ggplot2: comparing 2 groups through fraction of its members - r

Lets say we have 10000 users classified in 2 groups: lvl beginner and lvl pro.
Every user has a rank, going from 1 to 20.
The df:
# beginers
n <- 7000
user.id <- 1:n
lvl <- "beginer"
rank <- sample(1:20, n, replace = TRUE,
prob = seq(.9,0.1,length.out = 20))
df.beginer <- data.frame(user.id, rank, lvl)
# pros
n <- 3000
user.id <- 1:n
lvl <- "pro"
rank <- sample(1:20, n, replace = TRUE,
prob = seq(.9,0.3,length.out = 20))
df.pro <- data.frame(user.id, rank, lvl)
library(dplyr)
df <- bind_rows(df.beginer, df.pro)
df2 <- tbl_df(df) %>% group_by(lvl, rank) %>% mutate(count = n())
Problem 1:
I need a bar plot comparing each group side by side, but instead if giving me counts, I need percents, so the bars from each group will have the same max hight (100%)
The plot I got so far:
library(ggplot2)
plot <- ggplot(df2, aes(rank))
plot + geom_bar(aes(fill=lvl), position="dodge")
Problem 2:
I need a line plot comparing each group, so we will have 2 lines, but instead if giving me counts, I need percents, so the lines from each group will have the same max hight (100%)
The plot I got so far:
plot + geom_line(aes(y=count, color=lvl))
Problem 3:
Lets say that the ranks are cumulative, so a user who has rank 3, also has rank 1 and 2. A user who has rank 20 has all ranks from 1 to 20.
So, when plotting, I want the plot to start with rank 1 having 100% of users,
rank 2 will have something less, rank 3 even less and so on.
I got all this done on tableau but I really dislike it and want to show myself that R can handle all this stuff.
Thank you!

Three problems, three solutions:
problem 1 - calculate percentage and use geom_col
df %>%
group_by(rank, lvl)%>%
summarise(count = n()) %>%
group_by(lvl) %>%
mutate(count_perc = count / sum(count)) %>% # calculate percentage
ggplot(., aes(x = rank, y = count_perc))+
geom_col(aes(fill = lvl), position = 'dodge')
problem 2 - pretty much the same as problem 1 except use geom_line instead of geom_col
df %>%
group_by(rank, lvl)%>%
summarise(count = n()) %>%
group_by(lvl) %>%
mutate(count_perc = count / sum(count)) %>%
ggplot(., aes(x = rank, y = count_perc))+
geom_line(aes(colour = lvl))
problem 3 - make use of arrange and cumsum
df %>%
group_by(lvl, rank) %>%
summarise(count = n()) %>% # count by level and rank
group_by(lvl) %>%
arrange(desc(rank)) %>% # sort descending
mutate(cumulative_count = cumsum(count)) %>% # use cumsum
mutate(cumulative_count_perc = cumulative_count / max(cumulative_count)) %>%
ggplot(., aes(x = rank, y = cumulative_count_perc))+
geom_line(aes(colour = lvl))

Related

How to plot % positive cases (y-axis) by collection date (x-axis) and by other factors (R)?

