Re: [R] apply a color range (kind of like a heat map) to the values in each cell of a data frame
Hi Ding,
There are a number of "value to color" functions in various packages.
One is "color.scale" in the plotrix package:
library(plotrix)
s1 <-c(0.085,0.086,0.139,0.129,0.235,0.177,0.000,0.126,0.271,0.000,0.083,0.163)
s2 <-c(0.000,0.093,0.000,0.080,0.072,0.388,0.138,0.107,0.000,0.000,0.474,0.000)
s13 <-c(0.000,0.077,0.000,0.000,0.000,0.000,0.000,0.000,0.000,0.166,0.308,0.000)
s3 <-c(0.000,0.478,0.000,0.332,0.163,0.000,0.000,0.000,0.145,0.469,0.000,0.000)
test1 <-data.frame(s1,s2,s13,s3)
# generate a matrix of colors
test1.col<-color.scale(as.matrix(test1),extremes=c("white","blue"))
color.scale calculates colors using linear interpolation of the values
in three color spaces (RGB, HSV or HCL). You may be interested in some
of the plotting functions in plotrix that employ color.scale,
particularly "size_n_color".
Jim
On Fri, Jun 18, 2021 at 10:04 AM Yuan Chun Ding wrote:
>
> Dear R users,
>
> I have a numeric table with 140 rows and 30 columns, here I only made partial
> table, test1, as an example. I want to apply a blue color range to the
> value in each cell of the data frame test1.
> I found some R code using DT library. However, I only can see the colored
> table at my R studio viewer window, also only show the first 10 rows. I hope
> to save the colored table into a PNG file and want to modify the size of each
> cell, so I can apply the code to a much bigger table with 140 rows and 30
> column.
>
> Can you help me?
>
> Thank you very much!!
>
> Ding
>
> s1
> <-c(0.085,0.086,0.139,0.129,0.235,0.177,0.000,0.126,0.271,0.000,0.083,0.163)
> s2
> <-c(0.000,0.093,0.000,0.080,0.072,0.388,0.138,0.107,0.000,0.000,0.474,0.000)
> s13
> <-c(0.000,0.077,0.000,0.000,0.000,0.000,0.000,0.000,0.000,0.166,0.308,0.000)
> s3
> <-c(0.000,0.478,0.000,0.332,0.163,0.000,0.000,0.000,0.145,0.469,0.000,0.000)
> test1 <-data.frame(s1,s2,s13,s3)
> row.names(test1)
> library(DT)
>
> dtable1 <- datatable(test1, rownames=TRUE, options = list(lengthChange =
> FALSE, dom='t'))
>
> colRamp <- colorRamp(c("white","blue"))
> for(column in names(test1)){
> x <- na.omit(test1[[column]])
> brks <- quantile(x, probs = seq(.05, .95, .01))
> RGB <- colRamp(c(0, (brks-min(x))/(max(x)-min(x
> clrs <- apply(RGB, 1, function(rgb){
> sprintf("rgb(%s)", toString(round(rgb,0)))
> })
> dtable1 <- dtable1 %>%
> formatStyle(column, backgroundColor = styleInterval(brks, clrs))
> }
>
> dtable1
>
> --
>
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[R] apply a color range (kind of like a heat map) to the values in each cell of a data frame
Dear R users, I have a numeric table with 140 rows and 30 columns, here I only made partial table, test1, as an example. I want to apply a blue color range to the value in each cell of the data frame test1. I found some R code using DT library. However, I only can see the colored table at my R studio viewer window, also only show the first 10 rows. I hope to save the colored table into a PNG file and want to modify the size of each cell, so I can apply the code to a much bigger table with 140 rows and 30 column. Can you help me? Thank you very much!! Ding s1 <-c(0.085,0.086,0.139,0.129,0.235,0.177,0.000,0.126,0.271,0.000,0.083,0.163) s2 <-c(0.000,0.093,0.000,0.080,0.072,0.388,0.138,0.107,0.000,0.000,0.474,0.000) s13 <-c(0.000,0.077,0.000,0.000,0.000,0.000,0.000,0.000,0.000,0.166,0.308,0.000) s3 <-c(0.000,0.478,0.000,0.332,0.163,0.000,0.000,0.000,0.145,0.469,0.000,0.000) test1 <-data.frame(s1,s2,s13,s3) row.names(test1)% formatStyle(column, backgroundColor = styleInterval(brks, clrs)) } dtable1 -- -SECURITY/CONFIDENTIALITY WARNING- This message and any attachments are intended solely for the individual or entity to which they are addressed. This communication may contain information that is privileged, confidential, or exempt from disclosure under applicable law (e.g., personal health information, research data, financial information). Because this e-mail has been sent without encryption, individuals other than the intended recipient may be able to view the information, forward it to others or tamper with the information without the knowledge or consent of the sender. If you are not the intended recipient, or the employee or person responsible for delivering the message to the intended recipient, any dissemination, distribution or copying of the communication is strictly prohibited. If you received the communication in error, please notify the sender immediately by replying to this message and deleting the message and any accompanying files from your system. If, due to the security risks, you do not wish to receive further communications via e-mail, please reply to this message and inform the sender that you do not wish to receive further e-mail from the sender. (LCP301) __ 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-es] problemas para agrupar cadenas en una sola con str_replace_all
muchas gracias! no encontraba la solución de la forma que me passaste!
lo pude resolver de este modo:
cat_uno <- c("consultorio","consultorio externo","consultorio externos de
cp",
"consultorios cuidados paliativos","consultorios
externos cuidados paliativos",
"consultorios externos de cp","consultorios
externos de cp-",
"consultorios externos de cuidados paliativos","en
hospital: consultorios externos",
"hospital - consultorio
externo","hospital-cons.externo","hospital-cons.externos")
solucion_mult_p8$contexto_atencion <-
sapply(as.vector(solucion_mult_p8$contexto_atencion), function(x) if(x %in%
cat_uno) "Cosultorios Externos" else x )
El mié, 16 jun 2021 a las 20:23, INGESISTEL CIW ()
escribió:
> Podría servirle:
>
>
>
> > categorias <- c("CAMA UCI","CENTRO DE CUIDADOS CRONICOS","CLINICA
> PRIVADA: UTI","CONSULTORIO","CONSULTORIO EXTERNO","CONSULTORIO EXTERNOS DE
> CP","CONSULTORIOS CUIDADOS PALIATIVOS","CONSULTORIOS EXTERNOS CUIDADOS
> PALIATIVOS","CONSULTORIOS EXTERNOS DE CP","CONSULTORIOS EXTERNOS DE
> CP-","CONSULTORIOS EXTERNOS DE CUIDADOS PALIATIVOS","CONTROL TELEFONICO
> POSTALTA","CONVENTO","DISPOSITIVO TELEFONICO","EN CASA/COMUNIDAD","EN
> HOSPITAL: CONSULTORIOS EXTERNOS","EN UN HOGAR DE CUIDADO/HOGAR DE
> ANCIANOS","EN UN HOGAR DE CUIDADO/HOGAR DE ANCIANOS: OTRA SALA","EN UN
> HOGAR DE CUIDADO/HOGAR DE ANCIANOS: SALA PTES. COVID","EN UN HOSPICE O CASA
> DE CUIDADOS PALIATIVOS (NO ESPECIFICAMENTE PARA PACIENTES DE
> CORONAVIRUS)","EN UN HOSPITAL: OTRA SALA","EN UN HOSPITAL: SALA PTES.
