I'd like to use facet_zoom but for some reason the zoomed area results empty.
The two data sets I use are just numeric vectors of 1.000.000 numbers generated from a modified polynomial distribution. In the zoomed area there is a small spike that I'd like to show.
prova <-readRDS("probcond1.rds")
prova1 <-readRDS("probpoly.rds")
dfGamma <-data.frame(prova)
ggplot(dfGamma, aes(x=prova)) + stat_density(aes(y=..count..), color="black", fill="blue", alpha=0.3)
g <- ggplot(dfGamma, aes(x=prova)) +
stat_density(aes(y=..count..), color="black", fill="blue", alpha=0.3) +
scale_x_continuous(breaks=c(0,1,2,3,4,5,10,30,100,300,1000,4000,5000), trans="log1p", expand=c(0,0)) +
theme_bw()
g+expand_limits(x = c(1, 6000)) +facet_zoom(xlim = c(4000,5000))
I'm really new to R. sorry for my ignorance
Your axis is on a log1p scale, so your xlim should be wrapped inside log1p to do a zoom. You can do as follows:
g+expand_limits(x = c(1, 6000)) +facet_zoom(xlim = c(log1p(4000),log1p(5000)))
Here is a sample using the mtcars dataset.
library(ggplot2)
library(ggforce)
g <- ggplot(mtcars, aes(x=hp)) +
stat_density(aes(y=..count..), color="black", fill="blue", alpha=0.3) +
scale_x_continuous(breaks=c(0,1,2,3,4,5,10,30,100,300), trans="log1p", expand=c(0,0)) +
theme_bw()
If you use facet_zoom(xlim = c(100,300)) as follows will produce empty zoom output (flat values of 100 and 300 don't exist on the g's x-axis):
g+expand_limits(x = c(1, 300)) +facet_zoom(xlim = c(100,300))
Output-1 (flat value zoom)
If you transform the xlim using log1p, you can zoom on the corresponding values of the x-axis of plot g. You can do that as follows:
g+expand_limits(x = c(1, 300)) +facet_zoom(xlim = c(log1p(100),log1p(300)))
Output-2 (log1p zoom)
If you want to zoom in the axis independently, you can do as follows:
g+expand_limits(x = c(1, 300)) +facet_zoom(xlim = c(log1p(100),log1p(300)), ylim = c(5,10), split = TRUE)
Output
As you can see I did zoom the ylim between 5 and 10 and the split = TRUE makes the zoom independent and you can have multiple views of the zoom axis or if you just want one view, you can leave the split to its default value FALSE. The manual has a lot more information which you might want to consult, just in case it is available at Package ‘ggforce’
Hope that helps.
Related
I am pretty sure that this is easy to do but I can't seem to find a proper way to query this question into google or stack, so here we are:
I have a plot made in ggplot2 which makes use of geom_jitter(), efficiently creating one row for each element in a factor and plotting its values.
I would like to add a complementary geom_violin() to the plot, but just adding the extra geom_ function to the plot code returns two layers: the jitter and the violin, one on top of the other (as usually expected).
EDIT:
This is how the plot looks like:
How can I have the violin as a separate row, without generating a second plot?
