I have the following table in R (inspired by a cran help datasheet) :
> dfx <- data.frame(
+ group = c(rep('A', 108), rep('B', 115), rep('C', 106)),
+ sex = sample(c("M", "F","U"), size = 329, replace = TRUE),
+ age = runif(n = 329, min = 18, max = 54)
+ )
> head(dfx)
group sex age
1 A U 47.00788
2 A M 32.40236
3 A M 21.95732
4 A F 19.82798
5 A F 30.70890
6 A M 30.00830
I am interested in plotting the percentages of males (M), females (F) and "unknown"(U) in each group using barcharts, including error bars.
To do this graph, i plan to use the panel.ci/prepanel.ci commands.
I can easily build a proportion table for each group using the prop.table command :
> with(dfx, prop.table(table(group,sex), margin=1)*100)
sex
group F M U
A 29.62963 28.70370 41.66667
B 35.65217 35.65217 28.69565
C 37.73585 33.01887 29.24528
But now, i would like to build a similar table with error bars, and use these two tables to make a barchart.
If possible, i would like to use the ddply command, that i use for similar purposes (except that it was nor percentages but means).
Try something like this:
library(plyr)
library(ggplot2)
summary(dfx) # for example, each variable
dfx$interaction <- interaction(dfx$group, dfx$sex)
ddply(dfx, .(interaction), summary) #group by interaction, summary on dfx
ggplot(dfx, aes(x = sex, y = age, fill = group)) + geom_boxplot()
You can get a good on-line tutorial on building graphs here.
edit
I'm pretty sure you would need more than 1 value for the proportion in order to have any error. I only see 1 value for the proportion for each unique combination of variables group and sex.
This is the most I can help you with (below), but I'd be interested to see you post an answer to your own question when you find a suitable solution.
dfx$interaction <- interaction(dfx$group, dfx$sex)
dfx.summary <- ddply(dfx, .(group, sex), summarise, total = length(group))
dfx.summary$prop <- with(dfx.summary, total/sum(total))
dfx.summary
# group sex prop
# 1 A F 0.06382979
# 2 A M 0.12158055
# 3 A U 0.14285714
# 4 B F 0.12462006
# 5 B M 0.11854103
# 6 B U 0.10638298
# 7 C F 0.10334347
# 8 C M 0.12158055
# 9 C U 0.09726444
ggplot(dfx.summary, aes(sex, total, color = group)) + geom_point(size = 5)
Related
I have data that only shows a variable if it is not 0. However, I would like to have gaps representing these 0s in the graph.
(I will be working from a large dataframe, but have created an example data based on how I will be manipulating it for this purpose.)
library(tidyverse)
library(ggplot2)
A <- tibble(
name = c("CTX_M", "CblA_1"),
rpkm = c(350, 4),
sample = "A"
)
B <- tibble(
name = c("CTX_M", "OXA_1", "ampC"),
rpkm = c(324, 357, 99),
sample = "B"
)
plot <- bind_rows(A, B)
ggplot()+ geom_col(data = plot, aes(x = sample, y = rpkm, fill = name),
position = "dodge")
Sample A and B both have CTX_M, however the othre three "names" are only present in either sample A or sample B. When I run the code, the output graph shows two bars for sample A and three bars for sample B the resulting graph was:
Is there a way for me to add ClbA_1 to sample B with rpkm=0, and OXA_1 and ampC to sample A with rpkm=0, while maintaining sample separation? - so the tibble would look like this (order not important):
and the graph would therefore look like this:
You can use complete from tidyr.
plot <- plot %>% complete(name,sample,fill=list(rpkm=0))
# A tibble: 8 x 3
name sample rpkm
<chr> <chr> <dbl>
1 ampC A 0
2 ampC B 99
3 CblA_1 A 4
4 CblA_1 B 0
5 CTX_M A 350
6 CTX_M B 324
7 OXA_1 A 0
8 OXA_1 B 357
ggplot()+ geom_col(data = plot, aes(x = sample, y = rpkm, fill = name),
position = "dodge")
I'm pretty new to R and I have a problem with plotting a barplot out of my data which looks like this:
condition answer
2 H
1 H
8 H
5 W
4 M
7 H
9 H
10 H
6 H
3 W
The data consists of 100 rows with the conditions 1 to 10, each randomly generated 10 times (10 times condition 1, 10 times condition 8,...). Each of the conditions also has a answer which could be H for Hit, M for Miss or W for wrong.