Please help!
I have case data I need to prepare for a report soon and just cannot get the graphs to display properly.
From a dataset with CollectionDate as the "record" of cases (i.e. multiple rows with the same date means more cases that day), I want to display Number of positive cases/total (positive + negative) cases for that day as a percent on the y-axis, with collection dates along the x-axis. Then I want to break down by region. Goal is to look like this but in terms of daily positives/# of tests rather than just positives vs negatives. I also want to add a horizontal line on every graph at 20%.
I have tried manipulating it before, in and after ggplot:
ggplot(df_final, aes(x =CollectionDate, fill = TestResult)) +
geom_bar(aes(y=..prop..)) +
scale_y_continuous(labels=percent_format())
Which is, again, close. But the percents are wrong because they are just taking the proportion of that day against counts of all days instead of per day.
Then I tried using tally()in the following command to try and count per region and aggregate:
df_final %>%
group_by(CollectionDate, Region, as.factor(TestResult)) %>%
filter(TestResult == "Positive") %>%
tally()
and I still cannot get the graphs right.
Suggestions?
A quick look at my data:
head(df_final)
Well, I have to say that I am not 100% sure that I got what you want, but anyway, this can be helpful.
The data: Since you are new here, I have to let you know that using a simple and reproducible version of your data will make it easier to the rest of us to answer. To do this you can simulate a data frame o any other objec, or use dput function on it.
library(ggplot2)
library(dplyr)
data <- data.frame(
# date
CollectionDate = sample(
seq(as.Date("2020-01-01"), by = "day", length.out = 15),
size = 120, replace = TRUE),
# result
TestResult = sample(c("Positive", "Negative"), size = 120, replace = TRUE),
# region
Region = sample(c("Region 1", "Region2"), size = 120, replace = TRUE)
)
With this data, you can do ass follow to get the plots you want.
# General plot, positive cases proportion
data %>%
count(CollectionDate, TestResult, name = "cases") %>%
group_by(CollectionDate) %>%
summarise(positive_pro = sum(cases[TestResult == "Positive"])/sum(cases)) %>%
ggplot(aes(x = CollectionDate, y = positive_pro)) +
geom_col() +
geom_hline(yintercept = 0.2)
# positive proportion by day within region
data %>%
count(CollectionDate, TestResult, Region, name = "cases") %>%
group_by(CollectionDate, Region) %>%
summarise(
positive_pro = sum(cases[TestResult == "Positive"])/sum(cases)
) %>%
ggplot(aes(x = CollectionDate, y = positive_pro)) +
geom_col() +
# horizontal line at 20%
geom_hline(yintercept = 0.2) +
facet_wrap(~Region)
I can get you halfway there (refer to the comments in the code for clarifications). This code is for the counts per day per region (plotted separately for each region). I think you can tweak things further to calculate the counts per day per county too; and whole state should be a cakewalk. I wish you good luck with your report.
rm(list = ls())
library(dplyr)
library(magrittr)
library(ggplot2)
library(scales)
library(tidyr) #Needed for the spread() function
#Dummy data
set.seed(1984)
sdate <- as.Date('2000-03-09')
edate <- as.Date('2000-05-18')
dateslist <- as.Date(sample(as.numeric(sdate): as.numeric(edate), 10000, replace = TRUE), origin = '1970-01-01')
df_final <- data.frame(Region = rep_len(1:9, 10000),
CollectionDate = dateslist,
TestResult = sample(c("Positive", "Negative"), 10000, replace = TRUE))
#First tally the positve and negative cases
#by Region, CollectionDate, TestResult in that order
df_final %<>%
group_by(Region, CollectionDate, TestResult) %>%
tally()
#Then
#First spread the counts (in n)
#That is, create separate columns for Negative and Positive cases
#for each Region-CollectionDate combination
#Then calculate their proportions (as shown)
#Now you have Negative and Positive
#percentages by CollectionDate by Region
df_final %<>%
spread(key = TestResult, value = n) %>%
mutate(Negative = Negative/(Negative + Positive),
Positive = Positive/(Negative + Positive))
#Plotting this now
#Since the percentages are available already
#Use geom_col() instead of geom_bar()
df_final %>% ggplot() +
geom_col(aes(x = CollectionDate, y = Positive, fill = "Positive"),
position = "identity", alpha = 0.4) +
geom_col(aes(x = CollectionDate, y = Negative, fill = "Negative"),
position = "identity", alpha = 0.4) +
facet_wrap(~ Region, nrow = 3, ncol = 3)
This yields:

Percentages of a variable in another variable using dplyr and creating a boxplot with standard deviation