> COVID","EN UN HOSPITAL: UTI","GUARDIA SHOCKROOM","HOSPITAL","HOSPITAL -
> CONSULTORIO
> EXTERNO","HOSPITAL-CONS.EXTERNO","HOSPITAL-CONS.EXTERNOS","MEDIANTE VIDEO
> LLAMADAS","NO PROPORCIONE ATENCION AL PACIENTE","SALA DE REANIMACION Y
> SHOCK","SEGUIMIENTO TELEFONICO","TELECONSULTA","TELEFONICAMENTE","VIA
> TELEFONICA","VIEDOLLAMADA-MAILS")
>
>
>
> > CONSULTORIOs_EXTERNOS <- c(categorias[(grepl
> (toupper("consultorio"),categorias))])
>
>
>
> > CONSULTORIOs_EXTERNOS
>
> [1] "CONSULTORIO"
>
> [2] "CONSULTORIO EXTERNO"
>
> [3] "CONSULTORIO EXTERNOS DE CP"
>
> [4] "CONSULTORIOS CUIDADOS PALIATIVOS"
>
> [5] "CONSULTORIOS EXTERNOS CUIDADOS PALIATIVOS"
>
> [6] "CONSULTORIOS EXTERNOS DE CP"
>
> [7] "CONSULTORIOS EXTERNOS DE CP-"
>
> [8] "CONSULTORIOS EXTERNOS DE CUIDADOS PALIATIVOS"
>
> [9] "EN HOSPITAL: CONSULTORIOS EXTERNOS"
>
> [10] "HOSPITAL - CONSULTORIO EXTERNO"
>
>
>
>
>
> Nota: grepl busca la subcadena deseada
>
>
>
>
>
> Cordial saludo
>
>
>
>
>
> Enviado desde Correo
> para Windows 10
>
>
>
> *De: *juan manuel dias
> *Enviado: *miércoles, 16 de junio de 2021 15:27
> *Para: *Lista R
> *Asunto: *[R-es] problemas para agrupar cadenas en una sola con
> str_replace_all
>
>
>
> Hola, como andan!
>
>
>
> Tengo una base de datos de pacientes y una de las variables es contexto de
> atención en el que fue atendido. El problema es que hay respuestas que
> tiene que ser agrupadas en una misma categoría.
>
>
>
> Por ejemplo, todas estas categorías
>
>
>
> (CONSULTORIO, CONSULTORIO EXTERNO, CONSULTORIO EXTERNOS DE CP,
> CONSULTORIOS CUIDADOS PALIATIVOS,
>
> CONSULTORIOS EXTERNOS CUIDADOS PALIATIVOS, CONSULTORIOS EXTERNOS DE CP,
> CONSULTORIOS EXTERNOS DE CP-,
> CONSULTORIOS EXTERNOS DE CUIDADOS PALIATIVOS,CONSULTORIOS EXTERNOS DE
> CUIDADOS PALIATIVOS,
> CONSULTORIOS EXTERNOS DE CUIDADOS PALIATIVOS)
>
>
>
> Las debería agrupar en una única "CONSULTORIO EXTERNOS".
>
>
>
> Intenté de esta forma antes habiendo pasado la variable
> "contexto_atencion" toda a mayúsculas y sin acentos.
>
>
>
> pats_consext <- c("CONSULTORIO EXTERNO|CONSULTORIO EXTERNOS DE
> CP|CONSULTORIOS CUIDADOS PALIATIVOS|
> CONSULTORIOS EXTERNOS CUIDADOS PALIATIVOS|CONSULTORIOS EXTERNOS DE
> CP|CONSULTORIOS EXTERNOS DE CP-|
> CONSULTORIOS EXTERNOS DE CUIDADOS PALIATIVOS|CONSULTORIO")
>
> solucion_mult_p8<-solucion_mult_p8 %>%
> mutate(contexto_atencion = str_replace_all(contexto_atencion,
> pats_consext,'CONSULTORIOS EXTERNOS'))
>
>
>
> Pero no me resuelve el problema.
>
>
>
> Para la categoría
>
>
>
> CONSULTORIOS EXTERNOS CUIDADOS PALIATIVOS
>
>
>
> me trae
>
>
>
> CONSULTORIOS EXTERNOS EXTERNOS CUIDADOS PALIATIVOS
>
>
>
> Alguien sabe cuál puede ser el problema?
>
>
>
> Adjunto la base por las dudas!