Side quest: how I can I have the jitter and the violin geoms interleaved? (i.e. element A jitter row followed by element A violin row, and then element B jitter row followed by element B violin row)
This is the minimum required code to make it (without all the theme() embellishments):
P1 <- ggplot(data=TEST_STACK_SUB, aes(x=E, y=C, col=A)) +
theme(... , aspect.ratio=0.3) +
geom_point(position = position_jitter(w = 0.30, h = 0), alpha=0.2, size=0.5) +
geom_violin(data=TEST_STACK_SUB, mapping=aes(x=E, y=C), position="dodge") +
scale_x_discrete() +
scale_y_continuous(limits=c(0,1), breaks=seq(0,1,0.1),
labels=c(seq(0,1,0.1))) +
scale_color_gradient2(breaks=seq(0,100,20),
limits=c(0,100),
low="green3",
high="darkorchid4",
midpoint=50,
name="") +
coord_flip()
options(repr.plot.width=8, repr.plot.height=2)
plot(P1)
Here is a subset of the data to generate it (for you to try):
data
How about manipulating your factor as a continuous variable and nudging the entries across the aes() calls like so:
library(dplyr)
library(ggplot2)
set.seed(42)
tibble(x = rep(c(1, 3), each = 10),
y = c(rnorm(10, 2), rnorm(10))) -> plot_data
ggplot(plot_data) +
geom_jitter(aes(x = x - 0.5, y = y), width = 0.25) +
geom_violin(aes(x = x + 0.5, y = y, group = x), width = 0.5) +
coord_flip() +
labs(x = "x") +
scale_x_continuous(breaks = c(1, 3),
labels = paste("Level", 1:2),
trans = scales::reverse_trans())
I want to create a graph that looks something like this:
However, I would like to incorporate density based on the connected lines (and not individual plot points, as the graph above using geom_density_2d does). The data, in reality, looks something like this:
Where I am showing gene expression over a 4-point time series (y = gene expression value, x = time) In both examples, the centre line was created using LOESS curve fitting.
How can I create a density or contour plot based on the actual individual connecting lines that span from time=1 to time=4?
This is what have done so far:
# make a dataset
test <- data.frame(gene=rep(c((1:500)), each=4),
time=rep(c(1:4), 125),
value=rep(c(1,2,3,1), 125))
# add random noise to dataset
test$value <- jitter(test$value, factor=1,amount=2)
# first graph created as follows:
ggplot(data=test, aes(x=time, y=value)) +
geom_density_2d(colour="grey") +
scale_x_continuous(limits = c(0,5),
breaks = seq(1,4),
minor_breaks = seq(1)) +
scale_y_continuous(limits = c(-3,8)) +
guides(fill=FALSE) +
theme_classic()
# second plot created as follows
ggplot(test, aes(time, value)) +
geom_line(aes(group = gene),
size = 0.5,
alpha = 0.3,
color = "snow3") +
geom_point() +
scale_y_continuous(limits = c(-3, 8)) +
scale_x_continuous(breaks = seq(1,4), minor_breaks = seq(1)) +
theme_classic()
Thanks in advance for your help!
I want to create the next histogram density plot with ggplot2. In the "normal" way (base packages) is really easy:
set.seed(46)
vector <- rnorm(500)
breaks <- quantile(vector,seq(0,1,by=0.1))
labels = 1:(length(breaks)-1)
den = density(vector)
hist(df$vector,
breaks=breaks,
col=rainbow(length(breaks)),
probability=TRUE)
lines(den)
With ggplot I have reached this so far:
seg <- cut(vector,breaks,
labels=labels,
include.lowest = TRUE, right = TRUE)
df = data.frame(vector=vector,seg=seg)
ggplot(df) +
geom_histogram(breaks=breaks,
aes(x=vector,
y=..density..,
fill=seg)) +
geom_density(aes(x=vector,
y=..density..))
But the "y" scale has the wrong dimension. I have noted that the next run gets the "y" scale right.
ggplot(df) +
geom_histogram(breaks=breaks,
aes(x=vector,
y=..density..,
fill=seg)) +
geom_density(aes(x=vector,
y=..density..))
I just do not understand it. y=..density.. is there, that should be the height. So why on earth my scale gets modified when I try to fill it?
I do need the colours. I just want a histogram where the breaks and the colours of each block are directionally set according to the default ggplot fill colours.
