I've binned some data and currently have a dataframe that consists of two columns, one that specifies a bin range and another that specifies the frequency like this:-
> head(data)
binRange Frequency
1 (0,0.025] 88
2 (0.025,0.05] 72
3 (0.05,0.075] 92
4 (0.075,0.1] 38
5 (0.1,0.125] 20
6 (0.125,0.15] 16
I want to plot a histogram and density plot using this but I can't seem to find a way of doing so without having to generate new bins etc. Using this solution here I tried to do the following:-
p <- ggplot(data, aes(x= binRange, y=Frequency)) + geom_histogram(stat="identity")
but it crashes. Anyone know of how to deal with this?
Thank you
the problem is that ggplot doesnt understand the data the way you input it, you need to reshape it like so (I am not a regex-master, so surely there are better ways to do is):
df <- read.table(header = TRUE, text = "
binRange Frequency
1 (0,0.025] 88
2 (0.025,0.05] 72
3 (0.05,0.075] 92
4 (0.075,0.1] 38
5 (0.1,0.125] 20
6 (0.125,0.15] 16")
library(stringr)
library(splitstackshape)
library(ggplot2)
# extract the numbers out,
df$binRange <- str_extract(df$binRange, "[0-9].*[0-9]+")
# split the data using the , into to columns:
# one for the start-point and one for the end-point
df <- cSplit(df, "binRange")
# plot it, you actually dont need the second column
ggplot(df, aes(x = binRange_1, y = Frequency, width = 0.025)) +
geom_bar(stat = "identity", breaks=seq(0,0.125, by=0.025))
or if you don't want the data to be interpreted numerically, you can just simply do the following:
df <- read.table(header = TRUE, text = "
binRange Frequency
1 (0,0.025] 88
2 (0.025,0.05] 72
3 (0.05,0.075] 92
4 (0.075,0.1] 38
5 (0.1,0.125] 20
6 (0.125,0.15] 16")
library(ggplot2)
ggplot(df, aes(x = binRange, y = Frequency)) + geom_bar(stat = "identity")
you won't be able to plot a density-plot with your data, given its not continous but rather categorical, thats why I actually prefer the second way of showing it,
You can try
library(ggplot2)
ggplot(df, aes(x = binRange, y = Frequency)) + geom_col()
Related
I have a dataset in the following format
value1 value2 group
10 20 A
20 30 A
67 45 B
98 76 C
102 11 A
11 22 B
10 10 B
19 20 C
I am trying to make box plots for three groups (A, B and C) and the box plots for 1st and end column should be side by side. I can do two separate plots like following, but not able to figure out how to combine to put it side by side.
p1 <- ggplot(x, aes(x=group, y=value1)) + geom_boxplot()
p2 <- ggplot(x, aes(x=group, y=value)) + geom_boxplot()
I would appreciate any help. I am a newbie in R and ggplot.
Here's an option using pivot_longer from tidyr
x_new <- tidyr::pivot_longer(x, c(value1, value2))
ggplot(x_new, aes(x = group, y = value, col = name, fill = name)) + geom_boxplot(alpha = .5)
The gridExtra package can do this too. Assign your plots to variables then just use grid.arrange(plot1,plot2). Look up the documentation with ?grid.arrange for extra options.
I need help with this please.
I have searched here but not got the right output.
I am trying to plot this in R, so I can plot 3 files side-by-side in a single plot using GGplot.
The output I desire (plotted with excel) is this
What i am getting using GGplot is this
The R code i am using is this
A1 <- read.table("A1.txt", header = T, sep = "\t")
library(ggplot2)
ggplot(A1, aes(x = count)) + geom_bar()
The data is a tab-delimited file like this
length count
26 344776
27 289439
18 673395
28 338146
19 710702
20 928326
21 3491352
22 2724981
23 699007
24 726121
25 472509
The length, as it were will only be labels on the x axis for the counts plotted on the y-axis.
