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Yuan Chun Ding

2021-Jun-18 00:03 UTC

[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)<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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Jim Lemon

2021-Jun-18 03:29 UTC

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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

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)
>
> ______________________________________________
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R help - Jun 2021 - apply a color range (kind of like a heat map) to the values in each cell of a data frame

[R] apply a color range (kind of like a heat map) to the values in each cell of a data frame

[R] apply a color range (kind of like a heat map) to the values in each cell of a data frame