Hi all...
I assume there are a host of GGplot2 users out there.
I have circular plot - polar plot code questions
I needed to create circular ? polar plots of reproductive status for
bats.? I found a great sample of how to do this here:
https://stackoverflow.com/questions/41081376/how-to-create-a-circular-plot-showing-monthly-presence-or-absence-using-radial-p
I modified the sample code to meet the 3 data elements I am using the
"raw data" table below with T=testes enlarge, P= Pregnant and L=
Lactating.
library(data.table)
m <- fread("id?? ?T?? ?month?? ?P?? ?L
1?? ?0?? ?1?? ?0?? ?0
2?? ?0?? ?2?? ?0?? ?0
3?? ?0?? ?3?? ?0?? ?0
4?? ?1?? ?4?? ?0?? ?0
5?? ?1?? ?5?? ?1?? ?0
6?? ?1?? ?6?? ?1?? ?1
7?? ?0?? ?7?? ?1?? ?1
8?? ?0?? ?8?? ?1?? ?1
9?? ?0?? ?9?? ?0?? ?1
10?? ?0?? ?10?? ?0?? ?0
11?? ?0?? ?11?? ?0?? ?0
12?? ?0?? ?12?? ?0?? ?0")
# reshape from wide to long (as preferred by ggplot)
ml <- melt(m, measure.vars = c("T", "P", "L"))
# create factors to ensure desired order
ml[, variable := factor(variable, levels = c("T",
"P","L"))]
ml[, fct_month := factor(month, levels = 1:12, labels = month.abb)]
library(ggplot2)
ggplot(ml[value != 0], aes(x = fct_month, y = variable,
?????????????????????????? group = variable, colour = variable)) +
? geom_line(size = 3) +
? scale_y_discrete(expand = c(0, 1), breaks = NULL) +
? xlim(month.abb) +
? coord_polar() +
? theme_bw() + xlab(NULL) + ylab(NULL)
This is creating a plot more or less as needed.? 4 questions:
1 Do I even need the ID field? Seems not useful.
2 I assume the melt step can be avoided if my data is "Tidy" and long
format at the start, correct?
3? How can I increase the weight of the month lines and labels
4? Where can I add color choices for the 3 variables in the plot? Simply
adding an HTML color number to the ?colour=variable? then plots the data
and labeling one value as that color.
Tnx all. The list is always educational on a daily basis.
Cheers,
Bat Dude
[[alternative HTML version deleted]]
1) If you do not need it do not plot it. However, also consider how others will
use your content. Might it be a trivial piece of information for you, but a
critical piece of information for someone trying to use your content. A meta
analysis, or just wanting to try to relate your outcomes to the results from
their experiment.
2) There would be no need of melt() if the data is already in the proper format.
The long format is not always the right format, though more often than not it is
the right format (at least in my field of study).
3) google search something like "x-axis line weight ggplot" or
something like that. There are excellent online resources to answer focused
questions like that.
4) This might help:
https://www.datanovia.com/en/blog/ggplot-colors-best-tricks-you-will-love/
Tim
-----Original Message-----
From: R-help <r-help-bounces at r-project.org> On Behalf Of Bruce Miller
Sent: Sunday, April 23, 2023 1:19 PM
To: r-help at r-project.org
Subject: [R] Circular plot - polar plot code questions
[External Email]
Hi all...
I assume there are a host of GGplot2 users out there.
I have circular plot - polar plot code questions I needed to create circular -
polar plots of reproductive status for bats. I found a great sample of how to
do this here:
https://stackoverflow.com/questions/41081376/how-to-create-a-circular-plot-showing-monthly-presence-or-absence-using-radial-p
I modified the sample code to meet the 3 data elements I am using the "raw
data" table below with T=testes enlarge, P= Pregnant and L= Lactating.