I want to plot the number of Hits for each condition in a barplot (for example 8 Hits out of 10 for condition 1,...) for that I tried to do the following in ggplot2
ggplot(data=test, aes(x=test$condition, fill=answer=="H"))+
geom_bar()+labs(x="Conditions", y="Hitrate")+
coord_cartesian(xlim = c(1:10), ylim = c(0:10))+
scale_x_continuous(breaks=seq(1,10,1))
And it looked like this:
This actually exactly what I need except for the red color which covers everything. You can see that conditions 3 to 5 have no blue bar, because there are no hits for these conditions.
Is there any way to get rid of this red color and to maybe count the amount of hits for the different conditions? -> I tried the count function of dplyr but it only showed me the amount of H when there where some for this particular condition. 3-5 where just "ignored" by count, there wasn't even a 0 in the output.-> but I'd still need those numbers for the plot
I'm sorry for this particular long post but I'm really at the end of knowledge considering this. I'd be open for suggestions or alternatives! Thanks in advance!
This is a situation where a little preprocessing goes a long way. I made sample data that would recreate the issue, i.e. has cases where there won't be any "H"s.
Instead of relying on ggplot to aggregate data in the way you want it, use proper tools. Since you mention dplyr::count, I use dplyr functions.
The preprocessing task is to count observations with answer "H", including cases where the count is 0. To make sure all combinations are retained, convert condition to a factor and set .drop = F in count, which is in turn passed to group_by.
library(dplyr)
library(ggplot2)
set.seed(529)
test <- data.frame(condition = rep(1:10, times = 10),
answer = c(sample(c("H", "M", "W"), 50, replace = T),
sample(c("M", "W"), 50, replace = T)))
hit_counts <- test %>%
mutate(condition = as.factor(condition)) %>%
filter(answer == "H") %>%
count(condition, .drop = F)
hit_counts
#> # A tibble: 10 x 2
#> condition n
#> <fct> <int>
#> 1 1 0
#> 2 2 1
#> 3 3 4
#> 4 4 2
#> 5 5 3
#> 6 6 0
#> 7 7 3
#> 8 8 2
#> 9 9 1
#> 10 10 1
Then just plot that. geom_col is the version of geom_bar for where you have your y-values already, instead of having ggplot tally them up for you.
ggplot(hit_counts, aes(x = condition, y = n)) +
geom_col()
One option is to just filter out anything but where answer == "H" from your dataset, and then plot.
An alternative is to use a grouped bar plot, made by setting position = "dodge":
test <- data.frame(condition = rep(1:10, each = 10),
answer = sample(c('H', 'M', 'W'), 100, replace = T))
ggplot(data=test) +
geom_bar(aes(x = condition, fill = answer), position = "dodge") +
labs(x="Conditions", y="Hitrate") +
coord_cartesian(xlim = c(1:10), ylim = c(0:10)) +
scale_x_continuous(breaks=seq(1,10,1))
Also note that if the condition is actually a categorical variable, it may be better to make it a factor:
test$condition <- as.factor(test$condition)
This means that you don't need the scale_x_continuous call, and that the grid lines will be cleaner.
Another option is to pick your fill colors explicitly and make FALSE transparent by using scale_fill_manual. Since FALSE comes alphabetically first, the first value to specify is FALSE, the second TRUE.
ggplot(data=test, aes(x=condition, fill=answer=="H"))+
geom_bar()+labs(x="Conditions", y="Hitrate")+
coord_cartesian(xlim = c(1:10), ylim = c(0:10))+
scale_x_continuous(breaks=seq(1,10,1)) +
scale_fill_manual(values = c(alpha("red", 0), "cadetblue")) +
guides(fill = F)
I want to select the top 10 voted restaurants, and plot them together.
So i want to create a plot that shows the restaurant names and their votes.
I used:
topTenVotes <- top_n(dataSet, 10, Votes)
and it showed me data of the columns in dataset based on the top 10 highest votes, however i want just the number of votes and restaurant names.
