I have two separate data frames - each representing a feature (activity, and sleep) and the amount of days that each of these features were recorded by each id number. The amount of days need to reflect on the y-axis and the feature itself needs to reflect on the x-axis.
I managed to draw the boxplots separately, showing the outliers clearly esp for the one set, however if I want to place the two boxplots next to each other, the outliers do not show up clearly. Also, how do I get the names of the two features (activity and sleep) on my x-axis?
The dataframe for the "sleep "feature:
head(idday)
A tibble: 6 x 2
id days
<dbl> <int>
1 1503960366 25
2 1644430081 4
3 1844505072 3
4 1927972279 5
5 2026352035 28
6 2320127002 1
The dataframe for the "activity "feature:
head(iddaya)
A tibble: 6 x 2
id days
<dbl> <int>
1 1503960366 31
2 1624580081 31
3 1644430081 30
4 1844505072 31
5 1927972279 31
6 2022484408 31
My attempt for sleep:
ggplot(idday, aes(y = days), boxwex = 0.05) +
stat_boxplot(geom = "errorbar",
width = 0.2) +
geom_boxplot(alpha=0.9, outlier.color="red")
and for activity:
ggplot(iddaya, aes(y = days), boxwex = 0.05) +
stat_boxplot(geom = "errorbar",
width = 0.2) +
geom_boxplot(alpha=0.9, outlier.color="red")
I then combined them:
boxplot(summary(idday$days), summary(iddaya$days))
In this final image the outliers do not show clearly, and I want to name my x-axis and y-axis.
There are several ways to achieve your task. One way could be:
If your dataframes are coalled df_sleep and df_activity then we could combine them in a named list and add a new column feature, then plot:
df_sleep
df_activity
library(tidyverse)
bind_rows(list(sleep = df_sleep, activity = df_activity), .id = 'feature') %>%
ggplot(aes(x = feature, y=days, fill=feature))+
geom_boxplot()
If you want to compare these two boxplots with each other I recommend to use the same range for your y-axis. To achieve this you first have to combine both data frames. You can do this with inner_join() from the dplyr package.
data_combined <- inner_join(idday, iddaya,
by = "id",
suffix = c("_sleep", "_activity"))
Then you need to transform your data frame into long-format with pivot_longer() from the tidyr package:
data_combined_long <- data_combined %>%
pivot_longer(days_sleep:days_activity,
names_to = "features",
names_prefix = "days_",
values_to = "days")
After that you can again use ggplot() to create your boxplot. But now you have to define that you want your x-axis to represent your features:
ggplot(data_combined_long, aes(y = days, x = features), boxwex = 0.05)+
stat_boxplot(geom = "errorbar",
width = 0.5) +
geom_boxplot(alpha=0.9, outlier.color="red")
Your plot should then look like this:
Related
I have some experience with base R but am trying to learn tidyverse and ggplot. I have a dataframe with 4 columns of data. I want a simple x-y plot, where the first column of data is on the x-axis, and the data in the other 3 columns is plotted on the y-axis, resulting in 3 lines on one plot. The first 15 lines of my data look like this (sorry about the image - I don't know how to insert a sample of my data):
screen shot - first 15 rows of data
I tried to plot the second and third columns of data as follows: ,
ggplot(data=SWRC_SL, aes(x=SWRC_SL$pressure_head, y=SWRC_SL$UNSODA_theta)) +
geom_line(colour="red") + scale_x_log10() +
ggplot(data=SWRC_SL, aes(x=SWRC_SL$pressure_head, y=SWRC_SL$Vrugt_theta)) +
geom_line(colour="blue") + scale_x_log10()
I get this error:
Error: Don't know how to add ggplot(data = SWRC_SL, aes(x = SWRC_SL$pressure_head, y = SWRC_SL$Vrugt_theta)) to a plot
I believe I should be using something like "group=" to indicate which columns should be plotted, but I haven't been able to find an example that shows how you can use gglot to plot data across multiple columns. What am I missing ?
ggplot() is only ever called once when you create a chart. Try with the following:
ggplot() +
geom_line(data=SWRC_SL, aes(x=pressure_head, y=UNSODA_theta), colour="red") +
geom_line(data=SWRC_SL, aes(x=pressure_head, y=Vrugt_theta), colour="blue") +
scale_x_log10()
A better method would be to turn your data to long, where the UNSODA_theta and Vrugt_theta data are in the same column (say thetas), and have another column (say type_theta) indicating whether the data is for UNSODA_theta or Vrugt_theta. Then you could do the following:
ggplot(data=SWRC_SL, aes(x=pressure_head, y=thetas, colour=type_theta)) +
geom_line() +
scale_x_log10()
This is more desirable because ggplot2 will include a legend indicating what type of theta the colours are applied to.
