Jim Lemon
2021-Jun-18 03:29 UTC
[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 <ycding at coh.org>
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)<c("COH_001","COH_002","COH_003","COH_004","COH_005","COH_006","COH_007","COH_008","COH_009","COH_010","COH_011","COH_012")
>
> 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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Yuan Chun Ding
2021-Jun-18 18:46 UTC
[R] apply a color range (kind of like a heat map) to the values in each cell of a data frame
Hi Jim,
Thank you so much for your help!
I looked into the plotrix package, the addtable2plot function can do somewhat I
want by creating an empty plot first.
Ding
-----Original Message-----
From: Jim Lemon [mailto:drjimlemon at gmail.com]
Sent: Thursday, June 17, 2021 8:29 PM
To: Yuan Chun Ding <ycding at coh.org>
Cc: r-help at r-project.org
Subject: 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 <ycding at coh.org>
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)<c("COH_001","COH_002","COH_003","COH_004","COH_005","
>
COH_006","COH_007","COH_008","COH_009","COH_010","COH_011","COH_012")
>
> 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
>
> ----------------------------------------------------------------------
> ------------------------------------------------------------
> -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 at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://urldefense.com/v3/__https://stat.ethz.ch/mailman/listinfo/r-he
> lp__;!!Fou38LsQmgU!6XXGw94GkvcPBq4q8rUeHhiRqu21HG3c0QzMjapxzZvonoYhD6r
> 41_2EAHzW$ PLEASE do read the posting guide
> https://urldefense.com/v3/__http://www.R-project.org/posting-guide.htm
> l__;!!Fou38LsQmgU!6XXGw94GkvcPBq4q8rUeHhiRqu21HG3c0QzMjapxzZvonoYhD6r4
> 17wsEXst$ and provide commented, minimal, self-contained, reproducible
> code.