My Question is how to select only the top 10 highest votes and their restaurant names, and plotting them together?
expected output:
Restaurant Names Votes
A 300
B 250
C 230
D 220
E 210
F 205
G 200
H 194
I 160
J 120
K 34
And then a bar plot that shows these restaurant names and their votes
Another simple approach with base functions creating another variable:
df <- data.frame(Names = LETTERS, Votes = sample(40:400, length(LETTERS)))
x <- df$Votes
names(x) <- df$Names # x <- setNames(df$Votes, df$Names) is another approach
barplot(sort(x, decreasing = TRUE)[1:10], xlab = "Restaurant Name", ylab = "Votes")
Or a one-line solution with base functions:
barplot(sort(xtabs(Votes ~ Names, df), decreasing = TRUE)[1:10], xlab = "Restaurant Names")
I'm not seeing a data set to use, so here's a minimal example to show how it might work:
library(tidyverse)
df <-
tibble(
restaurant = c("res1", "res2", "res3", "res4"),
votes = c(2, 5, 8, 6)
)
df %>%
arrange(-votes) %>%
head(3) %>%
ggplot(aes(x = reorder(restaurant, votes), y = votes)) +
geom_col() +
coord_flip()
The top_n command also works in this case but is designed for grouped data.
Its more efficient, though less readable, to use base functions:
#toy data
d <- data.frame(list(Names = sample(LETTERS, size = 15), value = rnorm(25, 10, n = 15)))
head(d)
Names value
1 D 25.592749
2 B 28.362303
3 H 1.576343
4 L 28.718517
5 S 27.648078
6 Y 29.364797
#reorder by, and retain, the top 10
newdata <- data.frame()
for (i in 1:10) {
newdata <- rbind(newdata,d[which(d$value == sort(d$value, decreasing = T)[1:10][i]),])
}
newdata
Names value
8 W 45.11330
13 K 36.50623
14 P 31.33122
15 T 30.28397
6 Y 29.36480
7 Q 29.29337
4 L 28.71852
10 Z 28.62501
2 B 28.36230
5 S 27.64808
I am using the ..count.. transformation in geom_bar and get the warning
position_stack requires non-overlapping x intervals when some of my categories have few counts.
This is best explained using some mock data (my data involves direction and windspeed and I retain names relating to that)
#make data
set.seed(12345)
FF=rweibull(100,1.7,1)*20 #mock speeds
FF[FF>60]=59
dir=sample.int(10,size=100,replace=TRUE) # mock directions
#group into speed classes
FFcut=cut(FF,breaks=seq(0,60,by=20),ordered_result=TRUE,right=FALSE,drop=FALSE)
# stuff into data frame & plot
df=data.frame(dir=dir,grp=FFcut)
ggplot(data=df,aes(x=dir,y=(..count..)/sum(..count..),fill=grp)) + geom_bar()
This works fine, and the resulting plot shows the frequency of directions grouped according to speed. It is of relevance that the velocity class with the fewest counts (here "[40,60)") will have 5 counts.
However more velocity classes leads to a warning. For instance, with
FFcut=cut(FF,breaks=seq(0,60,by=15),ordered_result=TRUE,right=FALSE,drop=FALSE)
the velocity class with the fewest counts (now "[45,60)") will have only 3 counts and ggplot2 will warn that
position_stack requires non-overlapping x intervals
and the plot will show data in this category spread out along the x axis.
It seems that 5 is the minimum size for a group to have for this to work correctly.
I would appreciate knowing if this is a feature or a bug in stat_bin (which geom_bar is using) or if I am simply abusing geom_bar.
Also, any suggestions how to get around this would be appreciated.
Sincerely
This occurs because df$dir is numeric, so the ggplot object assumes a continuous x-axis, and aesthetic parameter group is based on the only known discrete variable (fill = grp).
As a result, when there simply aren't that many dir values in grp = [45,60), ggplot gets confused over how wide each bar should be. This becomes more visually obvious if we split the plot into different facets:
ggplot(data=df,
aes(x=dir,y=(..count..)/sum(..count..),
fill = grp)) +
geom_bar() +
facet_wrap(~ grp)
> for(l in levels(df$grp)) print(sort(unique(df$dir[df$grp == l])))
[1] 1 2 3 4 6 7 8 9 10
[1] 1 2 3 4 5 6 7 8 9 10
[1] 2 3 4 5 7 9 10
[1] 2 4 7
We can also check manually that the minimum difference between sorted df$dir values is 1 for the first three grp values, but 2 for the last one. The default bar width is thus wider.
The following solutions should all achieve the same result:
1. Explicitly specify the same bar width for all groups in geom_bar():
ggplot(data=df,
aes(x=dir,y=(..count..)/sum(..count..),
fill = grp)) +
geom_bar(width = 0.9)
2. Convert dir to a categorical variable before passing it to aes(x = ...):
ggplot(data=df,
aes(x=factor(dir), y=(..count..)/sum(..count..),
fill = grp)) +
geom_bar()
3. Specify that the group parameter should be based on both df$dir & df$grp:
ggplot(data=df,
aes(x=dir,
y=(..count..)/sum(..count..),
group = interaction(dir, grp),
fill = grp)) +
geom_bar()
This doesn't directly solve the issue, because I also don't get what's going on with the overlapping values, but it's a dplyr-powered workaround, and might turn out to be more flexible anyway.
