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

[Yuan Chun Ding]

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 using gmail.com] 
Sent: Thursday, June 17, 2021 8:29 PM
To: Yuan Chun Ding <ycding using coh.org>
Cc: r-help using 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 using 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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