As suggested by #Marius, the most efficient way to plot your data is to convert them into a long format.
Using tidyverse, you can have the use of pivot_longer function (from tidyr package) and write the following code:
library(tidyverse)
SWRC_SL %>% pivot_longer(.,-pressure_head, names_to = "variable", values_to = "value") %>%
ggplot(aes(x = pressure_head, y = value, color = variable))+
geom_line()+
scale_x_log10()
EDIT: Illustrating example
Using this dummy dataset:
pressure UNSODA_theta Vrugt_theta Cassel_theta
1 0 -1.4672500 1.4119747 -2.0553118
2 1 0.5210227 0.6189239 1.4817574
3 2 -0.1587546 1.4094018 2.2796175
4 3 1.4645873 2.6888733 -0.4631109
5 4 -0.7660820 2.5865884 -1.8799346
6 5 -0.4302118 0.6690922 0.9633620
First, you pivot your data into a long format:
df %>% pivot_longer(.,-pressure, names_to = "variable", values_to = "value")
# A tibble: 45 x 3
pressure variable value
<int> <chr> <dbl>
1 0 UNSODA_theta -1.47
2 0 Vrugt_theta 1.41
3 0 Cassel_theta -2.06
4 1 UNSODA_theta 0.521
5 1 Vrugt_theta 0.619
6 1 Cassel_theta 1.48
7 2 UNSODA_theta -0.159
8 2 Vrugt_theta 1.41
9 2 Cassel_theta 2.28
10 3 UNSODA_theta 1.46
# … with 35 more rows
Now, your data are suitable for the plotting with ggplot2, you can directly add ggplot command to the previous command by adding a "pipe" (%>%) between them:
library(tidyverse)
df %>% pivot_longer(.,-pressure, names_to = "variable", values_to = "value") %>%
ggplot(aes(x = pressure, y = value, color = variable))+
geom_line()+
scale_x_log10()
And you get the following plot with legend included:
Data example
structure(list(pressure = 0:14, UNSODA_theta = c(-1.46725002909224,
0.521022742648139, -0.158754604716016, 1.4645873119698, -0.766081999604665,
-0.430211753928547, -0.926109497377437, -0.17710396143654, 0.402011779486338,
-0.731748173119606, 0.830373167981674, -1.20808278630446, -1.04798441280774,
1.44115770684428, -1.01584746530465), Vrugt_theta = c(1.41197471231751,
0.61892394889108, 1.40940183965093, 2.68887328620405, 2.58658843344197,
0.669092199317234, -1.28523553529247, 3.49766158983416, 1.66706616676549,
1.5413273359637, 0.986600476854091, 1.51010842295293, 0.835624168230333,
1.42069464325451, 0.599753256022356), Cassel_theta = c(-2.05531181632119,
1.48175740118232, 2.27961753824932, -0.46311085383842, -1.87993463341154,
0.963361958516736, -0.0670637053409687, -2.59982761023726, 0.00319778952040447,
-0.945450500892219, -0.511452869790608, -1.73485854395378, 2.7047128618762,
-0.496698054586832, -2.40827011837962)), class = "data.frame", row.names = c(NA,
-15L))
My data is
PC_Name Electors_2009 Electors_2014 Electors_2019 Voters_2009 Voters_2014
1 Amritsar 1241099 1477262 1507875 814503 1007196
2 Anandpur Sahib 1338596 1564721 1698876 904606 1086563
3 Bhatinda 1336790 1525289 1621671 1048144 1176767
4 Faridkot 1288090 1455075 1541971 930521 1032107
5 Fatehgarh Sahib 1207556 1396957 1502861 838150 1030954
6 Ferozpur 1342488 1522111 1618419 956952 1105412
7 Gurdaspur 1318967 1500337 1595284 933323 1042699
8 Hoshiarpur 1299234 1485286 1597500 843123 961297
9 Jalandhar 1339842 1551497 1617018 899607 1040762
10 Khadoor Sahib 1340145 1563256 1638842 946690 1040518
11 Ludhiana 1309308 1561201 1683325 846277 1100457
12 Patiala 1344864 1580273 1739600 935959 1120933
13 Sangrur 1251401 1424743 1529432 931247 1099467
Voters_2019
1 859513
2 1081727
3 1200810
4 974947
5 985948
6 1172033
7 1103887
8 990791
9 1018998
10 1046032
11 1046955
12 1177903
13 1105888
I have written the code
data <- read.csv(file = "Punjab data 3.csv")
data
library(ggplot2)
library(reshape2)
long <- reshape2::melt(data, id.vars = "PC_Name")
ggplot(long, aes(PC_Name, value, fill = variable)) + geom_freqpoly(stat="identity",binwidth = 500)
I am trying to plot something like this
I tried line chart and geom line but I am not sure where problem resides. I am trying geom polygon now but its not plotting.I want to compare voters or electors not both of them according to year 2009 2014 2019.Sorry for bad english.
