I have 2 groups of data (top and bottom) that I have been able to make boxplots for separately, but cannot get them to show in the same graph. I want them side by side for comparison for each gene tested (12 total). So, I would like to have the x-axis labeled with the gene tested, and the y-axis with the ddCt values, with 2 boxplots (1 for the top, 1 for the bottom) for each gene. I have the code for each one separately that works below:
# boxplot of first group
boxplot(Top25[-1], main = "Top Performers Gene Expression Relative to 16S", ylab = "ddCt Values", xlab = "Biofilm Gene", cex.axis = 0.75)
# boxplot of second group
boxplot(Bottom25 [-1], main = "Bottom Performers Biofilm Gene Expression Relative to 16S", ylab = "ddCt Values", xlab = "Biofilm Gene", cex.axis = 0.75)
Any suggestions for what I may try? I've tried to "melt" them together following another ggplot2 question and got an error saying "object melt was not found". Thanks for any help!
Here is an example. The main idea is to use add = TRUE to add boxplot to an existing plot and specify the horizontal position of boxplot with at
#DATA
set.seed(42)
top = rnorm(40)
bottom = rnorm(40)
#Create Empty Plot
plot(1, 1, type = "n", xlim = c(0, 3), ylim = range(c(top, bottom)),
ann = FALSE, xaxt = "n")
#Add boxplots to existing plot
boxplot(x = top, at = 1, add = TRUE)
boxplot(x = bottom, at = 2, add = TRUE)
axis(1, at = c(1, 2), labels = c("top", "bottom"))
You can do this:
Top25 <- data.frame(gene=1:40, exp=rnorm(40, 2))
Bottom25 <- data.frame(gene=41:80, exp=rnorm(40, -2))
boxplot(list(Top25[, -1], Bottom25[, -1]), names=c("Top25", "Bottom25"))
Related
I need to map my Erosion values for different levels of tillage (colomns) with three levels of soil depth (rows (A1, A2, A3)). I want all of this to be shown as a barchart in a single plot.
Here is a reproducible example:
a<- matrix(c(1:36), byrow = T, ncol = 4)
rownames(a)<-(c("A1","B1","C1","A2","B2","C2","A3","B3","C3"))
colnames(a)<-(c("Int_till", "Redu_till", "mulch_till", "no_till"))
barplot(a[1,], xlab = "A1", ylab = "Erosion")
barplot(a[4,], xlab = "A2", ylab = "Erosion")
barplot(a[7,], xlab = "A3", ylab = "Erosion")
##I want these three barchart side by side in a single plot
## for comparison
### and need similar plots for all the "Bs" and "Cs"
### Lastly, i want these three plots in the same page.
I have seen people do similar things using "fill" in ggplot (for lines) and specifying the factor which nicely separates the chart for different categories but I tried doing it but always run into error maybe because my data is continuous.
If any body could help me with these two things.. It will be a great help. I will appreciate it.
Thank you!
We can use ggplot
library(reshape2)
library(ggplot2)
library(dplyr)
melt(a) %>%
ggplot(., aes(x = Var2, y = value, fill = Var1)) +
geom_bar(stat = 'identity',
position = position_dodge2(preserve = "single")) +
facet_wrap(~ Var1)
Set mfcol to specify a 3x3 grid and then for each row generate its bar plot. Also, you could consider adding the barplot argument ylim = c(0, max(a)) so that all graphs use the same Y axis. title and mtext can be used to set the overall title and various margin text as we do below. See ?par, ?title and ?mtext for more information.
opar <- par(mfcol = c(3, 3), oma = c(0, 3, 0, 0))
for(r in rownames(a)) barplot(a[r, ], xlab = r, ylab = "Erosion")
par(opar)
title("My Plots", outer = TRUE, line = -1)
mtext(LETTERS[1:3], side = 2, outer = TRUE, line = -1,
at = c(0.85, 0.5, 0.17), las = 2)
I have built two graphs in one (two different y axis but plotting on the same graph). I want to show the connection between the values on the left and the values on the right (Do they stay consistently > 0 or <0 or change?)
Now what I need is to link the two sides of the graph with a line to see if it decreases/increases. So I want a corresponding dot on the left to be linked to the corresponding dot on the right by a line.
But because the y axis values on the left and the right are different, I am not figuring out how this can work.
Here is my code to build the graph:
## Plot first set of data and draw its axis
plot(rep(1, length(DEG)), DEG, xlim = c(0,4), xaxt = "n",
ylim = c(-5, 5), col = "black", xlab = "", ylab = "")
axis(1, at = c(1))
## Allow a second plot on the same graph
par(new = TRUE)
## Plot the second plot and put axis scale on right
plot(rep(3, length(DMG)), DMG, axes = F, xlim = c(0, 4), xaxt = "n",
ylim = c(-80, 80), col = "black", xlab = "", ylab = "")
axis(1, at = c(3)))
axis(side = 4)
abline(h = 0, col = "red")
Does anyone have an idea? I tried the basic line:
lines(x$DEG[x$Genes == "FEX_0000936"], x$DMG[x$Genes == "FEX_0000936"],
type="o", pch=22, col="seagreen3")
Here is my graph perhaps it is clearer when seeing it:
Thanks for your help.