Manually, I added colors to your percentile bars. See if this works for you.
library(ggplot2)
ggplot(df, aes(x=vector)) +
geom_histogram(breaks=breaks,aes(y=..density..),colour="black",fill=c("red","orange","yellow","lightgreen","green","darkgreen","blue","darkblue","purple","pink")) +
geom_density(aes(y=..density..)) +
scale_x_continuous(breaks=c(-3,-2,-1,0,1,2,3)) +
ylab("Density") + xlab("df$vector") + ggtitle("Histogram of df$vector") +
theme_bw() + theme(plot.title=element_text(size=20),
axis.title.y=element_text(size = 16, vjust=+0.2),
axis.title.x=element_text(size = 16, vjust=-0.2),
axis.text.y=element_text(size = 14),
axis.text.x=element_text(size = 14),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank())
fill=seg results in grouping. You are actually getting a different histogram for each value of seg. If you don't need the colours, you could use this:
ggplot(df) +
geom_histogram(breaks=breaks,aes(x=vector,y=..density..), position="identity") +
geom_density(aes(x=vector,y=..density..))
If you need the colours, it might be easiest to calculate the density values outside of ggplot2.
Or an option with ggpubr
library(ggpubr)
gghistogram(df, x = "vector", add = "mean", rug = TRUE, fill = "seg",
palette = c("#00AFBB", "#E7B800", "#E5A800", "#00BFAB", "#01ADFA",
"#00FABA", "#00BEAF", "#01AEBF", "#00EABA", "#00EABB"), add_density = TRUE)
The confusion regarding interpreting the y-axis might be due to density is plotted rather than count. So, the values on the y-axis are proportions of the total sample, where the sum of the bars is equal to 1.
I am trying to make a labeled bubble plot with ggplot2 in R. Here is the simplified scenario:
I have a data frame with 4 variables: 3 quantitative variables, x, y, and z, and another variable that labels the points, lab.
I want to make a scatter plot, where the position is determined by x and y, and the size of the points is determined by z. I then want to place text labels beside the points (say, to the right of the point) without overlapping the text on top of the point.
If the points did not vary in size, I could try to simply modify the aesthetic of the geom_text layer by adding a scaling constant (e.g. aes(x=x+1, y=y+1)). However, even in this simple case, I am having a problem with positioning the text correctly because the points do not scale with the output dimensions of the plot. In other words, the size of the points remains constant in a 500x500 plot and a 1000x1000 plot - they do not scale up with the dimensions of the outputted plot.
Therefore, I think I have to scale the position of the label by the size (e.g. dimensions) of the output plot, or I have to get the radius of the points from ggplot somehow and shift my text labels. Is there a way to do this in ggplot2?
Here is some code:
# Stupid data
df <- data.frame(x=c(1,2,3),
y=c(1,2,3),
z=c(1,2,1),
lab=c("a","b","c"), stringsAsFactors=FALSE)
# Plot with bad label placement
ggplot(aes(x=x, y=y), data=df) +
geom_point(aes(size=z)) +
geom_text(aes(label=lab),
colour="red") +
scale_size_continuous(range=c(5, 50), guide="none")
EDIT: I should mention, I tried hjust and vjust inside of geom_text, but it does not produce the desired effect.
# Trying hjust and vjust, but it doesn't look nice
ggplot(aes(x=x, y=y), data=df) +
geom_point(aes(size=z)) +
geom_text(aes(label=lab), hjust=0, vjust=0.5,
colour="red") +
scale_size_continuous(range=c(5, 50), guide="none")
EDIT: I managed to get something that works for now, thanks to Henrik and shujaa. I will leave the question open just in case someone shares a more general solution.
Just a blurb of what I am using this for: I am plotting a map, and indicating the amount of precipitation at certain stations with a point that is sized proportionally to the amount of precipitation observed. I wanted to add a station label beside each point in an aesthetically pleasing manner. I will be making more of these plots for different regions, and my output plot may have a different resolution or scale (e.g. due to different projections) for each plot, so a general solution is desired. I might try my hand at creating a custom position_jitter, like baptiste suggested, if I have time during the weekend.
It appears that position_*** don't have access to the scales used by other layers, so it's a no go. You could make a clone of GeomText that shifts the labels according to the size mapped,
but it's a lot of effort for a very kludgy and fragile solution,
geom_shiftedtext <- function (mapping = NULL, data = NULL, stat = "identity",
position = "identity",
parse = FALSE, ...) {
GeomShiftedtext$new(mapping = mapping, data = data, stat = stat, position = position,
parse = parse, ...)
