I have a data frame like this:
nthreads ab_1 ab_2 ab_3 ab_4 ...
1 0 0 0 0 ...
2 1 0 12 1 ...
4 2 1 22 1 ...
8 10 2 103 8 ...
Each ab_X represents different causes that trigger an abort in my code. I want to summarize all abort causes in a barplot displaying nthreads vs aborts with different ab_X stacked in each bar.
I can do
ggplot(data, aes(x=factor(nthreads), y=ab_1+ab_2+ab_3+ab_4)) +
geom_bar(stat="identity")
But it only gives the total number of aborts. I know there is a fill aes, but I can not make it work with continuous variables.
You have to melt the data frame first
library(data.table)
dt_melt <- melt(data, id.vars = 'nthreads')
ggplot(dt_melt, aes(x = nthreads, y = value, fill = variable)) +
geom_bar(stat = 'identity')
It gives the total number of aborts because you are adding them together :)
You need to get your data from wide to long format first, i.e. create one column for the abort causes and a second for their values. You can use tidyr::gather for that. I also find geom_col more convenient than geom_bar:
library(tidyr)
library(ggplot2)
data %>%
gather(abort, value, -nthreads) %>%
ggplot(aes(factor(nthreads), value)) +
geom_col(aes(fill = abort)) +
labs(x = "nthreads", y = "count")
Note that the range of values makes some of the bars rather hard to see, so you might want to think about scales and maybe even facets.
Related
As an R-beginner, there's one hurdle that I just can't find the answer to. I have a table where I can see the amount of responses to a question according to gender.
Response
Gender
n
1
1
84
1
2
79
2
1
42
2
2
74
3
1
84
3
2
79
etc.
I want to plot these in a column chart: on the y I want the n (or its proportions), and on the x I want to have two seperate bars: one for gender 1, and one for gender 2. It should look like the following example that I was given:
The example that I want to emulate
However, when I try to filter the columns according to gender inside aes(), it returns an error! Could anyone tell me why my approach is not working? And is there another practical way to filter the columns of the table that I have?
ggplot(table) +
geom_col(aes(x = select(filter(table, gender == 1), Q),
y = select(filter(table, gender == 1), n),
fill = select(filter(table, gender == 2), n), position = "dodge")
Maybe something like this:
library(RColorBrewer)
library(ggplot2)
df %>%
ggplot(aes(x=factor(Response), y=n, fill=factor(Gender)))+
geom_col(position=position_dodge())+
scale_fill_brewer(palette = "Set1")
theme_light()
Your answer does not work, because you are assigning the x and y variables as if it was two different datasets (one for x and one for y). In line with the solution from TarJae, you need to think of it as the axis in a diagram - so you need for your x axis to assign the categorical variables you are comparing, and you want for the y axis to assign the numerical variables which determines the height of the bars. Finally, you want to compare them by colors, so each group will have a different color - that is where you include your grouping variable (here, I use fill).
library(dplyr) ## For piping
library(ggplot2) ## For plotting
df %>%
ggplot(aes(x = Response, y = n, fill = as.character(Gender))) +
geom_bar(stat = "Identity", position = "Dodge")
I am adding "Identity" because the default in geom_bar is to count the occurences in you data (i.e., if you data was not aggregated). I am adding "Dodge" to avoid the bars to be stacked. I will recommend you, to look at this resource for more information: https://r4ds.had.co.nz/index.html
So i have this data, that I would like to plot onto a graph - all the lines on the same graph
>ndiveristy
Quadrant nta.shannon ntb.shannon ntc.shannon
1 1 2.188984 0.9767274 1.8206140
2 2 1.206955 1.3240481 1.3007058
3 3 1.511083 0.5805081 0.7747041
4 4 1.282976 1.4222243 0.4843907
5 5 1.943930 1.7337267 1.5736545
6 6 2.030524 1.8604619 1.6860711
7 7 2.043356 1.5707110 1.5957869
8 8 1.421275 1.4363365 1.5456799
here is the code that I am using to try to plot it:
ggplot(ndiversity,aes(x=Quadrant,y=Diversity,colour=Transect))+
geom_point()+
geom_line(aes(y=nta.shannon),colour="red")+
geom_line(aes(y=ntb.shannon),colour="blue")+
geom_line(aes(y=ntc.shannon),colour="green")
But all I am getting is the error
data must be a data frame, or other object coercible by fortify(), not a numeric vector.
