Re: [R] Double buffering plots on Windows
Hi
Take a look at dev.hold() and dev.flush()
Paul
On 23/03/24 06:43, Bickis, Mikelis wrote:
Hello:
I want to present a sequence of plots as an animation. As a toy example
consider the code
function(n){for (i in 1:n){
plot(1:100,sin(i*(1:100)),type="l")
title(paste("n=",i))
segments(0,0,100,0,col=2)
}}
This sort-of works on a MacOS platform, but the rendering of the plots
is a bit choppy. Inserting a sleep function allows the plots to evolve
smoothly.
function(n){for (i in 1:n){
plot(1:100,sin(i*(1:100)),type="l")
title(paste("n=",i))
segments(0,0,100,0,col=2)
Sys.sleep(.2)
}}
However, on a Windows platform, only the last plot is rendered without
the Sys.sleep, so the dynamic element is lost. Inserting the Sys.sleep
does allow all the plots to be rendered, but they seem to be erased
before they are drawn again, so there is substantial flicker in the
appearance.
Is there some kind of double-buffering available within R, so that plots
are rendered only after they are fully drawn, leaving the previous plot
visible until it is replaced? I just used the default graphics driver on
Windows — is there perhaps a different driver that will the graphics
smoother?
Mik Bickis
Professor Emeritus
Department of Mathematics and Statistics
University of Saskatchewan
__
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--
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Te Kura Tatauranga | Department of Statistics
Waipapa Taumata Rau | The University of Auckland
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] geom_edge & color
Dear Kommo
Many thanks for the valuable solution.
Sibylle
-Original Message-
From: R-help On Behalf Of Kimmo Elo
Sent: Friday, March 22, 2024 12:10 PM
To: r-help@r-project.org
Subject: Re: [R] geom_edge & color
Hi,
this seems to work (assuming that your problem was the setting of
colours...):
--- snip ---
network %>%
ggraph(., layout = "auto") +
# This produces an error...
# geom_edge_arc(curvature=0.3, aes(width=(E(network)$weight/10),
color=c("darkblue", "red")[as.factor(edge_list$relationship)], alpha=0.5))
+
# ... this works :-)
geom_edge_arc(curvature=0.3, aes(width=E(network)$weight/10,
color=edge_list$relationship), alpha=.5) +
scale_edge_color_manual(values=c("pos"="darkblue", "neg"="red")) +
# This does not work either...
# geom_node_point(aes(size = V(network)$hub_score*200, color=
as.factor(V(network)$community))) +
# ... so try this :)
geom_node_point(aes(size = V(network)$hub_score*200,
color=V(network)$Subcategory_type)) +
geom_node_text(aes(label = V(network)$name), size=3, color="white",
repel=T)+
scale_color_scico_d(palette = "batlow")+
scale_edge_width(range = c(0.2,4))+
scale_size(range = c(0.5,15)) +
theme(plot.background = element_rect(fill = "black"),
legend.position = "right",
panel.background = element_rect(fill = "black"))
--- snip ---
At least in my data created with your code, the object "network" does not have
an attribute "community". I use the existing "Subcategory_type"
instead, because I had no time to debug this problem :-)
I do not know whether this produces what you expect or want to visualise.
HTH,
Kimmo
pe, 2024-03-22 kello 08:59 +0100, sibylle.stoec...@gmx.ch kirjoitti:
> Dear community
>
>
>
> Find enclosed the full working example.