}
require(proto)
GeomShiftedtext <- proto(ggplot2:::GeomText, {
objname <- "shiftedtext"
draw <- function(., data, scales, coordinates, ..., parse = FALSE, na.rm = FALSE) {
data <- remove_missing(data, na.rm,
c("x", "y", "label"), name = "geom_shiftedtext")
lab <- data$label
if (parse) {
lab <- parse(text = lab)
}
with(coord_transform(coordinates, data, scales),
textGrob(lab, unit(x, "native") + unit(0.375* size, "mm"),
unit(y, "native"),
hjust=hjust, vjust=vjust, rot=angle,
gp = gpar(col = alpha(colour, alpha),
fontfamily = family, fontface = fontface, lineheight = lineheight))
)
}
})
df <- data.frame(x=c(1,2,3),
y=c(1,2,3),
z=c(1.2,2,1),
lab=c("a","b","c"), stringsAsFactors=FALSE)
ggplot(aes(x=x, y=y), data=df) +
geom_point(aes(size=z), shape=1) +
geom_shiftedtext(aes(label=lab, size=z),
hjust=0, colour="red") +
scale_size_continuous(range=c(5, 100), guide="none")
This isn't a very general solution, because you'll need to tweak it every time, but you should be able to add to the x value for the text some value that's linear depending on z.
I had luck with
ggplot(aes(x=x, y=y), data=df) +
geom_point(aes(size=z)) +
geom_text(aes(label=lab, x = x + .06 + .14 * (z - min(z))),
colour="red") +
scale_size_continuous(range=c(5, 50), guide="none")
but, as the font size depends on your window size, you would need to decide on your output size and tweak accordingly. I started with x = x + .05 + 0 * (z-min(z)) and calibrated the intercept based on the smallest point, then when I was happy with that I adjusted the linear term for the biggest point.
Another alternative. Looks OK with your test data, but you need to check how general it is.
dodge <- abs(scale(df$z))/4
ggplot(data = df, aes(x = x, y = y)) +
geom_point(aes(size = z)) +
geom_text(aes(x = x + dodge), label = df$lab, colour = "red") +
scale_size_continuous(range = c(5, 50), guide = "none")
Update
Just tried position_jitter, but the width argument only takes one value, so right now I am not sure how useful that function would be. But I would be happy to find that I am wrong. Example with another small data set:
df3 <- mtcars[1:10, ]
ggplot(data = df3, aes(x = wt, y = mpg)) +
geom_point(aes(size = qsec), alpha = 0.1) +
geom_text(label = df3$carb, position = position_jitter(width = 0.1, height = 0)) +
scale_size_continuous(range = c(5, 50), guide = "none")
I am doing some research on non-defaulters and defaulters with regards to banking. In that context I am plotting their distributions relative to some score in a bar plot. The higher the score, the better the credit rating.
Since the number of defaults is very limited compared to the number of non-defaults plotting the defaults and non-defaults on the same bar plot is not very giving as you hardly can see the defaults. I then make a second bar plot based on the defaulters' scores only, but on the same interval scale as the full bar plot of both the scores of the defaulters and non-defaulters. I would then like to add vertical lines to the first bar plot indicating where the highest defaulter score is located and the lowest defaulter score is located. That is to get a view of where the distribution of the defaulters fit into that of the overall distribution of both defaulters and non-defaulters.