Can someone tell me what I'm doing wrong
Typically, rather than using multiple geom_line calls, we would only have a single call, by pivoting your data into long format. This would create a data frame of three columns: one for Quadrant, one containing labels nta.shannon, ntb.shannon and ntc.shannon, and a column for the actual values. This allows a single geom_line call, with the label column mapped to the color aesthetic, which automatically creates an instructive legend for your plot too.
library(tidyverse)
as.data.frame(ndiversity) %>%
pivot_longer(-1, names_to = 'Type', values_to = 'Shannon') %>%
mutate(Type = substr(Type, 1, 3)) %>%
ggplot(aes(Quadrant, Shannon, color = Type)) +
geom_line(size = 1.5) +
theme_minimal(base_size = 16) +
scale_color_brewer(palette = 'Set1')
For posterity:
convert to data frame
ndiversity <- as.data.frame(ndiversity)
get rid of the excess code
ggplot(ndiversity,aes(x=Quadrant))+
geom_line(aes(y=nta.shannon),colour="red")+
geom_line(aes(y=ntb.shannon),colour="blue")+
geom_line(aes(y=ntc.shannon),colour="green")
profit
not the prettiest graph I ever made
I'm currently trying to develop a surface plot that examines the results of the below data frame. I want to plot the increasing values of noise on the x-axis and the increasing values of mu on the y-axis, with the point estimate values on the z-axis. After looking at ggplot2 and ggplotly, it's not clear how I would plot each of these columns in surface or 3D plot.
df <- "mu noise0 noise1 noise2 noise3 noise4 noise5
1 1 0.000000 0.9549526 0.8908646 0.919630 1.034607
2 2 1.952901 1.9622004 2.0317115 1.919011 1.645479
3 3 2.997467 0.5292921 2.8592976 3.034377 3.014647
4 4 3.998339 4.0042379 3.9938346 4.013196 3.977212
5 5 5.001337 4.9939060 4.9917115 4.997186 5.009082
6 6 6.001987 5.9929932 5.9882173 6.015318 6.007156
7 7 6.997924 6.9962483 7.0118066 6.182577 7.009172
8 8 8.000022 7.9981131 8.0010066 8.005220 8.024569
9 9 9.004437 9.0066182 8.9667536 8.978415 8.988935
10 10 10.006595 9.9987245 9.9949733 9.993018 10.000646"
Thanks in advance.
Here's one way using geom_tile(). First, you will want to get your data frame into more of a Tidy format, where the goal is to have columns:
mu: nothing changes here
noise: need to combine your "noise0", "noise1", ... columns together, and
z: serves as the value of the noise and we will apply the fill= aesthetic using this column.
To do that, I'm using dplyr and gather(), but there are other ways (melt(), or pivot_longer() gets you that too). I'm also adding some code to pull out just the number portion of the "noise" columns and then reformatting that as an integer to ensure that you have x and y axes as numeric/integers:
# assumes that df is your data as data.frame
df <- df %>% gather(key="noise", value="z", -mu)
df <- df %>% separate(col = "noise", into=c('x', "noise"), sep=5) %>% select(-x)
df$noise <- as.integer(df$noise)
Here's an example of how you could plot it, but aesthetics are up to you. I decided to also include geom_text() to show the actual values of df$z so that we can see better what's going on. Also, I'm using rainbow because "it's pretty" - you may want to choose a more appropriate quantitative comparison scale from the RColorBrewer package.