>
>
>
> Muchas gracias!
>
>
>
> m
>
>
>
>
>
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Re: [R] Legend position in ggplot
Like this? theme(legend.position= 'top' On Thursday, June 17, 2021, 10:52:04 AM PDT, peri He wrote: Dear Friends, I would like to see my legend outside of a ggplot (at the top). This code is showing the legend inside of a plot: theme(legend.position=c(0.15,0.97)) But when I changed it to : theme(legend.position=c(-0.15,1.5)) , the legend disappears. I would appreciate it if you share your ideas. Regards, Peri [[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] Legend position in ggplot
Dear Friends, I would like to see my legend outside of a ggplot (at the top). This code is showing the legend inside of a plot: theme(legend.position=c(0.15,0.97)) But when I changed it to : theme(legend.position=c(-0.15,1.5)) , the legend disappears. I would appreciate it if you share your ideas. Regards, Peri [[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] Potential Bug: file.show does not support double-byte characters in the file path
Hi,
I may have come across a bug regarding the file.show function in the base
package.
### Bug Description
file.show does not support double-byte characters in the file path.
### Platform Info
> sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19043)
Matrix products: default
locale:
[1] LC_COLLATE=Chinese (Simplified)_China.936 LC_CTYPE=Chinese
(Simplified)_China.936
[3] LC_MONETARY=Chinese (Simplified)_China.936 LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_China.936
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.1.0 tools_4.1.0
### Steps to Reproduce
1. Install R-4.1.0 for Windows on Windows 10 x64 21H1 (Chinese-Simplified,
zh-CN)
2. Open RGui
3. Create a file named "test.txt" under "C:\Test", so that the full file path
does not include double-byte characters
4. Create a file named "test.txt" under "C:\测试", so that the full file path
includes double-byte characters
5. Run the following commands in the console
> t1 = "C:\\Test\\test.txt"
> t1
[1] "C:\\Test\\test.txt"
> file.show(t1)
>
> t2 = "C:\\测试\\test.txt"
> t2
[1] "C:\\测试\\test.txt"
> file.show(t2)
Warning message:
In file.show(t2) : file.show(): file 'C:\测试\test.txt' does not exist
Actual Result:
file.show() can correctly open the "C:\Test\test.txt" as the file path does not
contain double-byte characters, but it fails to do so for "C:\测试\test.txt".
### Additional information
For users with usernames that include double-byte characters, this bug even
prevents demo() from functioning properly.
> demo()
Warning message:
In file.show(outFile, delete.file = TRUE, title = paste("R", tolower(x$title)))
:
file.show():不存在'C:\Users\娴嬭瘯涓瓇1\AppData\Local\Temp\RtmpGuWTun\RpackageIQR197068c75431'这个文件
file.show() can correctly read from files containing double-byte characters if
the file paths do not. For example, the content for "C:\Test\test.txt" can be
"Testing 123 测试". file.show("C:\\Test\\test.txt") would open this file and
display its content correctly without specifying the encoding parameter.
Thanks,
Tim
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Re: [R] Can't add error bars to existing line graph
Hi Bruno,
The interaction.plot function plots the _levels_ of the x.factor
argument, not the values of the variable that is coerced to a factor.
