[R] Spicing Up Native Circular Plot Using ggplot2
I have some angle data from an animal behavior study that I would like to plot
for publication using ggplot2. What follows is my current workflow with some
example data.
### BEGIN SCRIPT ###
### Create two data frames of random Cartesian coordinates ###
df1 <- data.frame(
x = sample(10, 11, replace = TRUE),
y = sample(10, 11, replace = TRUE))
df2 <- data.frame(
x = sample(10, 11, replace = TRUE),
y = sample(10, 11, replace = TRUE))
### Write a function that converts continuous Cartesian coordinates to
velocities ###
get.polar <- function(df)
{
x <- diff(df$x)
y <- diff(df$y)
d <- complex(real = x, imaginary = y)
steps <- data.frame(speed = Mod(d), angle = Arg(d))
steps[-1,] # Deletes the first row as it does not contain an angle measurement
steps$time <- (1:nrow(steps))/30 # generates a time column in seconds (1 data
point = 1/30 of a second)
return(steps)
}
df1_polar <- get.polar(df1)
df2_polar <- get.polar(df2)
require(circular)
### Convert angles into an object of type 'circular' ###
df1_rad <- circular(df1_polar$angle, type = 'angles', units = 'radians',
zero=0, rotation = "counter")
df2_rad <- circular(df2_polar$angle, type = 'angles', units = 'radians',
zero=0, rotation = "counter")
### Convert radians to degrees with a clockwise rotation and zero at "north" ###
df1_deg <- conversion.circular(df1_rad, type = "angles", units = "degrees",
zero = pi/2, rotation = "clock")
df2_deg <- conversion.circular(df2_rad, type = "angles", units = "degrees",
zero = pi/2, rotation = "clock")
### Convert negative rotations to positive ###
df1_deg[df1_deg < 0] <- df1_deg[df1_deg < 0] + 360
df2_deg[df2_deg < 0] <- df2_deg[df2_deg < 0] + 360
par(pty = "s")
plot(df1_deg, units = "degrees")
ticks.circular(circular(seq(0,(11/6)*pi, pi/6)), zero = pi/2, rotation =
"clock", tcl = 0.075)
points(df2_deg, zero = pi/2, rotation = "clock", pch = 16, col = "darkgrey",
next.points = -0.2)
### END SCRIPT ###
Some suggestions for turning this rough plot into something publishable using
ggplot2?
Thank you!
Salvatore A. Sidoti
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Re: [R] inserting row(column) in array or dataframe at specified row(column)
> On May 1, 2016, at 10:53 AM, Jan Kacaba wrote:
>
> Hello dear R users,
>
> Is there a function or package which can insert row, column or array in
> another array at specified place (row or column)?
>
> I have made several attempts at this function optimizing both speed, code
> readability and ease of use. The functions are of following format:
>
> appcol=function(original_array, inserted_object, column_number,
> overwrite=FALSE)
This does not offer code, only the list of formals. If you want help with
coding, then you should provide some. I remember a posting by Gabor
Grothendieck on StackOverflow (where he cited another blogger) where he
demonstrated how to implement a postfix "+" function like that of C, that I
_think_ might address this question but without a MWE and desired result I
cannot do any testing.
>
> If overwrite=TRUE the columns after column_number are ovewritten by
> inserted_object else the columns after column_number are shifted.
>
> Now I have started using package dplyr and it seams that there is no
> inserting function either. One can only append at the end or at the
> beginning of tbl_df. Is it true?
Probably not. There's always:
> fortunes::fortune("Yoda")
Evelyn Hall: I would like to know how (if) I can extract some of the
information from the summary of my nlme.
Simon Blomberg: This is R. There is no if. Only how.
-- Evelyn Hall and Simon 'Yoda' Blomberg
R-help (April 2005)
> [[alternative HTML version deleted]]
One of _your_ tasks is now to learn "how" to tell gmail to post in plaintext.
