Histograms using ggplot2 within loop - r

I would like to create a grid of histograms using a loop and ggplot2. Say I have the following code:
library(gridExtra)
library(ggplot2)
df<-matrix(NA,2000,5)
df[,1]<-rnorm(2000,1,1)
df[,2]<-rnorm(2000,2,1)
df[,3]<-rnorm(2000,3,1)
df[,4]<-rnorm(2000,4,1)
df[,5]<-rnorm(2000,5,1)
df<-data.frame(df)
out<-NULL
for (i in 1:5){
out[[i]]<-ggplot(df, aes(x=df[,i])) + geom_histogram(binwidth=.5)
}
grid.arrange(out[[1]],out[[2]],out[[3]],out[[4]],out[[5]], ncol=2)
Note that all of the plots appear, but that they all have the same mean and shape, despite having set each of the columns of df to have different means.
It seems to only plot the last plot (out[[5]]), that is, the loop seems to be reassigning all of the out[[i]]s with out[[5]].
I'm not sure why, could someone help?

I agree with #GabrielMagno, facetting is the way to go. But if for some reason you need to work with the loop, then either of these will do the job.
library(gridExtra)
library(ggplot2)
df<-matrix(NA,2000,5)
df[,1]<-rnorm(2000,1,1)
df[,2]<-rnorm(2000,2,1)
df[,3]<-rnorm(2000,3,1)
df[,4]<-rnorm(2000,4,1)
df[,5]<-rnorm(2000,5,1)
df<-data.frame(df)
out<-list()
for (i in 1:5){
x = df[,i]
out[[i]] <- ggplot(data.frame(x), aes(x)) + geom_histogram(binwidth=.5)
}
grid.arrange(out[[1]],out[[2]],out[[3]],out[[4]],out[[5]], ncol=2)
or
out1 = lapply(df, function(x){
ggplot(data.frame(x), aes(x)) + geom_histogram(binwidth=.5) })
grid.arrange(out1[[1]],out1[[2]],out1[[3]],out1[[4]],out1[[5]], ncol=2)

I would recommend using facet_wrap instead of aggregating and arranging the plots by yourself. It requires you to specify a grouping variable in the data frame that separates the values for each distribution. You can use the melt function from the reshape2 package to create such new data frame. So, having your data stored in df, you could simply do this:
library(ggplot2)
library(reshape2)
ggplot(melt(df), aes(x = value)) +
facet_wrap(~ variable, scales = "free", ncol = 2) +
geom_histogram(binwidth = .5)
That would give you something similar to this:

Related

Iterating over a list using ggarrange

I have the following bit of code and don't understand why the for loop isn't working. I'm new to this, so excuse me if this is obvious, but it's not actually producing a combined set of graphs (as the more brute force method does below), it just prints out each graph individually
library(ggpubr)
graphs <- lapply(names(hemi_split), function(i){
ggplot(data=hemi_split[[i]], aes(x=type, y=shoot.mass))+
geom_point()+
facet_wrap(.~host, scales="free")+
theme_minimal()+
labs(title=i)
});graphs
for (i in 1:length(graphs)) {
ggarrange(graphs[[i]])
} ##not working
## this works, and is the desired output
ggarrange(graphs[[1]], graphs[[2]], graphs[[3]],
graphs[[4]], graphs[[5]], graphs[[6]],
graphs[[7]], graphs[[8]], graphs[[9]],
graphs[[10]], graphs[[11]])
thank you!
You can use do.call to provide all of the list elements of graphs as arguments of ggarrange:
library(ggpubr)
graphs <- lapply(names(mtcars)[2:5],function(x){
ggplot(mtcars,aes_string(x = x, y = "mpg")) +
geom_point()})
do.call(ggarrange,graphs)
another solution using purrr
library(tidyverse)
ggraphs <- map(names(mtcars)[2:5],
~ ggplot(mtcars,aes_string(x = .x, y = "mpg")) +
geom_point())
ggarrange(plotlist = ggraphs)