This question already has answers here:
How can I plot with 2 different y-axes?
(6 answers)
Closed 6 years ago.
i'm having troubles in a multi axis barplot. I have an X,Y axis with bars and dots in the same graph. The point is that I have to shown both of them in different scales
While I can shown both (bars and dots) correctly, the problem comes when I try to set different scales in left and right axis. I dont know how to change the aditional axis scale, and how to bind the red dots to the right axis, and the bars to the left one.
This is my code and what I get:
labels <- value
mp <- barplot(height = churn, main = title, ylab = "% churn", space = 0, ylim = c(0,5))
text(mp, par("usr")[3], labels = labels, srt = 45, adj = c(1.1,1.1), xpd = TRUE, cex=.9)
# Population dots
points(popul, col="red", bg="red", pch=21, cex=1.5)
# Churn Mean
media <- mean(churn)
abline(h=media, col = "black", lty=2)
# Population scale
axis(side = 4, col= "red")
ylim= c(0,50)
ylim= c(0,5)
What I want is to have left(grey) axis at ylim=c(0,5) with the bars bound to that axis. And the right(red) axis at ylim=c(0,50) with the dots bound to that axis...
The goal is to represent bars and points in the same graph with diferent axis.
Hope I explained myself succesfully.
Thanks for your assistance!
Here is a toy example. The only "trick" is to store the x locations of the bar centers and the limits of the x axis when creating the barplot, so that you can overlay a plot with the same x axis and add your points over the centers of the bars. The xaxs = "i" in the call to plot.window indicates to use the exact values given rather than expanding by a constant (the default behavior).
set.seed(1234)
dat1 <- sample(10, 5)
dat2 <- sample(50, 5)
par(mar = c(2, 4, 2, 4))
cntrs <- barplot(dat1)
xlim0 <- par()$usr[1:2]
par(new = TRUE)
plot.new()
plot.window(xlim = xlim0, ylim = c(0, 50), xaxs = "i")
points(dat2 ~ cntrs, col = "darkred")
axis(side = 4, col = "darkred")
I'd like to make a histogram of my variable "sex" with the values 1 = male and 2 = female. My code works properly, but I'd like to have only the values 1 and 2 on the x-axis (at the moment R prints all values between 0 and 1 in steps which makes less sense in the case of sex).
hist(g1_sex,
main = "Häufigkeitsverteilung Geschlecht",
sub = "1 = männlich, 2 = weiblich",
xlab = "Geschlecht",
ylab ="Häufigkeit",
ylim = c(0,120),
col = "lightblue",
labels = TRUE,
breaks=2)
I already tried to do it with
breaks = seq (1,2,1)
but this doesn't look nice too.
I would be very thankful for every hint of you!
Best wishes!
I think you really want barplot. See examples:
set.seed(0); x <- rbinom(500, 1, 0.3) ## generate toy 0-1 data
y <- table(x) ## make contingency table
names(y) <- c("male", "female")
ylim = c(0, 1.2 * max(y)) ## set plotting range
z <- barplot(y, space = 0, col = 5, main = "statistics", ylim = ylim)
text(z, y + 20, y, cex = 2, col = 5) ## add count number above each bar
I have also give solutions to add number above each bar, by setting extra space on the top using ylim, and use text to put texts.
Note that barplot also accepts main, etc, so you can add other annotations if you want.
I have a some data that I want to display graphically. Here's what it looks like:
data<- c(0.119197746, 0.054207788, 0.895580411, 0.64861727, 0.143249592,
0.284314897, 0.070027632, 0.297172433, 0.183569184, 0.713896071,
1.942425326, 1)
Using this command:
barplot(data, main="Ratio of Lipidated and Unlipidated LC3 I & II forms\nNormalized
to GAPDH", names.arg = c("PT250", "PT219", "PT165", "PT218", "PT244", "PT253", "PT279", "PT281",
"PT240", "PT262", "PT264", "CCD"), ylab = "Fold LC3 II/LC3I/GAPDH")
I produced this graph:
I would like to position the X-axis at 1 so that all values less-than-one will appear as down bars. I could achieve the desired affect by simply subtracting 1 from all of the values and plotting again but this would cause the numbers on the y-axis to be inaccurate. Is there some way to get R to plot values less than 1 as down bars?
Solution with custom axis.
barplot(data - 1, main="Ratio of Lipidated and Unlipidated LC3 I & II forms\nNormalized
to GAPDH", names.arg = c("PT250", "PT219", "PT165", "PT218", "PT244", "PT253", "PT279", "PT281",
"PT240", "PT262", "PT264", "CCD"), ylab = "Fold LC3 II/LC3I/GAPDH",
axes = F, ylim = c(-1, 1)
my_labs <- seq(-1, 1, by = 0.5)
axis(side = 2, at = my_labs, labels = my_labs + 1)