ggplot(df, aes(x=noise, y=mu, fill=z)) + theme_bw() +
geom_tile() +
geom_text(aes(label=round(z, 2))) +
scale_fill_gradientn(colors = rainbow(5))
EDIT: To answer OP's follow up, yes, you can also showcase this via plotly. Here's a direct transition:
p <- plot_ly(
df, x= ~noise, y= ~mu, z= ~z,
type='mesh3d', intensity = ~z,
colors= colorRamp(rainbow(5))
)
p
Static image here:
A much more informative way to show this particular set of information is to see the variation of df$z as it relates to df$mu by creating df$delta_z and then using that to plot. (you can also plot via ggplot() + geom_tile() as above):
df$delta_z <- df$z - df$mu
p1 <- plot_ly(
df, x= ~noise, y= ~mu, z= ~delta_z,
type='mesh3d', intensity = ~delta_z,
colors= colorRamp(rainbow(5))
)
Giving you this (static image here):
ggplot accepts data in the long format, which means that you need to melt your dataset using, for example, a function from the reshape2 package:
dfLong = melt(df,
id.vars = "mu",
variable.name = "noise",
value.name = "meas")
The resulting column noise contains entries such as noise0, noise1, etc. You can extract the numbers and convert to a numeric column:
dfLong$noise = with(dfLong, as.numeric(gsub("noise", "", noise)))
This converts your data to:
mu noise meas
1 1 0 1.0000000
2 2 0 2.0000000
3 3 0 3.0000000
...
As per ggplot documentation:
ggplot2 can not draw true 3D surfaces, but you can use geom_contour(), geom_contour_filled(), and geom_tile() to visualise 3D surfaces in 2D.
So, for example:
ggplot(dfLong,
aes(x = noise
y = mu,
fill = meas)) +
geom_tile() +
scale_fill_gradientn(colours = terrain.colors(10))
Produces:
I am looking to do a plot to look into the most common occuring FINAL_CALL_TYPE in my dataset by BOROUGH in NYC. I have a dataset with over 3 million obs. I broke this down into a sample of 2000, but have refined it even more to just the incident type and the borough it occured in.
Essentially, I want to create a plot that will visualize to the 5 most common call types in each borough, with the count of how many of each call types there was in each borough.
Below is a brief look of how my data looks with just Call Type and Borough
> head(df)
FINAL_CALL_TYPE BOROUGH
1804978 INJURY BRONX
1613888 INJMAJ BROOKLYN
294874 INJURY BROOKLYN
1028374 DRUG BROOKLYN
1974030 INJURY MANHATTAN
795815 CVAC BRONX
This shows how many unique values there are
> str(df)
'data.frame': 2000 obs. of 2 variables:
$ FINAL_CALL_TYPE: Factor w/ 139 levels "ABDPFC","ABDPFT",..: 50 48 50 34 50 25 17 138 28 28 ...
$ BOROUGH : Factor w/ 5 levels "BRONX","BROOKLYN",..: 1 2 2 2 3 1 4 2 4 4 ...
This is the code that I have tried
> ggplot(df, aes(x=BOROUGH, y=FINAL_CALL_TYPE)) +
+ geom_bar(stat = 'identity') +
+ facet_grid(~BOROUGH)
and below is the result
I have tried a few suggestions accross this community, but I have not found any that shows how to perform the action with 2 columns.
It would be much appreciated if there is someone who know a solution for this.
Thanks!
If I understand correctly, you can use tidyverse to doo something like:
df <- df %>%
group_by(BOROUGH, FINAL_CALL) %>%
summarise(count = n()) %>%
top_n(n = 5, wt = count)
then plot
ggplot(df, aes(x = FINAL_CALL, y = count) +
geom_col() +
facet(~BOROUGH, scales = "free")
creating the barplot
The first part of your problem is to create the barplot. With geom_bar you only need to supply the x variable, as the y-axis is the count of observations of that variable. You can then use the facet option to separate that count into different panels for another grouping variable.
library(ggplot2)
ggplot(data = diamonds, aes(x = color)) +
geom_bar() +
facet_grid(.~cut)
filtering to top 5 observations
The second part of your problem, limiting the data to only the top five in each group is slightly more complex. An easy way to do this is to first tally the data which will create a column n that has the count of observations. By adding the sort option we can filter the data to the first five rows in each group. tally, like summarize, automatically removes the last group.
In the ggplot call I now use geom_col instead of geom_bar and I explicitly specify that the y-variable is n (n is created by tally).
geom_bar plots the count of observations per x-variable, geom_col plots a y-variable value for each value of the x-variable.
scales = "free_x" removes values from the x-axis that are present in one cut panel but not another.
library(tidyverse)
df <- diamonds %>%
group_by(cut, color) %>%
tally(sort = TRUE) %>%
filter(row_number() <= 5)
ggplot(data = df, aes(x = color, y = n)) +
geom_col() +
facet_grid(.~cut, scales = "free_x")
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