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From: Debostuti G. <deb...@gm...> - 2023-05-17 04:52:14
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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? Thank you Debostuti -- Debostuti Ghosh Dastidar Research Associate PDB-India |
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From: Ethan M. <eam...@gm...> - 2023-05-17 16:06:12
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On Tue, May 16, 2023 at 9:52 PM Debostuti Ghoshdastidar <
deb...@gm...> 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
>
> _______________________________________________
> gnuplot-info mailing list
> gnu...@li...
> Membership management via:
> https://lists.sourceforge.net/lists/listinfo/gnuplot-info
>
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From: Debostuti G. <deb...@gm...> - 2023-05-17 16:48:02
|
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. Debostuti On Wed, 17 May 2023, 21:36 Ethan Merritt, <eam...@gm...> wrote: > On Tue, May 16, 2023 at 9:52 PM Debostuti Ghoshdastidar < > deb...@gm...> 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 >> >> _______________________________________________ >> gnuplot-info mailing list >> gnu...@li... >> Membership management via: >> https://lists.sourceforge.net/lists/listinfo/gnuplot-info >> > |
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From: Ethan M. <eam...@gm...> - 2023-05-17 20:40:10
|
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, <eam...@gm...> wrote:
>
> > On Tue, May 16, 2023 at 9:52 PM Debostuti Ghoshdastidar <
> > deb...@gm...> 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
> >>
> >> _______________________________________________
> >> gnuplot-info mailing list
> >> gnu...@li...
> >> Membership management via:
> >> https://lists.sourceforge.net/lists/listinfo/gnuplot-info
> >>
> >
>
|
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From: Debostuti G. <deb...@gm...> - 2023-05-18 01:01:12
|
That's great!! Thanks a lot Ethan... On Thu, 18 May 2023, 02:10 Ethan Merritt, <eam...@gm...> 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, <eam...@gm...> wrote: > > > > > On Tue, May 16, 2023 at 9:52 PM Debostuti Ghoshdastidar < > > > deb...@gm...> 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 > > >> > > >> _______________________________________________ > > >> gnuplot-info mailing list > > >> gnu...@li... > > >> Membership management via: > > >> https://lists.sourceforge.net/lists/listinfo/gnuplot-info > > >> > > > > > > > > > > |
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From: Debostuti G. <deb...@gm...> - 2023-05-18 11:34:37
|
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
--------------------------------------------------------------------------------------------------
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
On Thu, May 18, 2023 at 2:10 AM Ethan Merritt <eam...@gm...> 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, <eam...@gm...> wrote:
> >
> > > On Tue, May 16, 2023 at 9:52 PM Debostuti Ghoshdastidar <
> > > deb...@gm...> 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
> > >>
> > >> _______________________________________________
> > >> gnuplot-info mailing list
> > >> gnu...@li...
> > >> Membership management via:
> > >> https://lists.sourceforge.net/lists/listinfo/gnuplot-info
> > >>
> > >
> >
>
>
>
>
>
--
Debostuti Ghosh Dastidar
Research Associate
PDB-India
|
|
From: Ethan M. <eam...@gm...> - 2023-05-18 16:15:06
|
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 <eam...@gm...> 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, <eam...@gm...> wrote: > > > > > > > On Tue, May 16, 2023 at 9:52 PM Debostuti Ghoshdastidar < > > > > deb...@gm...> 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 > > > >> > > > >> _______________________________________________ > > > >> gnuplot-info mailing list > > > >> gnu...@li... > > > >> Membership management via: > > > >> https://lists.sourceforge.net/lists/listinfo/gnuplot-info > > > >> > > > > > > > > > > > > > > > > > > > |
|
From: Debostuti G. <deb...@gm...> - 2023-05-18 18:44:19
|
Dear Ethan I installed 5.4.6 but it is showing terminal type as unknown. pngcairo etc are no longer available to me. Looks like the reason is the absence of libgd (checked the config.log file). Could you point me to a resource that can help me in understanding what packages need to be installed for proper functioning of the current version? I do not want to do an update of my entire system for several reasons. Would rather install individual dependencies. Or is there a way to configure gnuplot so that pngcairo, etc are made available? I do not recall doing anything special for my earlier version of gnuplot...or maybe since it's been there since a very long time in my system I have forgotten. Debostuti On Thu, May 18, 2023 at 9:44 PM Ethan Merritt <eam...@gm...> wrote: > 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 <eam...@gm...> > 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, <eam...@gm...> > wrote: > > > > > > > > > On Tue, May 16, 2023 at 9:52 PM Debostuti Ghoshdastidar < > > > > > deb...@gm...> 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 > > > > >> > > > > >> _______________________________________________ > > > > >> gnuplot-info mailing list > > > > >> gnu...@li... > > > > >> Membership management via: > > > > >> https://lists.sourceforge.net/lists/listinfo/gnuplot-info > > > > >> > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- Debostuti Ghosh Dastidar Research Associate PDB-India |
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