I am trying to plot a volcano plot in R using the plot function and calibrate package in R and am trying to use the textxy function to plot only certain points.
Here is some data:
Metabolites <- data.frame(Metabolite = c("Glucose", "Galactose", "Creatine", "Lactose", "N-Acetylputrescine", "Tyramine", "Adenine", "Glycine", "Erythritol", "Choline"), Neg_pvalue = c(10, 8, 2, 1, 0.5, 0.7, 5, 3, 5.8, 4), LogFC = c(4, -3, 2, -1, 0.5, 0.7, 1, -2, -4, -1), padjust = c(1.453557e-19, 5.312771e-08, 4.983176e-02, 9.585447e-01, 2.449707e-01, 3.058580e-01, 4.223173e-02, 1.002379e-03, 4.466316e-27, 1.003879e-01))
Here is my code:
with(Metabolites, plot(LogFC, Neg_pvalue, pch=20, main="CNL", xlim=c(-5,6)))
with(subset(Metabolites, padjust <.05 ), points(LogFC, Neg_pvalue, pch=20, col="blue"))`
with(subset(Metabolites, padjust <.05 & abs(LogFC) > 2), points(LogFC, Neg_pvalue, ph=20, col="red"))
Now here is the issue:
with(subset(Metabolites, padjust <.05 & abs(LogFC) > 2), textxy(LogFC, Neg_pvalue, labs=Metabolite[1:3], cex=.5, offset = 0.2))`
If I plot this code, I get only the top 3 data points, as is indicated with the labs=Metabolite[1:3] part of the code. Alternatively, if I plot labs=Metabolite, then I get all labels.
If I wanted to plot the labels of only: Glycine, Lactose, and Erythritol as given in the Metabolites$Metabolite, am I able to do this?
Also, say I wanted to keep my top 3 data points labeled (labs=Metabolite[1:3]), but also want to label other metabolites of interest, say Tyramine and N-Acetylputrescine too; how can I do this?
This seems to work by slecting items that are in that set and using those character values as lables:
library(calibrate)
with(subset(Metabolites, Metabolite %in% c( 'Glycine', 'Lactose', 'Erythritol' )),
textxy(LogFC, Neg_pvalue, labs=c( 'Glycine', 'Lactose', 'Erythritol' ), cex=.5, offset = 0.2))
Related
I want to fit my points with logarithmic curve. Here is my data which contains x and y. I desire to plot x and y and the add a logarithmic fitting curve.
x<-structure(list(X2.y = c(39.99724745, 29.55541525, 23.39578201,
15.46797044, 10.52063652, 7.296161198, 6.232038434, 4.811851132,
4.641281547, 4.198523289, 3.325515839, 2.596563723, 1.894902523,
1.556380314), X5.y = c(62.76037622, 48.54726084, 37.71302646,
24.93942365, 17.71060023, 13.31130267, 10.36341862, 7.706914722,
7.170517624, 6.294292013, 4.917428837, 3.767836298, 2.891519878,
2.280974128), X10.y = c(77.83154815, 61.12151516, 47.19228808,
31.21034981, 22.47098182, 17.29384973, 13.09875178, 9.623698726,
8.845091983, 7.681873268, 5.971413758, 4.543320659, 3.551367285,
2.760718282), X25.y = c(96.87401383, 77.00911883, 59.16936025,
39.13368164, 28.48573658, 22.32580849, 16.55485248, 12.0455604,
10.96092113, 9.435085861, 7.303126501, 5.523147205, 4.385086234,