ggplot on grid with a grobList in R

I'm trying to plot multiple plots on a grid using ggplot2 in a for loop, followed by grid.arrange. But all the plots are identical afterwards.
library(ggplot2)
library(grid)
test = data.frame(matrix(rnorm(320), ncol=16 ))
names(test) = sapply(1:16, function(x) paste0("var_",as.character(x)))
plotlist = list()
for (i in 1:(dim(test)[2]-1)){
plotlist[[i]] = ggplot(test) +
geom_point(aes(get(x=names(test)[dim(test)[2]]), y=get(names(test)[i])))
}
pdf("output.pdf")
do.call(grid.arrange, list(grobs=plotlist, nrow=3))
dev.off(4)
When running this code, it seems like the get() calls are only evaluated at the time of the grid.arrange call, so all of the y vectors in the plot are identical as "var_15". Is there a way to force get evaluation immediately, so that I get 15 different plots?
Thanks!
Here are two ways that use purrr::map functions instead of a for-loop. I find that I have less of a clear sense of what's going on when I try to use loops, and since there are functions like the apply and map families that fit so neatly into R's vector operations paradigm, I generally go with mapping instead.
The first example makes use of cowplot::plot_grid, which can take a list of plots and arrange them. The second uses the newer patchwork package, which lets you add plots together—like literally saying plot1 + plot2—and add a layout. To do all those additions, I use purrr::reduce with + as the function being applied to all the plots.
library(tidyverse)
set.seed(722)
test = data.frame(matrix(rnorm(320), ncol=16 ))
names(test) = sapply(1:16, function(x) paste0("var_",as.character(x)))
# extract all but last column
xvars <- test[, -ncol(test)]
By using purrr::imap, I can map over all the columns and apply a function with 2 arguments: the column itself, and its name. That way I can set an x-axis label that specifies the column name. I can also easily access the column of data without having to use get or any tidyeval tricks (although for something for complicated, a tidyeval solution might be better).
plots <- imap(xvars, function(variable, var_name) {
df <- data_frame(x = variable, y = test[, ncol(test)])
ggplot(df, aes(x = x, y = y)) +
geom_point() +
xlab(var_name)
})
cowplot::plot_grid(plotlist = plots, nrow = 3)
library(patchwork)
# same as plots[[1]] + plots[[2]] + plots[[3]] + ...
reduce(plots, `+`) + plot_layout(nrow = 3)
Created on 2018-07-22 by the reprex package (v0.2.0).
Try this:
library(ggplot2)
library(grid)
library(gridExtra)
set.seed(1234)
test = data.frame(matrix(rnorm(320), ncol=16 ))
names(test) = sapply(1:16, function(x) paste0("var_",as.character(x)))
plotlist = list()
for (i in 1:(dim(test)[2]-1)) {
# Define here the dataset for the i-th plot
df <- data.frame(x=test$var_16, y=test[, i])
plotlist[[i]] = ggplot(data=df, aes(x=x, y=y)) + geom_point()
}
grid.arrange(grobs=plotlist, nrow=3)

Plot all columns from a data.frame in a subplot with ggplot2

as the title suggest, I want to plot all columns from my data.frame, but I want to do it in a generic way. All my columns are factor.
Here is my code so far:
nums <- sapply(train_dataset, is.factor) #Select factor columns
factor_columns <- train_dataset[ , nums]
plotList <- list()
for (i in c(1:NCOL(factor_columns))){
name = names(factor_columns)[i]
p <- ggplot(data = factor_columns) + geom_bar(mapping = aes(x = name))
plotList[[i]] <- p
}
multiplot(plotList, cols = 3)
where multiplot function came from here: http://www.cookbook-r.com/Graphs/Multiple_graphs_on_one_page_(ggplot2)/
And my dataset came from Kaggle (house pricing prediction): https://www.kaggle.com/c/house-prices-advanced-regression-techniques
What I get from my code is the image below, which appears to be the last column badly represented.
This would be the last column well represented:
EDIT:
Using gridExtra as #LAP suggest also doesn't give me a good result. I use this instead of multiplot.
nCol <- floor(sqrt(length(plotList)))
do.call("grid.arrange", c(plotList, ncol=nCol))
but what I get is this:
Again, SaleCondition is the only thing printed and not very well.
PD: I also tried cowplot, same result.
Using tidyr you can do something like the following:
factor_columns %>%
gather(factor, level) %>%
ggplot(aes(level)) + geom_bar() + facet_wrap(~factor, scales = "free_x")