library(data.table)
m <- fread("id T month P L
1 0 1 0 0
2 0 2 0 0
3 0 3 0 0
4 1 4 0 0
5 1 5 1 0
6 1 6 1 1
7 0 7 1 1
8 0 8 1 1
9 0 9 0 1
10 0 10 0 0
11 0 11 0 0
12 0 12 0 0")
# reshape from wide to long (as preferred by ggplot) ml <- melt(m,
measure.vars = c("T", "P", "L"))
# create factors to ensure desired order ml[, variable := factor(variable,
levels = c("T", "P","L"))]
ml[, fct_month := factor(month, levels = 1:12, labels = month.abb)]
library(ggplot2)
ggplot(ml[value != 0], aes(x = fct_month, y = variable,
group = variable, colour = variable)) +
geom_line(size = 3) +
scale_y_discrete(expand = c(0, 1), breaks = NULL) +
xlim(month.abb) +
coord_polar() +
theme_bw() + xlab(NULL) + ylab(NULL)
This is creating a plot more or less as needed. 4 questions:
1 Do I even need the ID field? Seems not useful.
2 I assume the melt step can be avoided if my data is "Tidy" and long
format at the start, correct?
3 How can I increase the weight of the month lines and labels
4 Where can I add color choices for the 3 variables in the plot? Simply adding
an HTML color number to the "colour=variable" then plots the data and
labeling one value as that color.
Tnx all. The list is always educational on a daily basis.
Cheers,
Bat Dude
[[alternative HTML version deleted]]
______________________________________________
R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.r-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Hi Bruce,
Reading your message, I get the idea that you want a radial.plot with
arcs to indicate "at least one bat is in this state'.This can be done
with an addition to the rp.type= argument. If you already have what
you want in this format, it may not be worth programming it. However,
if you want "how many bats are in this state":
m <- read.table(
text="id T month P L
1 0 1 0 0
2 0 2 0 0
3 0 3 0 0
4 1 4 0 0
5 1 5 1 0
6 1 6 1 1
7 0 7 1 1
8 0 8 1 1
9 0 9 0 1
10 0 10 0 0
11 0 11 0 0
12 0 12 0 0",
header=TRUE)
library(plotrix)
png("batstate.png",width=600)
kiteChart(t(m[,c("T","P","L")]),
main="Bat state by month",
xlab="Month",ylab="State",
varlabels=c("Testiular
enlargement","Pregnant","Lactatins"),
timelabels=month.abb)
dev.off()
Jim
On Mon, Apr 24, 2023 at 7:22?PM Bruce Miller <batsncats at gmail.com>
wrote:>
> Hi all...
> I assume there are a host of GGplot2 users out there.
> I have circular plot - polar plot code questions
> I needed to create circular ? polar plots of reproductive status for
> bats. I found a great sample of how to do this here:
>
https://stackoverflow.com/questions/41081376/how-to-create-a-circular-plot-showing-monthly-presence-or-absence-using-radial-p
>
> I modified the sample code to meet the 3 data elements I am using the
> "raw data" table below with T=testes enlarge, P= Pregnant and L=
Lactating.
>
> library(data.table)
>
>
> m <- fread("id T month P L
> 1 0 1 0 0
> 2 0 2 0 0
> 3 0 3 0 0
> 4 1 4 0 0
> 5 1 5 1 0
> 6 1 6 1 1
> 7 0 7 1 1
> 8 0 8 1 1
> 9 0 9 0 1
> 10 0 10 0 0
> 11 0 11 0 0
> 12 0 12 0 0")
> # reshape from wide to long (as preferred by ggplot)
> ml <- melt(m, measure.vars = c("T", "P",
"L"))
>
> # create factors to ensure desired order
> ml[, variable := factor(variable, levels = c("T",
"P","L"))]
>
> ml[, fct_month := factor(month, levels = 1:12, labels = month.abb)]
> library(ggplot2)
> ggplot(ml[value != 0], aes(x = fct_month, y = variable,
> group = variable, colour = variable)) +
> geom_line(size = 3) +
> scale_y_discrete(expand = c(0, 1), breaks = NULL) +
> xlim(month.abb) +
> coord_polar() +
> theme_bw() + xlab(NULL) + ylab(NULL)
>
> This is creating a plot more or less as needed. 4 questions:
> 1 Do I even need the ID field? Seems not useful.
> 2 I assume the melt step can be avoided if my data is "Tidy" and
long
> format at the start, correct?
> 3 How can I increase the weight of the month lines and labels
> 4 Where can I add color choices for the 3 variables in the plot? Simply
> adding an HTML color number to the ?colour=variable? then plots the data
> and labeling one value as that color.
>
> Tnx all. The list is always educational on a daily basis.
> Cheers,
> Bat Dude
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
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