This means that the temperature locations on the x axis are c(1,2),
not c(12,17). The code below works for me:
readscaphfileNEW<-read.table(text="EXPERIMENT TEMP SCAPH.BPM
12021 1282
22021 1258
32021 1278
42021 1259
52021 1280
62021 12 100
72021 1261
82021 12 103
92021 1261
10 2021 17 100
11 2021 1770
12 2021 1783
13 2021 1773
14 2021 17 143
15 2021 17 103
16 2021 1773
17 2021 17 158
18 2021 1795
19 2021 1780
20 1939 12 158
21 1939 12 148
22 1939 12 152
23 1939 12 148
24 1939 12 160
25 1939 12 168
26 1939 12 152
27 1939 12 150
28 1939 12 187
29 1939 17 300
30 1939 17 302
31 1939 17 291
32 1939 17 240
33 1939 17 253
34 1939 17 207
35 1939 17 184
36 1939 17 224
37 1939 17 242
38 1939 17 236",
header=TRUE,stringsAsFactors=FALSE)
interaction.plot(readscaphfileNEW$TEMP,
readscaphfileNEW$EXPERIMENT, readscaphfileNEW$SCAPH.BPM,
xlab = "Temperature (°C)", ylab = "Scaphognathite Rate (BPM)",
main = "Scaphognathite",
ylim = c(0,300), trace.label = "Year",
type = "b", pch = c(19,17), fixed = TRUE)
library(plotrix)
Scaphmeans <-as.vector(by(readscaphfileNEW$SCAPH.BPM,
readscaphfileNEW[,c("EXPERIMENT","TEMP")],mean))
Scaphse = as.vector(by(readscaphfileNEW$SCAPH.BPM,
readscaphfileNEW[,c("EXPERIMENT","TEMP")],std.error))
dispersion(c(1,1,2,2),Scaphmeans,Scaphse)
Note that you can get much the same plot using brkdn.plot (plotrix):
brkdn.plot(SCAPH.BPM~EXPERIMENT+TEMP,data=readscaphfileNEW,
xlab="Temperature C",pch=c(1,2))
legend(15,160,c(1939,2021),pch=c(1,2))
Jim
On Thu, Jun 17, 2021 at 3:38 AM Bruno.Salonen wrote:
>
>
> Hi all,
>
> I'm trying to add error bars to an existing line graph in base R.
>
> The basic line graph comes up just fine, but it does not show my error
> bars...
>
> Data frame = readscaphfileNEW
> Plot name = SCAPHLINEGRAPHNEW
> x axis = TEMP
> y axis = SCAPH.BPM
> Tracer = Year (SAME AS 'EXPERIMENT)
> Scaphmeans = means of SCAPH.BPM
> Scaphse = standard error of SCAPH.BPM
>
> Here is the code..
>
> SCAPHLINEGRAPHNEW <- interaction.plot(readscaphfileNEW$TEMP,
> readscaphfileNEW$EXPERIMENT, readscaphfileNEW$SCAPH.BPM,
> xlab = "Temperature (°C)", ylab = "Scaphognathite Rate (BPM)",
> main = "Scaphognathite",
> ylim = c(0,300), trace.label = "Year",
> type = "b", pch = c(19,17), fixed = TRUE)
> arrows(SCAPHLINEGRAPHNEW,Scaphmeans+Scaphse,SCAPHLINEGRAPHNEW,Scaphmeans-Scaphse,code=3,
> angle=90, length=0.1)
>
> Why are my error bars not showing? Is the 'arrows' line wrong?
>
> Thanks a million for your help, everybody.
>
> Here is my data set:
>
> > readscaphfileNEW
>EXPERIMENT TEMP SCAPH.BPM
> 12021 1282
> 22021 1258
> 32021 1278
> 42021 1259
> 52021 1280
> 62021 12 100
> 72021 1261
> 82021 12 103
> 92021 1261
> 10 2021 17 100
> 11 2021 1770
> 12 2021 1783
> 13 2021 1773
> 14 2021 17 143
> 15 2021 17 103
> 16 2021 1773
> 17 2021 17 158
> 18 2021 1795
> 19 2021 1780
> 20 1939 12 158
> 21 1939 12 148
> 22 1939 12 152
> 23 1939 12 148
> 24 1939 12 160
> 25 1939 12 168
> 26 1939 12 152
> 27 1939 12 150
> 28 1939 12 187
> 29 1939 17 300
> 30 1939 17 302
> 31 1939 17 291
> 32 1939 17 240
> 33 1939 17 253
> 34 1939 17 207
> 35 1939 17 184
> 36 1939 17 224
> 37 1939 17 242
> 38 1939 17 236
>
> Bruno
>
>
>
> --
> Sent from: https://r.789695.n4.nabble.com/R-help-f789696.html
>
> __
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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.
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