Re: Regarding plotting stacked histograms with custom colors

On Thursday, 18 May 2023 05:08:36 PDT Debostuti Ghoshdastidar wrote:

> 
> However the bars are not getting colored according to col i+1, although the
> key is (please see attached image). Could you please help me understand
> whats going wrong?
> 
> Debostuti

I am guessing that your gnuplot executable is not current.
There was a bug that affected this specific kind of plot, fixed in
the September 2022 gnuplot release (version 5.4 patchlevel 5).
I should have remembered that and mentioned it before.

The current release level is 5.4.6, with 5.4.7 queued for later
this month.

	Ethan


> Hi Ethan
> 
> I followed your suggestions and made little tweaks to the script as follows:
> -----------------------------------------------
> set lt 101 lw 4 lc "red"
> set lt 102 lw 4 lc "pink"
> set lt 103 lw 4 lc "dark-blue"
> set lt 104 lw 4 lc "blue"
> set lt 105 lw 4 lc "royalblue"
> .
> .
> .
> set lt 120 lw 4 lc 'white' #*set 20 custom colors*
> set style data histogram
> set style histogram rows
> set style fill solid border lc "black"
> #set style line 2 lc  'black' lt 1 lw 2
> set boxwidth 0.80
> alphabet = "GAVLIPWFYSTCMNQHKRDE"
>     color(category) = 100 + strstrt(alphabet, category)
>     plot for [i=3:10:2] 'test.dat' using
> (column(i)):(color(strcol(i+1))):xtic(1):x2tic(2) lc variable
> -----------------------------------------------------------------------------------------------------------------------
> 
> for the following test data (the real data will have all 20 amino acids in
> a row):
> 
> test.dat:
> 1       Gly     0.03    G       0       A       0       V       0       I
> 2       Met     0.03    M       0       A       0       V       0       I
> 3       Arg     0.94    R       0       A       0       V       0       I
> 5       Arg     0.94    R       0       A       0       V       0       I
> 6       Tyr     0.97    Y       0       A       0       V       0       I
> 7       Val     0.03    V       0       G       0       A       0       I
> 8       Cys     0.88    C       0       G       0       A       0       V
> 9       Glu     1.00    E       0       G       0       A       0       V
> 11      Pro     0.03    R       0.09    P       0       A       0       G
> 12      Ser     0.58    S       0       G       0       A       0       V
> 13      His     0.03    S       0.15    R       0.21    A       0.61    H
> 14      Gly     0.03    A       0.06    S       0.61    G       0       V
> 15      Gly     0.06    S       0.12    A       0.21    G       0       V
> 
> --------------------------------------------------------------------------------------------------
> 
> 
> 
> On Thu, May 18, 2023 at 2:10 AM Ethan Merritt <[email protected]> wrote:
> 
> > On Wednesday, 17 May 2023 09:47:43 PDT Debostuti Ghoshdastidar wrote:
> > > Hi Ethan
> > >
> > > Thank you for the solution. Each Y column will be a score for a
> > particular
> > > amino acid. The Y columns will be in increasing order of the score value.
> > > Each Z will always correspond to a particular color we use to represent
> > the
> > > amino acid that will be in the corresponding y column. We will use a set
> > of
> > > 20 colors to represent 20 amino Acids.
> >
> > Ah. In that case you probably don't want "lc palette", which assumes
> > a continuous range of values and a smoothly-varying color palette.
> > Instead define 20 distinct colors in a convenient range of linetypes,
> > say lt 101 through lt 120, indexed by the value in column Zn.
> > That matches this demo from the on-line collection very closely:
> >
> >     https://gnuplot.sourceforge.net/demo_5.4/histogram_colors.html
> >
> > If you have the one letter code in the Z column (P for Proline, etc)
> > you could use pieces of the demo code directly.
> >
> >     alphabet = "ABCDEFGHIJKLMNOPQRSTUVWXYZ"
> >     color(category) = 100 + strstrt(alphabet, category)
> >     plot for [i=2:*:2] DATA using (column(i)):(color(strcol(i+1)) lc
> > variable
> >
> > Otherwise you could define a slightly more complicated color() function
> > that
> > for instance maps from the 3-letter code, e.g.
> >     array AA = ["Ala", "Cys", "Asp", "Glu", ...]
> >     color(category) = 100 + sum [1:20] (category eq AA[i]) ? i : 0)
> >
> > cheers,
> >
> >         Ethan
> > >
> > > Debostuti
> > >
> > > On Wed, 17 May 2023, 21:36 Ethan Merritt, <[email protected]> wrote:
> > >
> > > > On Tue, May 16, 2023 at 9:52 PM Debostuti Ghoshdastidar <
> > > > [email protected]> wrote:
> > > >
> > > >> Dear Users
> > > >>
> > > >> I have data in the following format
> > > >>
> > > >> X1 Y1 Z1 Y2 Z2...Yn Zn
> > > >> X2 Y1 Z1 Y2 Z2...Yn Zn
> > > >> .
> > > >> .
> > > >> .
> > > >> Xn Y1 Z1 Y2 Z2...Yn Zn
> > > >>
> > > >> I would like to draw a rowstacked histogram (which I know how to)
> > where
> > > >> the
> > > >> colors for the bars are specified by the corresponding Z columns. For
> > > >> example Y1 should be colored based on Z1 value, Y2 based on Z2 value,
> > and
> > > >> so on...mush like the use of cbrange. Could you suggest how I can
> > > >> accomplish this?
> > > >>
> > > >
> > > > set style data histogram
> > > > set style histogram rows
> > > > set style fill solid border lc "black"
> > > > set cbrange [0:<something>]
> > > > plot for [i=2:*:2] DATA using (column(i)):(column(i+1)) lc palette
> > title
> > > > "???"
> > > >
> > > > It is not clear to me how you would label or construct a legend
> > describing
> > > > this in a way that is easy for the viewer to understand.  Perhaps
> > > > superimpose
> > > > a label on top of each individual box?
> > > >
> > > >     Ethan
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >> Thank you
> > > >>
> > > >> Debostuti
> > > >> --
> > > >> Debostuti Ghosh Dastidar
> > > >> Research Associate
> > > >> PDB-India
> > > >>
> > > >> _______________________________________________
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> > > >> [email protected]
> > > >> Membership management via:
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> > > >>
> > > >
> > >
> >
> >
> >
> >
> >
> 
> 






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