2009,
mCases = rpois(23, 3),
pVac = sample(55:80, 23, T))
par(mar = c(5, 5, 5, 5))
with(someData, {
# Generate the barplot
BP <- barplot(mCases, ylim = c(0, 18), names = Year,
yaxt = "n", xlab = "", ylab = "Measles cases in Thousands")
axis(side = 2, at = 2*1:9, las = 1)
box()
# Add the % Vaccinated
par(new = T)
plot(BP, pVac, type = "l", ylim = c(0, 100), axes = F, ylab = "", xlab = "")
axis(side = 4, las = 1)
nudge <- ifelse(pVac > median(pVac), 2, -2)
text(BP, pVac + nudge, pVac)
mtext(side = 4, "% Vaccinated", line = 3)
par(new = F)
})
Try library(plotrix)
library(plotrix)
## Create sample data
y2<-sample(0:80,20,rep=TRUE)
x2<-sort(sample(1980:2010,20,rep=F))
y1<-sample(0:18,20,rep=TRUE)
x1<-sort(sample(1980:2010,20,rep=F))
x<-1980:2010
twoord.plot(x1,y1,x2,y2,
lylim=c(0,18),rylim=c(0,100),type=c("bar","l"),
ylab="Measles Cases in thousands",rylab="% Vaccinated",
lytickpos=seq(0,18,by=2),rytickpos=seq(0,100,by=10),ylab.at=9,rylab.at=50,
lcol=3,rcol=4)
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)