3.366876291), X50.y = c(111.0008027, 88.79545082, 68.05463659,
45.01166182, 32.94782526, 26.05880295, 19.11878542, 13.84223574,
12.53056405, 10.73571912, 8.291067088, 6.25003851, 5.003586577,
3.81655893), X100.y = c(125.0232816, 100.4947544, 76.87430545,
50.84623991, 37.37696657, 29.76423356, 21.66378667, 15.6256447,
14.08861698, 12.0267487, 9.271712877, 6.971562563, 5.61752001,
4.262921183)), class = "data.frame", row.names = c(NA, -14L))
I tried this:
single_idf<-function(x) {
idf<-x
durations = c(5/60, 10/60, 15/60, 30/60, 1, 2, 3, 4, 5, 6, 8, 12, 18, 24)
nd = length(durations)
Tp = c(2, 5, 10, 25, 50, 100)
nTp = length(Tp)
psym = seq(1, nTp)
# open new window for this graph, set plotting parameters for a single graph panel
windows()
par(mfrow = c(1,1), mar = c(5, 5, 5, 5), cex = 1)
# set up custom axis labels and grid line locations
ytick = c(1,2,3,4,5,6,7,8,9,10,20,30,40,50,60,70,80,90,100,
200,300,400,500,600,700,800,900,1000,1100,1200,1300,1400)
yticklab = as.character(ytick)
xgrid = c(5,6,7,8,9,10,15,20,30,40,50,60,120,180,240,300,360,
420,480,540,600,660,720,840,960,1080,1200,1320,1440)
xtick = c(5,10,15,20,30,60,120,180,240,300,360,480,720,1080,1440)
xticklab = c("5","10","15","20","30","60","2","3","4","5","6","8","12","18","24")
ymax1 = max(idf)
durations = durations*60
plot(durations, col=c("#FF00FF") ,lwd=c(1), idf[, 1],
xaxt="n",yaxt="n",
pch = psym[1], log = "xy",
xlim = c(4, 24*60), ylim = range(c(1,idf+150)),
xlab = "(min) Duration (hr)",
ylab = "Intensity (mm/hr)"
)
for (iT in 2:nTp) {
points(durations, idf[, iT], pch = psym[iT], col="#FF00FF",lwd=1)
}
for (iT in 1:nTp) {
mod.lm = lm(log10(idf[, iT]) ~ log10(durations))
b0 = mod.lm$coef[1]
b1 = mod.lm$coef[2]
yfit = log(10^(b0 + b1*log10(durations)))
lines(durations,col=c("#FF00FF"),yfit, lty = psym[iT],lwd=1)
}
}
But when I run this, the curves stands far away from the points. I want to see curves over the points. How can I arrange this?
single_idf(x)
Consider this as an option for you using ggplot2 and dplyr. Also added method='lm' to match OP expected output (Many thanks and credits to #AllanCameron for his magnificent advice):
library(ggplot2)
library(dplyr)
#Data
df <- data.frame(x,y)
#Plot
df %>%
pivot_longer(-y) %>%
ggplot(aes(x=log(y),y=log(value),color=name,group=name))+
geom_point()+
stat_smooth(geom = 'line',method = 'lm')
Output:
The main problem is that you were plotting the natural log of the fit rather than the fit itself.
If you change the line
yfit = log(10^(b0 + b1*log10(durations)))
To
yfit = 10^(b0 + b1*log10(durations))
And rerun your code, you get
I want to make the fontsize of the y-axis labels adjustable to the input data size on the y-axis like in Fig. 3, in contrast to the current situation in Fig. 1-2 where labels are not next to the corresponding lines.