--
David Winsemius
Alameda, CA, USA
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Re: [R] row names, coulmn names
> On May 1, 2016, at 11:09 AM, Jan Kacaba wrote: > > Hello dear R helpers, > > Is it possible to have more than 1 row for column names in data.frame, > array, tbl_df? I would like to have column numbers in the first row, string > names in the second row, physical unit in third row. It's possible to embed "\n" in names but whether that will deliver desired results with plotting and printing functions may be another matter. You would always need to quote names, even when using "$". > How would I do it? > > Derek > > [[alternative HTML version deleted]] > > __ > R-help@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. David Winsemius Alameda, CA, USA __ R-help@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.
Re: [R] Aggregate FIPS data to State and Census divisions
> On May 1, 2016, at 9:30 AM, Miluji Sb wrote:
>
> Dear Dennis,
>
> Thank you for your reply. I can use the dplyr/data.table packages to
> aggregate - its the matching FIPS codes to their states that I am having
> trouble. Thanks again.
So post some example code that demonstrate you paid attention to the answer
given. Both dplyr and data.table not limited for aggregation. They do several
versions of matching. So does the base function `merge`. We do not yet know
what sort of efforts you have made. r-help@r-project.org is not an online
code-writing service.
--
David
>
> Sincerely,
>
> Milu
>
> On Sun, May 1, 2016 at 6:20 PM, Dennis Murphy wrote:
>
>> Hi:
>>
>> Several such packages exist. Given the size of your data, it's likely
>> that the dplyr and data.table packages would be worth investigating.
>> Both are well documented.
>>
>> Dennis
>>
>> On Sun, May 1, 2016 at 8:30 AM, Miluji Sb wrote:
>>> Dear all,
>>>
>>> I have the following data by US FIPS code. Is there a package to
>> aggregate
>>> the data by State and Census divisions?
>>>
>>> temp <- dput(head(pop1,5))
>>> structure(list(FIPS = c("01001", "01003", "01005", "01007", "01009"
>>> ), death_2050A1 = c(18.19158, 101.63088, 13.18896, 10.30068,
>>> 131.91798), death_2050A2 = c(22.16349, 116.58387, 15.85324, 12.78564,
>>> 155.20506), death_2050B1 = c(21.38906, 76.23018, 21.38218, 17.14269,
>>> 151.64466), death_2050B2 = c(23.43543, 81.39378, 22.96802, 18.76926,
>>> 161.86404), death_2050BC = c(21.89947, 93.88002, 18.60352, 15.1032,
>>> 152.43414)), .Names = c("FIPS", "death_2050A1", "death_2050A2",
>>> "death_2050B1", "death_2050B2", "death_2050BC"), row.names = c(NA,
>>> 5L), class = "data.frame")
>>>
>>> Thank you!
>>>
>>> Sincerely,
>>>
>>> Milu
>>>
>>>[[alternative HTML version deleted]]
>>>
>>> __
>>> R-help@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.
>>
>
> [[alternative HTML version deleted]]
>
> __
> R-help@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.
David Winsemius
Alameda, CA, USA
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] inserting row(column) in array or dataframe at specified row(column)
If you can address your columns by name then order shouldn't matter. If the column order does matter, perhaps a matrix is a better structure to use? On Sun, May 1, 2016, 10:56 AM Jan Kacaba wrote: > Hello dear R users, > > Is there a function or package which can insert row, column or array in > another array at specified place (row or column)? > > I have made several attempts at this function optimizing both speed, code > readability and ease of use. The functions are of following format: > > appcol=function(original_array, inserted_object, column_number, > overwrite=FALSE) > > # If overwrite=TRUE the columns after column_number are ovewritten by > inserted_object else the columns after column_number are shifted. > > Now I have started using package dplyr and it seams that there is no > inserting function either. One can only append at the end or at the > beginning of tbl_df. Is it true? > > [[alternative HTML version deleted]] > > __ > R-help@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. > [[alternative HTML version deleted]] __ R-help@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.