Below is the code I am using replaced with (seeded) random data instead.
library(ggplot2)
#NDS represents non-defaults and DS defaults on the same scale
#although here being just some random normals for the sake of simplicity.
set.seed(10)
NDS<-rnorm(10000,sd=1)-2
DS<-rnorm(100,sd=2)-5
#Cutoffs are constructed such that intervals of size 0.3
#contain all values of NDS & DS
minCutoff<--9.3
maxCutoff<-2.1
#Generate the actual interval "bins"
NDS_CUT<-cut(NDS,breaks=seq(minCutoff, maxCutoff, by = 0.3))
DS_CUT<-cut(DS,breaks=seq(minCutoff, maxCutoff, by = 0.3))
#Manually generate where to put the vertical lines for min(DS) and max(DS)
minDS_bar<-levels(cut(NDS,breaks=seq(minCutoff, maxCutoff, by = 0.3)))[1]
maxDS_bar<-levels(cut(NDS,breaks=seq(minCutoff, maxCutoff, by = 0.3)))[32]
#Generate data frame - seems stupid, but makes sense
#when the "real" data is used :-)
NDSdataframe<-cbind(as.data.frame(NDS_CUT),rep(factor("State-1"),length(NDS_CUT)))
colnames(NDSdataframe)<-c("Score","Action")
DSdataframe<-cbind(as.data.frame(DS_CUT),rep(factor("State-2"),length(DS_CUT)))
colnames(DSdataframe)<-c("Score","Action")
fulldataframe<-rbind(NDSdataframe,DSdataframe)
attach(fulldataframe)
#Plot the full distribution of NDS & DS
# with geom_vline(xintercept = minDS_bar) + geom_vline(xintercept = maxDS_bar)
# that unfortunately does not show :-(
fullplot<-ggplot(fulldataframe, aes(Score, fill=factor(Action,levels=c("State-2","State-1")))) + geom_bar(position="stack") + opts(axis.text.x = theme_text(angle = 45)) + opts (legend.position = "none") + xlab("Scoreinterval") + ylab("Antal pr. interval") + geom_vline(xintercept = minDS_bar) + geom_vline(xintercept = maxDS_bar)
#Generate dataframe for DS only
#It might seem stupid, but again makes sense
#when using the original data :-)
DSdataframe2<-cbind(as.data.frame(DS_CUT),rep(factor("State-2"),length(DS_CUT)))
colnames(DSdataframe2)<-c("theScore","theAction")
#Calucate max number of observations to adjust bar plot of DS only
myMax<-max(table(DSdataframe2))+1
attach(DSdataframe2)
#Generate bar plot of DS only
subplot<-ggplot(fulldataframe, aes(theScore, fill=factor(theAction))) + geom_bar (position="stack") + opts(axis.text.x = theme_text(angle = 45)) + opts(legend.position = "none") + ylim(0, myMax) + xlab("Scoreinterval") + ylab("Antal pr. interval")
#plot on a grid
grid.newpage()
pushViewport(viewport(layout = grid.layout(2, 1)))
vplayout <- function(x, y)
viewport(layout.pos.row = x, layout.pos.col = y)
print(fullplot, vp = vplayout(1, 1))
print(subplot, vp = vplayout(2, 1))
#detach dataframes
detach(DSdataframe2)
detach(fulldataframe)
Furthermore, if anybody has an idea of how I can align the to plot so that correct intervals are just below/above each other on the grid plot
Hope somebody is able to help!
Thanks in advance,
Christian
Wrap aes around the xintercept in the geom_vline layer:
... + geom_vline(aes(xintercept = minDS_bar)) + geom_vline(aes(xintercept = maxDS_bar))
Question 1:
Since you provide the vertical lines as data, you have to map the aesthetics first, using aes()
fullplot <-ggplot(
fulldataframe,
aes(Score, fill=factor(Action,levels=c("State-2","State-1")))) +
geom_bar(position="stack") +
opts(axis.text.x = theme_text(angle = 45)) +
opts (legend.position = "none") +
xlab("Scoreinterval") +
ylab("Antal pr. interval") +
geom_vline(aes(xintercept = minDS_bar)) +
geom_vline(aes(xintercept = maxDS_bar))
Second question:
To align the plots, you can use the align.plots() function in package ggExtra
install.packages("dichromat")
install.packages("ggExtra", repos="http://R-Forge.R-project.org")
library(ggExtra)
ggExtra::align.plots(fullplot, subplot)