Is this what you wanted?
ggplot(A1, aes(x = as.character(length), y=count)) + geom_bar(stat="identity")
Here is my script (example inspired from here and using the reorder option from here):
library(ggplot2)
Animals <- read.table(
header=TRUE, text='Category Reason Species
1 Decline Genuine 24
2 Improved Genuine 16
3 Improved Misclassified 85
4 Decline Misclassified 41
5 Decline Taxonomic 2
6 Improved Taxonomic 7
7 Decline Unclear 10
8 Improved Unclear 25
9 Improved Bla 10
10 Decline Hello 30')
fig <- ggplot(Animals, aes(x=reorder(Animals$Reason, -Animals$Species), y=Species, fill = Category)) +
geom_bar(stat="identity", position = "dodge")
This gives the following output plot:
What I would like is to order my barplot only on condition 'Decline', and all the 'Improved' would not be inserted in the middle. Here is what I would like to get (after some svg editing):
So now all the whole 'Decline' condition is sorted and the 'Improved' condition comes after. Besides, ideally, the bars would all be at the same width, even if the condition is not represented for the value (e.g. "Bla" has no "Decline" value).
Any idea on how I could do that without having to play with SVG editors? Many thanks!
First let's fill your data.frame with missing combinations like this.
library(dplyr)
Animals2 <- expand.grid(Category=unique(Animals$Category), Reason=unique(Animals$Reason)) %>% data.frame %>% left_join(Animals)
Then you can create an ordering variable for the x-scale:
myorder <- Animals2 %>% filter(Category=="Decline") %>% arrange(desc(Species)) %>% .$Reason %>% as.character
An then plot:
ggplot(Animals2, aes(x=Reason, y=Species, fill = Category)) +
geom_bar(stat="identity", position = "dodge") + scale_x_discrete(limits=myorder)
Define new data frame with all combinations of "Category" and "Reason", merge with data of "Species" from data frame "Animals". Adapt ggplot by correct scale_x_discrete:
Animals3 <- expand.grid(Category=unique(Animals$Category),Reason=unique(Animals$Reason))
Animals3 <- merge(Animals3,Animals,by=c("Category","Reason"),all.x=TRUE)
Animals3[is.na(Animals3)] <- 0
Animals3 <- Animals3[order(Animals3$Category,-Animals3$Species),]
ggplot(Animals3, aes(x=Animals3$Reason, y=Species, fill = Category)) + geom_bar(stat="identity", position = "dodge") + scale_x_discrete(limits=as.character(Animals3[Animals3$Category=="Decline","Reason"]))
To achieve something like that I would adjust the data frame when working with ggplot. Add the missing categories with a value of zero.
Animals <- rbind(Animals,
data.frame(Category = c("Improved", "Decline"),
Reason = c("Hello", "Bla"),
Species = c(0,0)
)
)
Along the same lines as the answer from user Alex, a less manual way of adding the categories might be
d <- with(Animals, expand.grid(unique(Category), unique(Reason)))
names(d) <- names(Animals)[1:2]
Animals <- merge(d, Animals, all.x=TRUE)
Animals$Species[is.na(Animals$Species)] <- 0
I have two data frames z (1 million observations) and b (500k observations).
z= Tracer time treatment
15 0 S
20 0 S
25 0 X
04 0 X
55 15 S
16 15 S
15 15 X
20 15 X
b= Tracer time treatment
2 0 S
35 0 S
10 0 X
04 0 X
20 15 S
11 15 S
12 15 X
25 15 X
I'd like to create grouped boxplots using time as a factor and treatment as colour. Essentially I need to bind them together and then differentiate between them but not sure how. One way I tried was using:
zz<-factor(rep("Z", nrow(z))
bb<-factor(rep("B",nrow(b))
dumB<-merge(z,zz) #this won't work because it says it's too big
dumB<-merge(b,zz)
total<-rbind(dumB,dumZ)
But z and zz merge won't work because it says it's 10G in size (which can't be right)
The end plot might be similar to this example: Boxplot with two levels and multiple data.frames
Any thoughts?