Code
library("corrgram")
# https://stackoverflow.com/a/40387233/54964
ids <- seq(1,18)
x_at <- seq(0.075, 0.925, length.out = length(ids))
y_at <- seq(0.075, 0.91, length.out = length(ids))
createLabels <- function(xlab, ylab, x_labels, y_labels){
ids <- y_labels # assume here
x_at <- seq(0.075, 0.925, length.out = length(ids))
y_at <- seq(0.075, 0.91, length.out = length(ids))
mtext(xlab, side = 1, line = 4)
mtext(ylab, side = 2, line = 3)
axis(1, at=x_at, labels=x_labels, line = 1.5, tick=F, cex.axis=.7)
axis(2, at=y_at, labels=y_labels, line = 1, tick=F, cex.axis=.7, las=1) # horizontal y-axis labels; rawr
}
corrgram(baseball,main="Baseball data PC2/PC1 order")
createLabels(xlab="Patient 1 ID", ylab="Patient 2 ID", x_labels=ids, y_labels=ids)
Fig. 1 Output with the limited test data baseball,
Fig. 2 Output with the real case,
Fig. 3 Expected output
Expected output: automatically adjustable label font size to the input data size on the y-axis; example of the output created by makeMatrixPlot(list, ids, title) found here in Fig. 3
Testing Istrel's answer with big data set where long IDs
Complete code here which visualises correctly but gives backside strange outputs an NULLs, here some key points about optimised parameters
# https://stackoverflow.com/a/40485734/54964
cex_lab<-0.9 # little smaller fontsize for matrix >= 20x20
oma<-c(4, 4, 6, 4)
gap<-0
las<-2 # both axis labels always perpendicular
Output complications as the warning and many NULLs
In max(l.wid) : no non-missing arguments to max; returning -Inf
[[1]]
[[1]][[1]]
NULL
...
[[1]][[7]]
NULL
[[2]]
[[2]][[1]]
NULL
...
[[2]][[7]]
NULL
[[3]]
[[3]][[1]]
NULL
...
[[3]][[7]]
NULL
Call it for instance by
library("corrplot")
library("psych")
ids <- seq(1,11)
M.cor <- cor(mtcars)
colnames(M.cor) <- ids
rownames(M.cor) <- ids
p.mat <- psych::corr.test(M.cor, adjust = "none", ci = F)
p.mat <- p.mat[["r"]]
corrplot(M.cor,
method = "color",
type = "upper",
tl.col = 'black',
diag = TRUE,
p.mat = p.mat,
sig.level = 0.0000005
)
createLabels(xlab="Patient 1 ID", ylab="Patient 2 ID and Ages", x_labels=ids, y_labels="")
R: 3.3.1
Used graphic objects: corrplot, corrgram, ...
OS: Debian 8.5
Corrgram uses mfrow from par() for squares drawing. We can use that for labeling. The number of labels should be equal to the number of columns in the matrix. If you set oma or gap arguments in corrgram function, you have to specify same parameters in createLabels function.
BTW, if you use corrgram without main argument, you will need oma=c(4,4,4,4) in createLabels
createLabels <- function(xlab, ylab, x_labels, y_labels,
cex_lab=1.3, oma=c(4, 4, 6, 4), gap=0, las=0){
# oma and gap args same as in corrgram
nc <- length(x_labels) # get number of columns
# Inititate mfrow partition as in corrgram
opar <- par(mfrow = c(nc, nc), mar = rep.int(gap/2, 4), oma = oma) #save old par parameters
# Create matrix of outer cells indexes and positions
left_side <- matrix(c(nc:1, rep(1, nc), rep(2, nc)), nc)
bottom_side <- matrix(c(rep(nc, nc), 1:nc, rep(1, nc)), nc)
sides <- rbind(left_side, bottom_side)
# Dublicate labels vector
labels <- c(y_labels, x_labels)
# Loop over each outer cell
for (i in c(1:(nc*2))){
