[R] Help with color.scale {plotrix}

[Sarah Goslee]

This is the error message:

> > Error in cellcol[x < 0.33] <- color.scale(x[x < 0.33], c(1, 0.8), c(0,  :
> >   NAs are not allowed in subscripted assignments

x has NA values, but is being used for subscripting.

either use

cellcol[!is.na(x) & x < 0.33]

or specify a NA value for color.scale() and let it handle the missing values.

> cellcol[x<0.33]<-color.scale(x[x<0.33],c(1,0.8),c(0,0.8),0, na.color=NA)
Error in cellcol[x < 0.33] <- color.scale(x[x < 0.33], c(1, 0.8), c(0,  :
  NAs are not allowed in subscripted assignments


vs

> cellcol <- color.scale(x, c(1,0.8),c(0,0.8),0, na.color=NA)

Which doesn't help with the < 0.33 part, but you could set the values
> 0.33 to NA first.




On Fri, Oct 9, 2015 at 5:49 PM, William Dunlap <wdunlap at tibco.com> wrote:
> Try setting the na.color argument of color.scale to a color string,
> not NA.  "#00000000" (alpha = 0 is the key part) is transparent so it it
> might
> suit your needs.
>
> Bill Dunlap
> TIBCO Software
> wdunlap tibco.com
>
> On Fri, Oct 9, 2015 at 12:26 PM, Kumar Mainali <kpmainali at gmail.com> wrote:
>>
>> Hi Sarah,
>>
>> Thanks for the explanation. This solves my first problem. I hope somebody
>> will be able to answer my second question. Copied here from previous email
>> >>
>>
>> Another question: some of my matrices have missing cells and I do not want
>> to assign any colors to the missing cells. The following code gives me
>> error. I am trying to use the output (cellcol) to the
>> function color2D.matplot.
>>
>> > cellcol<-matrix("#000000", nrow=nrow(plotdata),ncol=ncol(plotdata))
>> > cellcol[x<0.33]<-color.scale(x[x<0.33],c(1,0.8),c(0,0.8),0, na.color=NA)
>> Error in cellcol[x < 0.33] <- color.scale(x[x < 0.33], c(1, 0.8), c(0,  :
>>   NAs are not allowed in subscripted assignments
>> In addition: Warning messages:
>> 1: In min(x) : no non-missing arguments to min; returning Inf
>> 2: In max(x) : no non-missing arguments to max; returning -Inf
>> ᐧ
>>
>> Postdoctoral Associate
>> Department of Biology
>> University of Maryland, College Park
>>
>> On Fri, Oct 9, 2015 at 11:48 AM, Sarah Goslee <sarah.goslee at gmail.com>
>> wrote:
>>
>> > Hi Kumar,
>> >
>> > You're overthinking it:
>> >
>> > in RGB, colorspace, cs1 is red, cs2 is green, cs3 is blue.
>> > So if cs1=c(1,1),cs2=(c(0,1),cs3=0 (or c(0,0) because of R's recycling)
>> > the first color in the sequence is c(1, 0, 0) or red ##FF0000 and the
>> > second color is c(1, 1, 0) #FFFF00 or yellow.
>> >
>> > Sarah
>> >
>> > On Fri, Oct 9, 2015 at 11:16 AM, Kumar Mainali <kpmainali at gmail.com>
>> > wrote:
>> > > Hi Jim,
>> > >
>> > > Thank you! Your color code does work. I still do not understand how
>> > > red
>> > to
>> > > yellow in RGB space translates to cs1=c(1,1),cs2=(c(0,1),cs3=0. In
>> > > other
>> > > words, I have RGB values for red and yellow. How do I go from there to
>> > the
>> > > code you sent?
>> > >
>> > > Another question: some of my matrices have missing cells and I do not
>> > want
>> > > to assign any colors to the missing cells. The following code gives me
>> > > error. I am trying to use the output (cellcol) to the
>> > > function color2D.matplot.
>> > >
>> > >> cellcol<-matrix("#000000", nrow=nrow(plotdata),ncol=ncol(plotdata))
>> > >> cellcol[x<0.33]<-color.scale(x[x<0.33],c(1,0.8),c(0,0.8),0,
>> > >> na.color=NA)
>> > > Error in cellcol[x < 0.33] <- color.scale(x[x < 0.33], c(1, 0.8), c(0,
>> > > :
>> > >   NAs are not allowed in subscripted assignments
>> > > In addition: Warning messages:
>> > > 1: In min(x) : no non-missing arguments to min; returning Inf
>> > > 2: In max(x) : no non-missing arguments to max; returning -Inf
>> > > ᐧ
>> > >
>> > > Postdoctoral Associate
>> > > Department of Biology
>> > > University of Maryland, College Park
>> > >
>> > > On Fri, Oct 9, 2015 at 7:24 AM, Jim Lemon <drjimlemon at gmail.com>
>> > > wrote:
>> > >
>> > >> Hi Kumar,
>> > >> The color.scale function translates numeric values into one or more
>> > >> intervals of color by a linear transformation into the numeric values
>> > that
>> > >> specify colors. One of three color spaces (rgb, hcl and hsv) can be
>> > >> specified, and the endpoints can be specified as "extremes=c(<minimum
>> > >> color>,<maximum color>" or as three vectors of numbers. By default,
>> > >> the
>> > RGB
>> > >> color space is used, so:
>> > >>
>> > >> # starts at RGB #FF0000 and finishes at RGB #FFFF00
>> > >> red to yellow - extremes=c("red","yellow") OR
>> > cs1=c(1,1),cs2=(c(0,1),cs3=0
>> > >> # starts at RGB #FFFF00 and finishes at RGB #00FF00
>> > >> yellow to green - extremes=c("yellow","green") OR
>> > >> cs1=c(1,0),cs2=(c(1,1),cs3=0
>> > >>
>> > >> Obviously the shades of colors that you want may differ from the
>> > >> above,
>> > so
>> > >> you have to play with the values to get the ones you want. In many
>> > cases,
>> > >> you will have to specify more than two numbers for the color specs to
>> > get
>> > >> the "in between" colors right, especially if the span of the colors
>> > >> is
>> > >> large.
>> > >>
>> > >> Jim
>> > >>
>> > >> On Fri, Oct 9, 2015 at 4:15 PM, Kumar Mainali <kpmainali at gmail.com>
>> > wrote:
>> > >>
>> > >>> Hi Jim and others:
>> > >>>
>> > >>> I needed color code for some color gradients in color.scale
>> > >>> function. I
>> > >>> found that the following translates to green to yellow to
>> > >>> red: c(0,1,1),c(1,1,0),0. How does this string translate to the
>> > >>> color
>> > >>> gradient? I would like to know the gradient code for red to yellow,
>> > yellow
>> > >>> to green and other ranges.
>> > >>>
>> > >>> Thanks,
>> > >>> Kumar Mainali
>> > >>>
>> >