I have this df. I wish to make glasses into a factor with a level <=1.5 and >1.5. hereafter I want to examine how many percent of in both levels have a ciss value above 16. Each levels are considered as one group, so that should count as 100%.
glasses <- c(1.0,1.1,1.1,1.6,1.2,1.7,2.2,5.2,8.2,2.5,3.0,3.3,3.0,3.0)
ciss <- c(2,9,10,54,65,11,70,54,0,65,8,60,47,2)
df <- cbind(glasses, ciss)
df
I want a outcome looking like
glasses Percentages ciss > 16
<=1.5 xx%
>1.5 xx%
I tried using dplyr
dfnew <- df %>% mutate(ani=cut(glasses, breaks=c(-Inf, 1.5, Inf),
labels=c("<=1.5",">1.5")))
dfnew %>% group_by(ani) %>% mutate(perc = ciss>16 / sum(ciss))
And lastly, I would like to demonstrate the percentages in boxplot (glasses on the x axis, percentages of ciss above 16 on the y axis).
try this.
require(tidyverse)
require(ggplot2)
require(reshape2)
#Input data
glasses = c(1.0,1.1,1.1,1.6,1.2,1.7,2.2,5.2,8.2,2.5,3.0,3.3,3.0,3.0)
ciss = c(2,9,10,54,65,11,70,54,0,65,8,60,47,2)
#Bind in dataframe
df = as.data.frame(cbind(glasses,ciss))
df %>%
mutate(typglass = if_else(glasses > 1.5,">1.5","<=1.5")) %>%
filter(ciss > 16) %>%
group_by(typglass) %>%
summarise (n = n()) %>%
mutate(freq = n / sum(n)) %>%
ggplot() +
geom_bar(aes(x = typglass, y = freq, fill = typglass), stat = "identity", width = 0.5) +
theme_classic()
Gives the following result:

Barplot with set x, y and fill categories R

I have the following type of data and would like to create a stacked barplot, which would show the sum of Number on y axis for different bins of Distance on x axis which would indicate distance. In fact, that would be a sort of histogram, but not with frequencies on y but the sums of Number per set bin. This would be cumulative for all categories in Dest which would be marked with different colours.
Thanks so much.
library(ggplot2)
df <- data.frame(c(rep("A",20),rep("B",25),rep("C",35)),sample(1:30, 80,replace = TRUE),
rnorm(80,45,8))
colnames(df) <- c("Dest","Number","Distance")
ggplot(data = df, aes(x = Distance, y = Number, fill = Dest)) +
geom_histogram(colour = c("red","blue","green"))
Here are 2 solutions in case you want to be the one that specifies the (Distance) bins and not the histogram:
Option 1 (using ntile)
Here's a solution that allows you to specify the number of bins using ntile, which means that those bins will have more or less the same number of observations:
library(tidyverse)
df <- data.frame(c(rep("A",20),rep("B",25),rep("C",35)),sample(1:30, 80,replace = TRUE),
rnorm(80,45,8))
colnames(df) <- c("Dest","Number","Distance")
df %>%
group_by(bin = ntile(Distance, 3)) %>% # specify number of bins you want
mutate(DistRange = paste0(round(min(Distance)), " - ", round(max(Distance)))) %>%
ungroup() %>%
group_by(Dest, bin, DistRange = fct_reorder(DistRange, bin)) %>%
summarise(sum_number = sum(Number)) %>%
ungroup() %>%
ggplot(aes(DistRange, sum_number, fill=Dest))+
geom_col()
Option 2 (using cut)
An alternative option using cut to specify ranges:
df %>%
mutate(bin = cut(Distance, breaks = c(min(Distance)-1, 40, 50, 55, max(Distance)))) %>% # specify ranges
group_by(Dest, bin) %>%
summarise(sum_number = sum(Number)) %>%
ungroup() %>%
ggplot(aes(bin, sum_number, fill=Dest))+
geom_col()