Re: [R] row names, coulmn names
I think what you ask isn't ideal.Each column in a dataframe should be the same data type. While column names are stored in the first row when the df is exported to CSV, they are not stored as columns in the data frame. Instead the column names are stored as a separate attribute of the df. This is why you need to use names(df) to access them, not df[1,]. I don't have access to R right now, but I think ?attributes or ??"attributes" should point you in the correct direction. On Sun, May 1, 2016, 11:11 AM Jan Kacaba wrote: > Hello dear R helpers, > > Is it possible to have more than 1 row for column names in data.frame, > array, tbl_df? I would like to have column numbers in the first row, string > names in the second row, physical unit in third row. > How would I do it? > > Derek > > [[alternative HTML version deleted]] > > __ > R-help@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. > [[alternative HTML version deleted]] __ R-help@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.
[R] row names, coulmn names
Hello dear R helpers, Is it possible to have more than 1 row for column names in data.frame, array, tbl_df? I would like to have column numbers in the first row, string names in the second row, physical unit in third row. How would I do it? Derek [[alternative HTML version deleted]] __ R-help@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.
[R] inserting row(column) in array or dataframe at specified row(column)
Hello dear R users, Is there a function or package which can insert row, column or array in another array at specified place (row or column)? I have made several attempts at this function optimizing both speed, code readability and ease of use. The functions are of following format: appcol=function(original_array, inserted_object, column_number, overwrite=FALSE) # If overwrite=TRUE the columns after column_number are ovewritten by inserted_object else the columns after column_number are shifted. Now I have started using package dplyr and it seams that there is no inserting function either. One can only append at the end or at the beginning of tbl_df. Is it true? [[alternative HTML version deleted]] __ R-help@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.
Re: [R] Aggregate FIPS data to State and Census divisions
Dear Dennis,
Thank you for your reply. I can use the dplyr/data.table packages to
aggregate - its the matching FIPS codes to their states that I am having
trouble. Thanks again.
Sincerely,
Milu
On Sun, May 1, 2016 at 6:20 PM, Dennis Murphy wrote:
> Hi:
>
> Several such packages exist. Given the size of your data, it's likely
> that the dplyr and data.table packages would be worth investigating.
> Both are well documented.
>
> Dennis
>
> On Sun, May 1, 2016 at 8:30 AM, Miluji Sb wrote:
> > Dear all,
> >
> > I have the following data by US FIPS code. Is there a package to
> aggregate
> > the data by State and Census divisions?
> >
> > temp <- dput(head(pop1,5))
> > structure(list(FIPS = c("01001", "01003", "01005", "01007", "01009"
> > ), death_2050A1 = c(18.19158, 101.63088, 13.18896, 10.30068,
> > 131.91798), death_2050A2 = c(22.16349, 116.58387, 15.85324, 12.78564,
> > 155.20506), death_2050B1 = c(21.38906, 76.23018, 21.38218, 17.14269,
> > 151.64466), death_2050B2 = c(23.43543, 81.39378, 22.96802, 18.76926,
> > 161.86404), death_2050BC = c(21.89947, 93.88002, 18.60352, 15.1032,
> > 152.43414)), .Names = c("FIPS", "death_2050A1", "death_2050A2",
> > "death_2050B1", "death_2050B2", "death_2050BC"), row.names = c(NA,
> > 5L), class = "data.frame")
> >
> > Thank you!
> >
> > Sincerely,
> >
> > Milu
> >
> > [[alternative HTML version deleted]]
> >
> > __
> > R-help@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.
>
[[alternative HTML version deleted]]
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Removing NAs from dataframe (for use in Vioplot)
> On May 1, 2016, at 12:15 AM, Mike Smith wrote:
>
On Apr 30, 2016, at 12:58 PM, Mike Smith wrote:
>
Hi
>
First post and a relative R newbie
>
I am using the vioplot library to produce some violin plots.