I want to plot PC_Name on x-axis and compare Electors_2009 with Voters_2009 and Electors_2014 with Voters_2014 and all these on same graph. So on y axis I will have 'values' after melting.
It sounds like you were interested in PC_Name on horizontal axis, and value (after melting) on vertical axis. Perhaps you might be interested in a barplot with and compare electors and voters side-by-side?
As suggested by #camille, you could split your data frame's variable column after melting into two columns (one with either Electors or Voters, and the other column with the year). This would provide flexibility in plot options.
Here are a couple of possibilities to start with:
You could order your variable factor how you would like (e.g., Electors_2009, Voters_2009, Electors_2014, etc. for comparison) and use geom_bar.
You could use facet_wrap to make comparisons between Electors and Voters by year.
library(ggplot2)
library(reshape2)
long <- reshape2::melt(data, id.vars = "PC_Name")
# Split electors/voters from year into 2 columns
long <- cbind(long, colsplit(long$variable, "_", c("type", "year")))
# Change order of variable factor for comparisons
long$variable <- factor(long$variable, levels =
c("Electors_2009", "Voters_2009",
"Electors_2014", "Voters_2014",
"Electors_2019", "Voters_2019"))
# Plot value vs. PC_Name using barplot (all years together)
ggplot(long, aes(PC_Name, value, fill = variable)) +
geom_bar(position = "dodge", stat = "identity")
# Show example plot faceted by year
ggplot(long, aes(PC_Name, value, fill = type)) +
geom_bar(position = "dodge", stat = "identity") +
facet_wrap(~year, ncol = 1)
Please let me know if this is what you had in mind. There would be alternative options available.
Sorry if this question already exists - was googling for a while now already and didn't find anything.
I am relatively new to R and learning while doing all of this.
I'm supposed to create some PDF via r markdown that analyses patient-data with specific main-diagnosis and secondary-diagnosis. For this I'm supposed to plot some numbers via ggplot (geom_bar and geom_boxplot).
So what I do so far is, I retrieve data-sets that include both codes via SQL and load them into data.table-objects afterwards. Afterwards I join them to get the data I need.
After this I add columns that consist sub-strings of those codes and others that consist the count of those certain sub-strings (so I can plot the occurrences of every code).
I wanted now for example to put certain data.table into a geom_bar or geom_boxplot and make it visible. This actually works, but my y-axis has a weird scale that doesn't fit the numbers it actually should show. The proportions of the bars are also not accurate.
For example: one diagnoses appears 600 times and the other one 1000 times. The y-axis shows steps of 0 - 500.000 - 1.000.000 - 1.500.000 - ....
The Bar that shows 600 is super small and the bar with 1000 goes up to 1.500.000
If I create a new variable before and count what I need via count() and plot this it just works. The rows I put for the y-axis have in both variable the same datatype (integer)
So here is just how I create the data.table that I use for plotting
exazerbationsHdComorbiditiesNd <- allExazerbationsHd[allComorbiditiesNd, on="encounter_num", nomatch=0]
exazerbationsHdComorbiditiesNd <- exazerbationsHdComorbiditiesNd[, c("i.DurationGroup", "i.DurationInDays", "i.start_date", "i.end_date", "i.duration", "i.patient_num"):=NULL]
exazerbationsHdComorbiditiesNd[ , IcdHdCodeCount := .N, by = concept_cd]
exazerbationsHdComorbiditiesNd[ , IcdHdCodeClassCount := .N, by = IcdHdClass]
If I want to bar-plot now for example IcdHdClass by IcdHdCodeClassCount I do following:
ggplot(exazerbationsHdComorbiditiesNd, aes(exazerbationsHdComorbiditiesNd$IcdHdClass, exazerbationsHdComorbiditiesNd$IcdHdCodeClassCount, label=exazerbationsHdComorbiditiesNd$IcdHdCodeClassCount)) + geom_bar(stat = "identity") + geom_text(vjust = 0, size = 5)
It outputs said bar-plot with weird proportions.