Cheers,
EDIT: Added boxplot
I would approach it as follows:
# create a list of your data.frames
l <- list(z,b)
# assign names to the dataframes in the list
names(l) <- c("z","b")
# bind the dataframes together with rbindlist from data.table
# the id parameter will create a variable with the names of the dataframes
# you could also use 'bind_rows(l, .id="id")' from 'dplyr' for this
library(data.table)
zb <- rbindlist(l, id="id")
# create the plot
ggplot(zb, aes(x=factor(time), y=Tracer, color=treatment)) +
geom_boxplot() +
facet_wrap(~id) +
theme_bw()
which gives:
Other alternatives for creating your plot:
# facet by 'time'
ggplot(zb, aes(x=id, y=Tracer, color=treatment)) +
geom_boxplot() +
facet_wrap(~time) +
theme_bw()
# facet by 'time' & color by 'id' instead of 'treatment'
ggplot(zb, aes(x=treatment, y=Tracer, color=id)) +
geom_boxplot() +
facet_wrap(~time) +
theme_bw()
In respons to your last comment: to get everything in one plot, you use interaction to distinguish between the different groupings as follows:
ggplot(zb, aes(x=treatment, y=Tracer, color=interaction(id, time))) +
geom_boxplot(width = 0.7, position = position_dodge(width = 0.7)) +
theme_bw()
which gives:
The key is you do not need to perform a merge, which is computationally expensive on large tables. Instead assign a new variable and value (source c(b,z) in my code below) to each dataframe and then rbind. Then it becomes straight forward, my solution is very similar to #Jaap's just with different faceting.
library(ggplot2)
#Create some mock data
t<-seq(1,55,by=2)
z<-data.frame(tracer=sample(t,size = 10,replace = T), time=c(0,15), treatment=c("S","X"))
b<-data.frame(tracer=sample(t,size = 10,replace = T), time=c(0,15), treatment=c("S","X"))
#Add a variable to each table to id itself
b$source<-"b"
z$source<-"z"
#concatenate the tables together
all<-rbind(b,z)
ggplot(all, aes(source, tracer, group=interaction(treatment,source), fill=treatment)) +
geom_boxplot() + facet_grid(~time)
Let's say I have data consisting of the time I leave the house and the number of minutes it takes me to get to work. I'll have some repeated values:
08:00, 20
08:04, 25
08:30, 40
08:20, 23
08:04, 22
And some numbers will repeat (like 08:04). What I want to do is a run a scatter plot that is correctly scaled at the x-axis but allows these multiple values per entry so that I could view the trend.
Is a time-series even what I want to be using? I've been able to plot a time series graph that has one value per time, and I've gotten multiple values plotted but without the time-series scaling. Can anyone suggest a good approach? Preference for ggplot2 but I'll take standard R plotting if it's easier.
First lets prepare some more data
set.seed(123)
df <- data.frame(Time = paste0("08:", sample(35:55, 40, replace = TRUE)),
Length = sample(20:50, 40, replace = TRUE),
stringsAsFactors = FALSE)
df <- df[order(df$Time), ]
df$Attempt <- unlist(sapply(rle(df$Time)$lengths, function(i) 1:i))
df$Time <- as.POSIXct(df$Time, format = "%H:%M") # Fixing y axis
head(df)
Time Length Attempt
6 08:35 24 1
18 08:35 43 2
35 08:35 34 3
15 08:37 37 1
30 08:38 33 1
38 08:39 38 1
As I understand, you want to preserve the order of observations of the same leaving house time. At first I ignored that and got a scatter plot like this:
ggplot(data = df, aes(x = Length, y = Time)) +
geom_point(aes(size = Length, colour = Length)) +
geom_path(aes(group = Time, colour = Length), alpha = I(1/3)) +
scale_size(range = c(2, 7)) + theme(legend.position = 'none')
but considering three dimensions (Time, Length and Attempt) scatter plot no longer can show us all the information. I hope I understood you correctly and this is what you are looking for:
ggplot(data = df, aes(y = Time, x = Attempt)) + geom_tile(aes(fill = Length))