>
> DW> It's a package, not a library.
>
I have an input CSV with columns off irregular length that contain NAs. I
want to strip the NAs out and produce a multiple violin plot automatically
labelled using the headers. At the moment I do this
>
Code:
ds1 = read.csv("http://www.lecturematerials.co.uk/data/spelling.csv";)
library(vioplot)
y6<-na.omit(ds1$y6)
y5<-na.omit(ds1$y5)
y4<-na.omit(ds1$y4)
y3<-na.omit(ds1$y3)
y2<-na.omit(ds1$y2)
y1<-na.omit(ds1$y1)
vioplot(y6, y5, y4,y3,y2,y1,horizontal=TRUE, names=c("Y6",
"Y5","Y4","Y3","Y2","Y1"), col = "lightblue")
>
>
Two queries:
>
1. Is there a more elegant way of automatically stripping the NAs, passing
the columns to the function along with the header names??
>
>
>>> ds2 <- lapply( ds1, na.omit)
>
>
> Fantastic - that does the trick! Easy when you know how!!
>
> Follow-on: is there a way feed all the lists from ds2 to vioplot? It is now a
> series of lists (rather than a dataframe - is that right?). So this works,
>
> library(vioplot)
> ds1 = read.csv("http://www.lecturematerials.co.uk/data/spelling.csv";)
> ds2 <- lapply( ds1, na.omit)
> vioplot(ds2$y1,ds2$y2)
>
> but this doesnt
>
> library(vioplot)
> ds1 = read.csv("http://www.lecturematerials.co.uk/data/spelling.csv";)
> ds2 <- lapply( ds1, na.omit)
> vioplot(ds2)
>
Error in min(data) : invalid 'type' (list) of argument
I had trouble, too. I thought, "Oh, this is easy, just use `do.call`", but I
failed in getting any successful argument passing that way.
> do.call('vioplot', list(x=ds2[[6]], ds2[-6]) )
Error in min(data) : invalid 'type' (list) of argument
> do.call('vioplot', c(x=ds2[[6]], ds2[-6]) )
Error in vioplot(x1 = 5L, x2 = 10L, x3 = 6L, x4 = 7L, x5 = 7L, x6 = 6L, :
argument "x" is missing, with no default
Eventually I re-wrote the first line of vioplot's body to behave the way I
thought made the most sense:
vioplot <-
function (x, ..., range = 1.5, h = NULL, ylim = NULL, names = NULL,
horizontal = FALSE, col = "magenta", border = "black", lty = 1,
lwd = 1, rectCol = "black", colMed = "white", pchMed = 19,
at, add = FALSE, wex = 1, drawRect = TRUE)
{
datas <- c(list(x), ...)
# but keep the rest the same.
# I then get success with:
vioplot(ds2[['y1']], ds2[-6]) # success
do.call('vioplot', list(x=ds2[[6]], ds2[-6]) ) # also successes
do.call('vioplot', list(x=ds2[['y1']], ds2[-6]) )
This is retracing a route explored 8 years ago:
http://markmail.org/search/?q=list%3Aorg.r-project.r-help+list+argument+to+vioplot#query:list%3Aorg.r-project.r-help%20list%20argument%20to%20vioplot+page:1+mid:j6lapgri46utcod7+state:results
It's probably easier to use that helper-function approach than my efforts at
hacking.
Best of luck;
David
2. Can I easily add the sample size to each violin plotted??
>
?violplot
>>> No documentation for ‘violplot’ in specified packages and libraries:
>>> you could try ‘??violplot’
>
> DW> I see that I mispled that _package_ name. However, after loading
> DW> it I realized that I had no way of replicating what you are
> DW> seeing, because you didn't provide that file (or even something
> DW> that resembles it. It's rather unclear how you wanted this information
> presented.