cell_ind <- sides[i, ]
par(mfg=c(cell_ind[1], cell_ind[2], nc, nc)) # set current plotting cell
usr<-par("usr")
clip(usr[1], -2, usr[3], usr[4]) # alter clipping region
axis(cell_ind[3], at=0.5, labels=labels[i],
outer=TRUE, xpd=NA, lwd=NA, mgp=c(3,0,0.2), cex.axis=cex_lab, las=las)
}
# Add labels
par(opar)
mtext(xlab, side = 1, line = -1.5, outer=TRUE, xpd=NA)
mtext(ylab, side = 2, line = -1.5, outer=TRUE, xpd=NA)
}
corrgram(baseball,main="Baseball data PC2/PC1 order")
createLabels(xlab="Patient 1 ID", ylab="Patient 2 ID", 1:18, 1:18)
The corrgram package has been updated (version 1.11) with better support for labels along the axes. I've used the basic idea from Leo and added it to the package. For example:
require(corrgram)
labs=colnames(state.x77)
corrgram(state.x77, oma=c(7, 7, 2, 2),
outer.labels=list(bottom=list(labels=labs,cex=1.5,srt=60),
left=list(labels=labs,cex=1.5,srt=30)))
mtext("Bottom", side=1, cex=2, line = -1.5, outer=TRUE, xpd=NA)
mtext("Left", side=2, cex=2, line = -1.5, outer=TRUE, xpd=NA)
I'm using boxplot() in R. My code is:
#rm(list=ls())
#B2
fps_error <- c(0.058404273, 0.028957446, 0.026276044, 0.07084294, 0.078438563, 0.024000178, 0.120678965, 0.081774358, 0.025644741, 0.02931614)
fps_error = fps_error *100
fps_qp_error <-c(1.833333333, 1.69047619, 1.666666667, 3.095238095, 2.738095238, 1.714285714, 3.634146341, 5.142857143, 1.238095238, 2.30952381)
bit_error <- c(0.141691737, 0.136173785, 0.073808209, 0.025057931, 0.165722097, 0.004276999, 0.365353752, 0.164757488, 0.003362543, 0.022423845)
bit_error = bit_error *100
bit_qp_error <-c(0.666666667, 0.785714286, 0.428571429, 0.142857143, 0.785714286, 0.023809524, 1.523809524, 0.976190476, 0.023809524, 0.142857143)
ssim_error <-c(0.01193773, 0.015151569, 0.003144532, 0.003182908, 0.008125274, 0.013796366, 0.00359078, 0.019002591, 0.005031524, 0.004370175)
ssim_error = ssim_error * 100
ssim_qp_error <-c(3.833333333, 1.80952381, 0.69047619, 0.571428571, 2, 1.904761905, 0.761904762, 2.119047619, 0.857142857, 0.976190476)
all_errors = cbind(fps_error, bit_error, ssim_error)
all_qp_errors = cbind(fps_qp_error, bit_qp_error, ssim_qp_error)
modes = cbind(rep("FPS error",10), rep("Bitrate error",10), rep("SSIM error",10))
journal_linear_data <-data.frame(fps_error, fps_qp_error,bit_error,bit_qp_error,ssim_error,ssim_qp_error )
yvars <- c("fps_error","bit_error","ssim_error")
yvars_qp <-c("fps_qp_error","bit_qp_error","ssim_qp_error")
xvars <- c("FPS", "Bitrate", "SSIM")
graphics.off()
bmp(filename="boxplot_B2_error.bmp")
op <- par(mfrow = c(1, 3), #matrix of plots
oma = c(0,0,2,0),mar=c(5.1, 7.1, 2.1, 2.1),mgp=c(4,1,0)) #outer margins
par(cex.lab=3)
par(cex.axis=3)
for (i in 1:3) {boxplot(journal_linear_data[,yvars[i]], xlab=xvars[i], ylab="Percentage error", outcex = 2)}
par(op)
mtext(text="Percentage error per mode for B2",side=3, line=1.5, font=2, cex=2,adj=0.95, col='black')
dev.off()
The image output is shown below. As you can see the y-axis does not have the same range for all graphs. How can I fix this? For example starting in 0.5 or 0.
You can simply put an ylim = c(0, 5) in all your boxplot() call. This sets y-axis range (roughly) between 0 and 5.