>
>
>
> Many thanks
>
> Sibylle
>
>
>
> Test_cat.csv
>
>
> Names
>
> Subcategory_type
>
> sources.cyto
>
> source
>
> Factor
>
>
> A.A
>
> material
>
> "A"
>
> A
>
> 1
>
>
> B.B
>
> material
>
> "B"
>
> B
>
> 1
>
>
> C.C
>
> regulation
>
> "C"
>
> C
>
> 1
>
>
> D.D
>
> regulation
>
> "D"
>
> D
>
> 1
>
>
> E.E
>
> habitat
>
> "E"
>
> E
>
> 1
>
>
> F.F
>
> cultural
>
> "F"
>
> F
>
> 1
>
>
>
> Test_adjac.csv
>
>
> A.A
>
> B.B
>
> C.C
>
> D.D
>
> E.E
>
> F.F
>
>
> A.A
>
> 0
>
> 0
>
> 5
>
> 5
>
> 5
>
> 5
>
>
> B.B
>
> 4
>
> 0
>
> 1
>
> 1
>
> 1
>
> 1
>
>
> C.C
>
> 5
>
> 5
>
> 0
>
> 5
>
> 4
>
> 2
>
>
> D.D
>
> 5
>
> 0
>
> 5
>
> 0
>
> 5
>
> 3
>
>
> E.E
>
> 5
>
> 1
>
> 5
>
> 5
>
> 0
>
> 4
>
>
> F.F
>
> 1
>
> 2
>
> 3
>
> 4
>
> 5
>
> 5
>
>
>
>
>
> Edges_table-Test.csv
>
>
>
>
> Names
>
> target
>
> weight
>
> relationship
>
>
> B.B
>
> A.A
>
> 4
>
> pos
>
>
> C.C
>
> A.A
>
> 5
>
> pos
>
>
> D.D
>
> A.A
>
> 5
>
> neg
>
>
> E.E
>
> A.A
>
> 5
>
> pos
>
>
> F.F
>
> A.A
>
> 1
>
> pos
>
>
> C.C
>
> B.B
>
> 5
>
> pos
>
>
> E.E
>
> B.B
>
> 1
>
> pos
>
>
> F.F
>
> B.B
>
> 2
>
> neg
>
>
> A.A
>
> C.C
>
> 5
>
> pos
>
>
> B.B
>
> C.C
>
> 1
>
> pos
>
>
> D.D
>
> C.C
>
> 5
>
> pos
>
>
> E.E
>
> C.C
>
> 5
>
> pos
>
>
> F.F
>
> C.C
>
> 3
>
> pos
>
>
> A.A
>
> D.D
>
> 5
>
> neg
>
>
> B.B
>
> D.D
>
> 1
>
> pos
>
>
> C.C
>
> D.D
>
> 5
>
> pos
>
>
> E.E
>
> D.D
>
> 5
>
> pos
>
>
> F.F
>
> D.D
>
> 4
>
> pos
>
>
> A.A
>
> E.E
>
> 5
>
> pos
>
>
> B.B
>
> E.E
>
> 1
>
> pos
>
>
> C.C
>
> E.E
>
> 4
>
> pos
>
>
> D.D
>
> E.E
>
> 5
>
> pos
>
>
> F.F
>
> E.E
>
> 5
>
> pos
>
>
> A.A
>
> F.F
>
> 5
>
> pos
>
>
> B.B
>
> F.F
>
> 1
>
> neg
>
>
> C.C
>
> F.F
>
> 2
>
> pos
>
>
> D.D
>
> F.F
>
> 3
>
> pos
>
>
> E.E
>
> F.F
>
> 4
>
> pos
>
>
> F.F
>
> F.F
>
> 5
>
> pos
>
>
>
>
>
>
>
> #upload librairies
>
> library(circlize)
>
> library(ggplot2)
>
> library(igraph)
>
> library(tidyverse)
>
> library(RColorBrewer)
>
> library(stringi)
>
> library(scico)
>
> library(plotly)
>
> library(ggraph)
>
>
>
> #upload
>
> aes<-read.csv("Test_adjac.csv", row.names = 1)
>
> details<-read.csv("Test_cat.csv")
>
>
>
>
>
> # adjacency table
>
> aes_collapsed<-aes %>%
>
> rownames_to_column(var='Names') %>%
>
> tidyr::gather(target, weight, 1:ncol(aes)+1) %>%
>
> dplyr::filter(weight != 0) %>%
>
> mutate(weight = ifelse(weight == "-1", 0, weight)) # here 0 =
> negative values
>
>
>
> write.csv(aes_collapsed, "edges_table-Test.csv", row.names = F)
>
> edge_list<-read.csv("edges_table-Test.csv")
>
>
>
>
>
> #create network and add some necessary attributes (vertices) for the
> plot
>
>
>
> network <- graph_from_data_frame(aes_collapsed, directed= FALSE,
>
> vertices = details)
>
>
>
> ### network and vertex with 'subcategory_type'
>
>
>
> temp<-cluster_optimal(network)
>
> temp<-cbind(membership=temp$membership,
[R] an issue about subsetting a vector
To the R-Help list, I would like to have a clarification about an issue that I observe when subsetting a vector. This is R version 4.3.3 on Windows 10. -- Example with a vector: > a <- 1:5 > a [1] 1 2 3 4 5 So we have, with a negative index: > a[-3] [1] 1 2 4 5 But when the index is integer(0), we have this: > a[integer(0)] integer(0) > a[-integer(0)] integer(0) When it comes to the function integer(), the R Help file says: "Value: integer creates a integer vector of the specified length. Each element of the vector is equal to 0." But we see below that integer(0) is some kind of null vector, that is, no numbers are represented by integer(0): > class(integer(0)) [1] "integer" > length(integer(0)) [1] 0 So my question: in the expression a[-integer(0)], what happens exactly with the index -integer(0)? We see that integer(0), although of class integer, does not represent any numbers, as its length is zero, so it seems to me that it makes no sense to calculate its negative -integer(0). What exactly is -integer(0)? In particular, why a[-integer(0)] is not the whole vector a, that is, [1] 1 2 3 4 5? In the example below, if the invalid index -99 is presented to a, the result is the whole vector: > a[-99] [1] 1 2 3 4 5 If -integer(0) is an invalid index, why do we have this? > a[-integer(0)] integer(0) Why a[-integer(0)] is not the whole vector a? Thank you very much. Paulo Barata Rio de Janeiro, Brazil __ 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] an issue about subsetting a vector