Combining two ecdf plots with different

At the moment I`m writing my bachelor thesis and all of my plots are created with ggplot2. Now I need a plot of two ecdfs but my problem is that the two dataframes have different lengths. But by adding values to equalize the length I would change the distribution, therefore my first thought isn't possible. But a ecdf plot with two different dataframes with a different length is forbidden.
daten <- peptidPSMotherExplained[peptidPSMotherExplained$V3!=-1,]
daten <- cbind ( daten , "scoreDistance"= daten$V2-daten$V3 )
daten2 <- peptidPSMotherExplained2[peptidPSMotherExplained2$V3!=-1,]
daten2 <- cbind ( daten2 , "scoreDistance"= daten2$V2-daten2$V3 )
p <- ggplot(daten, aes(x = scoreDistance)) + stat_ecdf()
p <- p + geom_point(aes(x = daten2$lengthDistance))
p
with the normal plot function of R it is possible
plot(ecdf(daten$scoreDistance))
plot(ecdf(daten2$scoreDistance),add=TRUE)
but it looks different to all of my other plots and I dislike this.
Has anybody a solution for me?
Thank you,
Tobias
Example:
df <-data.frame(scoreDifference = rnorm(10,0,12))
df2 <- data.frame(scoreDifference = rnorm(5,-3,9))
plot(ecdf(df$scoreDifference))
plot(ecdf(df2$scoreDifference),add=TRUE)
So how can I achieve this kind of plot in ggplot?
I don't know what geom one should use for such plots, but for combining two datasets you can simply specify the data in a new layer,
ggplot(df, aes(x = scoreDifference)) +
stat_ecdf(geom = "point") +
stat_ecdf(data=df2, geom = "point")
I think, reshaping your data in the right way will probably make ggplot2 work for you:
df <-data.frame(scoreDiff1 = rnorm(10,0,12))
df2 <- data.frame(scoreDiff2 = rnorm(5,-3,9))
library('reshape2')
data <- merge(melt(df),melt(df2),all=TRUE)
Then, with data in the right shape, you can simply go on to plot the stuff with colour (or shape, or whatever you wish) to distinguish the two datasets:
p <- ggplot(daten, aes(x = value, colour = variable)) + stat_ecdf()
Hope this is what you were looking for!?

ggplot2 equivalent of matplot() : plot a matrix/array by columns?

matplot() makes it easy to plot a matrix/two dimensional array by columns (also works on data frames):
a <- matrix (rnorm(100), c(10,10))
matplot(a, type='l')
Is there something similar using ggplot2, or does ggplot2 require data to be melted into a dataframe first?
Also, is there a way to arbitrarily color/style subsets of the matrix columns using a separate vector (of length=ncol(a))?
Maybe a little easier for this specific example:
library(ggplot2)
a <- matrix (rnorm(100), c(10,10))
sa <- stack(as.data.frame(a))
sa$x <- rep(seq_len(nrow(a)), ncol(a))
qplot(x, values, data = sa, group = ind, colour = ind, geom = "line")
The answers to questions posed in the past have generally advised the melt strategy before specifying the group parameter:
require(reshape2); require(ggplot2)
dataL = melt(a, id="x")
qplot(a, x=Var1, y=value, data=dataL, group=Var2)
p <- ggplot(dataL, aes_string(x="Var1", y="value", colour="Var2", group="Var2"))
p <- p + geom_line()
Just somewhat simplifying what was stated before (matrices are wrapped in c() to make them vectors):
require(ggplot2)
a <- matrix(rnorm(200), 20, 10)
qplot(c(row(a)), c(a), group = c(col(a)), colour = c(col(a)), geom = "line")

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