If I do first:
plotTest <- count(exazerbationsHdComorbiditiesNd, exazerbationsHdComorbiditiesNd$IcdHdClass)
And then bar-plot it:
ggplot(plotTest, aes(plotTest$`exazerbationsHdComorbiditiesNd$IcdHdClass`, plotTest$n, label=plotTest$n)) + geom_bar(stat = "identity") + geom_text(vjust = 0, size = 5)
Its all perfect and works.
I checked also data-types of the columns I needed:
sapply(exazerbationsHdComorbiditiesNd, class)
sapply(plotTest, class)
In both variables the columns I need are of the type character and integer
Edit:
Unfortunately I cant post images. So here are just the links to those.
Here is a screenshot of the plot with wrong y-axis:
https://ibb.co/CbxX1n7
And here is a screenshot of the plot shown right:
https://ibb.co/Xb8gyx1
Here is some example-data that I copied out the data.table object:
Exampledata
Since you added the class counts as an additional column--rather than aggregating--what’s happening is that for each row in your data, the class counts get stacked on top of each other:
library(tidyverse)
set.seed(42)
df <- tibble(class = sample(letters[1:3], 10, replace = TRUE)) %>%
add_count(class, name = "count")
df # this is essentially what your data looks like
#> # A tibble: 10 x 2
#> class count
#> <chr> <int>
#> 1 a 5
#> 2 a 5
#> 3 a 5
#> 4 a 5
#> 5 b 3
#> 6 b 3
#> 7 b 3
#> 8 a 5
#> 9 c 2
#> 10 c 2
ggplot(df, aes(class, count)) + geom_bar(stat = "identity")
You could use position = "identity" so that the bars don’t get stacked:
ggplot(df, aes(class, count)) +
geom_bar(stat = "identity", position = "identity")
However, that creates a whole bunch of unnecessary layers in your plot that you can’t see. A better approach would be to drop the extra rows from your data before plotting:
df %>%
distinct(class, count)
#> # A tibble: 3 x 2
#> class count
#> <chr> <int>
#> 1 a 5
#> 2 b 3
#> 3 c 2
df %>%
distinct(class, count) %>%
ggplot(aes(class, count)) +
geom_bar(stat = "identity")
Created on 2019-09-05 by the reprex package (v0.3.0.9000)
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()
Long time fan of this site, first time user though.
Been searching for a similar/working result for this question.
I am trying to show the PROPORTION that each level of a 2 level factor appear at three locations. All in a side by side bar chart in ggplot.
Here is the code I've been using to (try) to create the chart. The result has been two charts: one using geom_bar and geom_col, respectively. What I'd like is essentially a combination of the two. The first, but with the colors and Y axis of the second.
Thank you!
ggplot(df,aes(x = Stream,fill = death)) +
geom_bar(position = "dodge")+
scale_fill_manual(values = c(rep(c("gray45", "gray75"))))+
labs(fill="Time of Death")
death_stream <-df %>%
group_by(Stream,Tree_Death)%>%
summarise (n = n()) %>%
mutate(rel.freq = paste0(round(100 * n/sum(n), 0), "%"))
death_stream %>%
ggplot(aes(x = Stream,y = rel.freq)) +
geom_col(position = "dodge",fill = "grey50", colour = "black")+
labs(fill="Time of Death")
Thanks Axeman, I figured it out.
the "class" of "rel.freq." was character. I tried specifying as numeric, but instead of
<int>
it produced
<dbl>
turns out all i had to do was revert the tibble BACK to data.frame and specify as numeric. Another way is to export as excel file and change the column "rel.freq" to NUMBERS in Excel.
death_stream
# A tibble: 6 x 4
Stream Tree_Death n percent
<int> <int> <int> <int>
1 1 0 25 33
2 1 1 50 67
3 2 0 17 30
4 2 1 40 70
5 3 0 120 70
6 3 1 51 30