As with a lot of things in R, the behaviour is counterintuitive but (arguably) logical. The key (maybe) is that `a[-x]` does not mean "take all of the elements of a except those indicated by `x`, but rather, "negate x, then take all but the negative elements". In other words, -integer(0) is integer(0) (we multiply *each of the elements of integer(0)* by -1, but integer(0) has no elements) that reduces to a[integer(0)] and from there you get "select none of the elements". A related point is explained in the R Inferno https://www.burns-stat.com/pages/Tutor/R_inferno.pdf section 8.1.13, "negative nothing is something". See also https://stackoverflow.com/questions/42615728/subsetting-vector-how-to-programatically-pass-negative-index-safely https://stackoverflow.com/questions/40026975/subsetting-with-negative-indices-best-practices/40029485#40029485 On 2024-03-24 2:19 p.m., Paulo Barata wrote: To the R-Help list, I would like to have a clarification about an issue that I observe when subsetting a vector. This is R version 4.3.3 on Windows 10. -- Example with a vector: > a <- 1:5 > a [1] 1 2 3 4 5 So we have, with a negative index: > a[-3] [1] 1 2 4 5 But when the index is integer(0), we have this: > a[integer(0)] integer(0) > a[-integer(0)] integer(0) When it comes to the function integer(), the R Help file says: "Value: integer creates a integer vector of the specified length. Each element of the vector is equal to 0." But we see below that integer(0) is some kind of null vector, that is, no numbers are represented by integer(0): > class(integer(0)) [1] "integer" > length(integer(0)) [1] 0 So my question: in the expression a[-integer(0)], what happens exactly with the index -integer(0)? We see that integer(0), although of class integer, does not represent any numbers, as its length is zero, so it seems to me that it makes no sense to calculate its negative -integer(0). What exactly is -integer(0)? In particular, why a[-integer(0)] is not the whole vector a, that is, [1] 1 2 3 4 5? In the example below, if the invalid index -99 is presented to a, the result is the whole vector: > a[-99] [1] 1 2 3 4 5 If -integer(0) is an invalid index, why do we have this? > a[-integer(0)] integer(0) Why a[-integer(0)] is not the whole vector a? Thank you very much. Paulo Barata Rio de Janeiro, Brazil __ 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-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: [ESS] Displaying R plots within an Emacs buffer
Wow! This is really nice! Thanks, Stephen and Rodney!! A few comments: - I works perfectly for me in two different machines (both running Debian and Emacs 29.2.50) - Maybe I am not understanding https://github.com/sje30/ess-unigd#adjust-to-size-of-buffer--dynamically-update , but resize of image (on changing frame and window sizes) happens automagically for me. - The only minor thing is that, for some reason, the svg is shown in Fundamental mode (if I find-file other svgs, they are shown as images directly); I guess it is something with my setup. revert-buffer solves it. Best, R. P.S. FWIW, for a while I've been using a kind of similar thing with browsers that run inside Emacs. First I started using xwidget-webkit-browse-url, but since this recently broke or will be broken soon[1], I then started using EAF (Emacs Application Framework). With a browser one gets the browse history of plots, mentioned in https://github.com/sje30/ess-unigd#browse-history-of-plots . The procedure is similar to what Stephen does: first, in R load library httpgd and launch hgd. Then have xwidget-webkit-browse-url or eaf-open-browser open the URL returned by hgd. [1] https://mail.gnu.org/archive/html/bug-gnu-emacs/2023-09/msg02681.html , https://debbugs.gnu.org/db/66/66068.html On Fri, 22-March-2024, at 16:43:23, "Sparapani, Rodney via ESS-help" wrote: > Oh, yeah, sorry that was stupid. So now I have execute permission. > But, this is what latest.svg shows now… > Status: 404 > Reason: Not Found -- Ramon Diaz-Uriarte Department of Biochemistry, Lab B-31 Facultad de Medicina Universidad Autónoma de Madrid Arzobispo Morcillo, 4 28029 Madrid Spain Phone: +34-91-497-2412 Email: rdia...@gmail.com r.d...@uam.es ramon.d...@iib.uam.es https://ligarto.org/rdiaz __ ESS-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/ess-help