Perhaps you did not see ylim argument in ?boxplot; the "Arguments" section also does not mention it. But ylim is just a trivial graphical parameter passed via "...". You can also find such example in the "Examples" session of ?boxplot:
boxplot(len ~ dose, data = ToothGrowth,
boxwex = 0.25, at = 1:3 - 0.2,
subset = supp == "VC", col = "yellow",
main = "Guinea Pigs' Tooth Growth",
xlab = "Vitamin C dose mg",
ylab = "tooth length",
xlim = c(0.5, 3.5), ylim = c(0, 35), yaxs = "i")
I am learning latex graphics. I generated latex graphs with standalone, but I am trying to generate R plots with latex fonts. Through online tutorials, here is my code with the Iris dataset in RStudio (I modified example code to get it working. Once I know how to fix the frame, I can study the code in more details):
library(tikzDevice)
options(tikzMetricPackages = c("\\usepackage[utf8]{inputenc}",
"\\usepackage[T1]{fontenc}", "\\usetikzlibrary{calc}",
"\\usepackage{amssymb}"))
## I need the amssymb package because I use \mathcal and \mathbb
tikz("formula.tex", width = 4, height = 4, standAlone = TRUE,
packages = c("\\usepackage{tikz}",
"\\usepackage[active,tightpage,psfixbb]{preview}",
"\\PreviewEnvironment{pgfpicture}",
"\\setlength\\PreviewBorder{0pt}",
"\\usepackage{amssymb}"))
par(mar = c(4, 4, 0.1, 0.1), mgp = c(2, 0.9, 0))
library(tikzDevice)
options(tikzMetricPackages = c("\\usepackage[utf8]{inputenc}",
"\\usepackage[T1]{fontenc}", "\\usetikzlibrary{calc}",
"\\usepackage{amssymb}"))
## I need the amssymb package because I use \mathcal and \mathbb
tikz("formula.tex", width = 4, height = 4, standAlone = TRUE,
packages = c("\\usepackage{tikz}",
"\\usepackage[active,tightpage,psfixbb]{preview}",
"\\PreviewEnvironment{pgfpicture}",
"\\setlength\\PreviewBorder{0pt}",
"\\usepackage{amssymb}"))
par(mar = c(4, 4, 0.1, 0.1), mgp = c(2, 0.9, 0))
plot(iris$Sepal.Length, iris$Sepal.Width, main="Iris sepal length vs width measurements", xlab="Length", ylab="Width")
dev.off()
tools::texi2pdf("formula.tex")
system(paste(getOption("pdfviewer"), "formula.pdf"))
Which gives me:
I would like to have a bit more white space on the right, so the 8 comes fully, and fix the title. The inner picture should be smaller and the title lower as well, if possible.
Sorry for this. I looked at the code and figured it out! I needed to remove
par(mar = c(4, 4, 0.1, 0.1), mgp = c(2, 0.9, 0))
which gives me:
So it works!!! :D
I want to place 2 sets of y-axis labels on the graph I created using levelplot function from lattice library at R. I was able to get two sets of labels to show but they are overlapping. Below please see a minimum example. I also tried a few options at par.settings such as ylab.axis.padding and axis.components padding, but nothing seemed to change the superimposition of 2 y-labels. Perhaps they have been overwritten somehow? Any ideas will be appreciated.
My example codes :
A = matrix( c(3, 1, 0, 1, 2, 3, 1, 0,
rep(1,4), 2, 0, 1), nrow=3, ncol=5, byrow = TRUE)
colnames(A)= c("XXX5", "XXX4", "XXX3", "XXX2", "XXX1")
axis.build=function(side,...){
if(side == "left"){
panel.axis(side=side, outside=TRUE, at=1:5,tck=0,
text.col="black", labels=colnames(A), text.cex=0.5)
panel.axis(side=side, outside=TRUE, at=1:5,tck=0,
text.col="brown", labels=seq(ncol(A)), text.cex=0.9 )
} else axis.default(side=side, ...)
}
levelplot(A, aspect="iso", shrink = c(0.8, 0.8),
scales= list(x=list(draw=F),cex=0.5, font=2),
axis=axis.build,, xlab= NULL, ylab=NULL,
col.regions=c("black", "orange", "red","purple"),
at=c(-1, 0, 1, 2, 3), colorkey = FALSE,
par.settings = list(axis.line=list(col="transparent"),
axis.components=list(bottom=list(pad1=1, pad2=3)) ))
I think I have found the solution. In case anyone interested : I changed the first tck=0 to tck=2, and added line.col= "transparent", thus two left axis are stacked next to each other. Voila ! However, I can't seem to find where the documentation is for using pad1 and pad2 parameters. Any suggestion?