Instead of relying on geom_bar to take the cut factor and give you shares via ..count../sum(..count..), you can easily enough just calculate those shares yourself up front, and then plot your bars. I personally like having this type of control over my data and exactly what I'm plotting.
First, I put dir and FF into a data frame/tbl_df, and cut FF. Then count lets me group the data by dir and grp and count up the number of observations for each combination of those two variables, then calculate the share of each n over the sum of n. I'm using geom_col, which is like geom_bar but when you have a y value in your aes.
library(tidyverse)
set.seed(12345)
FF <- rweibull(100,1.7,1) * 20 #mock speeds
FF[FF > 60] <- 59
dir <- sample.int(10, size = 100, replace = TRUE) # mock directions
shares <- tibble(dir = dir, FF = FF) %>%
mutate(grp = cut(FF, breaks = seq(0, 60, by = 15), ordered_result = T, right = F, drop = F)) %>%
count(dir, grp) %>%
mutate(share = n / sum(n))
shares
#> # A tibble: 29 x 4
#> dir grp n share
#> <int> <ord> <int> <dbl>
#> 1 1 [0,15) 3 0.03
#> 2 1 [15,30) 2 0.02
#> 3 2 [0,15) 4 0.04
#> 4 2 [15,30) 3 0.03
#> 5 2 [30,45) 1 0.01
#> 6 2 [45,60) 1 0.01
#> 7 3 [0,15) 6 0.06
#> 8 3 [15,30) 1 0.01
#> 9 3 [30,45) 2 0.02
#> 10 4 [0,15) 6 0.06
#> # ... with 19 more rows
ggplot(shares, aes(x = dir, y = share, fill = grp)) +
geom_col()
Here is my simplified data :
company <-c(rep(c(rep("company1",4),rep("company2",4),rep("company3",4)),3))
product<-c(rep(c(rep(c("product1","product2","product3","product4"),3)),3))
week<-c( c(rep("w1",12),rep("w2",12),rep("w3",12)))
mydata<-data.frame(company=company,product=product,week=week)
mydata$rank<-c(rep(c(1,3,2,3,2,1,3,2,3,2,1,1),3))
mydata=mydata[mydata$company=="company1",]
And, R code I used :
ggplot(mydata,aes(x = week,fill = as.factor(rank))) +
geom_bar(position = "fill")+
scale_y_continuous(labels = percent_format())
In the bar plot, I want to label the percentage by week, by rank.
The problem is the fact that the data doesn't have percentage of rank. And the structure of this data is not suitable to having one.
(of course, the original data has much more observations than the example)
Is there anyone who can teach me How I can label the percentage in this graph ?
I'm not sure I understand why geom_text is not suitable. Here is an answer using it, but if you specify why is it not suitable, perhaps someone might come up with an answer you are looking for.
library(ggplot2)
library(plyr)
mydata = mydata[,c(3,4)] #drop unnecessary variables
data.m = melt(table(mydata)) #get counts and melt it
#calculate percentage:
m1 = ddply(data.m, .(week), summarize, ratio=value/sum(value))
#order data frame (needed to comply with percentage column):
m2 = data.m[order(data.m$week),]
#combine them:
mydf = data.frame(m2,ratio=m1$ratio)
Which gives us the following data structure. The ratio column contains the relative frequency of given rank within specified week (so one can see that rank == 3 is twice as abundant as the other two).
> mydf
week rank value ratio
1 w1 1 1 0.25
4 w1 2 1 0.25
7 w1 3 2 0.50
2 w2 1 1 0.25
5 w2 2 1 0.25
8 w2 3 2 0.50
3 w3 1 1 0.25
6 w3 2 1 0.25
9 w3 3 2 0.50
Next, we have to calculate the position of the percentage labels and plot it.
#get positions of percentage labels:
mydf = ddply(mydf, .(week), transform, position = cumsum(value) - 0.5*value)
#make plot
p =
ggplot(mydf,aes(x = week, y = value, fill = as.factor(rank))) +
geom_bar(stat = "identity")
#add percentage labels using positions defined previously
p + geom_text(aes(label = sprintf("%1.2f%%", 100*ratio), y = position))
Is this what you wanted?