R - ggplot2 parallel categorical plot

I am working with categorical longitudinal data. My data has 3 simple variables such as :
id variable value
1 1 1 c
2 1 2 b
3 1 3 c
4 1 4 c
5 1 5 c
...
Where variable is basically time, and value are the 3 possible categories one id can take.
I am interested in producing a "parallel" longitudinal graph, similar to this with ggplot2
I am struggling a bit to get it right. What I came up for now is this :
dt0 %>% ggplot(aes(variable, value, group = id, colour = id)) +
geom_line(colour="grey70") +
geom_point(aes(colour=value, size = nn), size=4) +
scale_colour_brewer(palette="Set1") + theme_minimal()
The issue with this graph is that we can't really see the "thickness" of the "transition" (the id lines).
I wondered if you could help me for :
a) help make visible the id lines, or make it "thicker" according to the number of id going form one state to the other
b) I also would like to re-size the point according to the number of id in this state. I tried to do it with geom_point(aes(colour=value, size = nn), size=4) but it doesn't seem to work.
Thanks.
# data #
library(dplyr)
library(ggplot2)
set.seed(10)
# generate random sequences #
dt = as.data.frame( cbind(id = 1:1000, replicate(5, sample( c('a', 'b', 'c'), prob = c(0.1,0.2,0.7), 1000, replace = T)) ) )
# transform to PP file #
dt = dt %>% melt(id.vars = c('id'))
# create a vector 1-0 if the activity was performed #
dt0 = dt %>% group_by(id) %>% mutate(variable = 1:n()) %>% arrange(id)
# create the number of people in that state #
dt0 = dt0 %>% count(id, variable, value)
dt0 = dt0 %>% group_by(variable, value, n) %>% mutate(nn = n())
# to produce the first graph # 
library(vcrpart)
otsplot(dt0$variable, factor(dt0$value), dt0$id)
you were so close with geom_point(aes(colour=value, size = nn), size=4), the problem was that with you redefined size after defining it in aes() ggplot overwrote the variable reference with the constant 4. Assuming you want to use nn to scale line thinkness as well, you could tweak your code to this:
dt0 %>% ggplot(aes(variable, value, group = id, colour = id)) +
geom_line(colour="grey70", aes(size = nn)) +
geom_point(aes(colour=value, size = nn)) +
scale_colour_brewer(palette="Set1") + theme_minimal()
If you wanted to use a lag value for the line thickness I would suggests adding that as a new column in dt0.

split data into groups in R

My data frame looks like this:
plant distance
one 0
one 1
one 2
one 3
one 4
one 5
one 6
one 7
one 8
one 9
one 9.9
two 0
two 1
two 2
two 3
two 4
two 5
two 6
two 7
two 8
two 9
two 9.5
I want to split distance of each level into groups by interval(for instance,interval=3), and compute percentage of each group. Finally, plot the percentages of each level of each group similar like this:
my code:
library(ggplot2)
library(dplyr)
dat <- data %>%
mutate(group = factor(cut(distance, seq(0, max(distance), 3), F))) %>%
group_by(plant, group) %>%
summarise(percentage = n()) %>%
mutate(percentage = percentage / sum(percentage))
p <- ggplot(dat, aes(x = plant, y = percentage, fill = group)) +
geom_bar(stat = "identity", position = "stack")+
scale_y_continuous(labels=percent)
p
But my plot is shown below: the group 4 was missing.
And I found that the dat was wrong, the group 4 was NA.
The likely reason is that the length of group 4 was less than the interval=3, so my question is how to fix it? Thank you in advance!
I have solved the problem.The reason is that the cut(distance, seq(0, max(distance), 3), F) did not include the maximum and minimum values.
Here is my solution:
dat <- my_data %>%
mutate(group = factor(cut(distance, seq(from = min(distance), by = 3, length.out = n()/ 3 + 1), include.lowest = TRUE))) %>%
count(plant, group) %>%
group_by(plant) %>%
mutate(percentage = n / sum(n))

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