>
> The original code *should* have worked as the csv was online. There doesnt
> seem to be any option in vioplot to add the sample size (these are all small
> samples which I wanted to highlight) so I dont know if this is easily done
> elsewhere.
>
> Thanks again!!
> ---
> Mike Smith
>
David Winsemius
Alameda, CA, USA
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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[R] Aggregate FIPS data to State and Census divisions
Dear all,
I have the following data by US FIPS code. Is there a package to aggregate
the data by State and Census divisions?
temp <- dput(head(pop1,5))
structure(list(FIPS = c("01001", "01003", "01005", "01007", "01009"
), death_2050A1 = c(18.19158, 101.63088, 13.18896, 10.30068,
131.91798), death_2050A2 = c(22.16349, 116.58387, 15.85324, 12.78564,
155.20506), death_2050B1 = c(21.38906, 76.23018, 21.38218, 17.14269,
151.64466), death_2050B2 = c(23.43543, 81.39378, 22.96802, 18.76926,
161.86404), death_2050BC = c(21.89947, 93.88002, 18.60352, 15.1032,
152.43414)), .Names = c("FIPS", "death_2050A1", "death_2050A2",
"death_2050B1", "death_2050B2", "death_2050BC"), row.names = c(NA,
5L), class = "data.frame")
Thank you!
Sincerely,
Milu
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Removing NAs from dataframe (for use in Vioplot)
>>> On Apr 30, 2016, at 12:58 PM, Mike Smith wrote:
>>> Hi
>>> First post and a relative R newbie
>>> I am using the vioplot library to produce some violin plots.
DW> It's a package, not a library.
>>> I have an input CSV with columns off irregular length that contain NAs. I
>>> want to strip the NAs out and produce a multiple violin plot automatically
>>> labelled using the headers. At the moment I do this
>>> Code:
>>> ds1 = read.csv("http://www.lecturematerials.co.uk/data/spelling.csv";)
>>> library(vioplot)
>>> y6<-na.omit(ds1$y6)
>>> y5<-na.omit(ds1$y5)
>>> y4<-na.omit(ds1$y4)
>>> y3<-na.omit(ds1$y3)
>>> y2<-na.omit(ds1$y2)
>>> y1<-na.omit(ds1$y1)
>>> vioplot(y6, y5, y4,y3,y2,y1,horizontal=TRUE, names=c("Y6",
>>> "Y5","Y4","Y3","Y2","Y1"), col = "lightblue")
>>> Two queries:
>>> 1. Is there a more elegant way of automatically stripping the NAs, passing
>>> the columns to the function along with the header names??
>> ds2 <- lapply( ds1, na.omit)
Fantastic - that does the trick! Easy when you know how!!
Follow-on: is there a way feed all the lists from ds2 to vioplot? It is now a
series of lists (rather than a dataframe - is that right?). So this works,
library(vioplot)
ds1 = read.csv("http://www.lecturematerials.co.uk/data/spelling.csv";)
ds2 <- lapply( ds1, na.omit)
vioplot(ds2$y1,ds2$y2)
but this doesnt
library(vioplot)
ds1 = read.csv("http://www.lecturematerials.co.uk/data/spelling.csv";)
ds2 <- lapply( ds1, na.omit)
vioplot(ds2)
>>> 2. Can I easily add the sample size to each violin plotted??
>>> ?violplot
>> No documentation for ‘violplot’ in specified packages and libraries:
>> you could try ‘??violplot’
DW> I see that I mispled that _package_ name. However, after loading
DW> it I realized that I had no way of replicating what you are
DW> seeing, because you didn't provide that file (or even something
DW> that resembles it. It's rather unclear how you wanted this information
presented.
The original code *should* have worked as the csv was online. There doesnt seem
to be any option in vioplot to add the sample size (these are all small samples
which I wanted to highlight) so I dont know if this is easily done elsewhere.
Thanks again!!
---
Mike Smith
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
