Visualize a string/sequence, emphasizing certain substrings

up vote
3
down vote

favorite

I need to visualize a sequence, with the ability to emphasize certain segments.

For example, take this sequence seq:

seq = -----------------DTLCIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDKHNGKLCK
LRGVAPLHLGKCNIAGWILGNPECESLSTASSWSYIVETPSSDNGTCYPGDFIDYEELREQLSSVSSFER
FEIFPKTSSWPNHDSNKGVTAACPHAGAKSFYKNLIWLVKKGNSYPKLSKSYINDKGKEVLVLWGIHHPS
TSADQQSLYQNADTYVFVGSSRYSKKFKPEIAIRPKVRDQEGRMNYYWTLVEPGDKITFEATGNLVVPRY
AFAMERNAGSGIIISDTPVHDCNTTCQTPKGAINTSLPFQNIHPITIGKCPKYVKSTKLRLATGLRNIPS
G----LFGAIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADLKSTQNAIDEITNKVNSVIEKMNTQFTAV
GKEFNHLEKRIENLNKKVDDGFLDIWTYNAELLVLLENERTLDYHDSNVKNLYEKVRSQLKNNAKEIGNG
CFEFYHKCDNTCMESVKNGTYDYPKYSEEAKLNREEIDS-------------------------------
--------------------------------------------------------------------

The list of segments I want to emphasize: segments = "AGSGIIISDTPVHDC", "AIDEITNKVNSVIEK", AKSFYKNLIWLVKKG.

I'm thinking that something that looks like this would work for the emphasis, where the black line is the length of the sequence, and the blue boxes are the segments:

enter image description here

To get start and ending positions of each segment, we can use StringPosition[seq, #] & /@ segments.

Now I'm not sure which visualization tool would help me visualize this sequence and emphasize the segment using these start and end positions.

edited 1 hour ago

J. M. is somewhat okay.â™¦

94.6k10293454

asked 2 hours ago

briennakh

3669

how about StringReplace[seq, s : Alternatives @@ segments :> ToString[Style[s, Red, Bold], StandardForm]]?
â€“Â kglr
1 hour ago

That's definitely good, and I actually already had something similar to that, but I need something that's more pictorial, thanks though! @kglr
â€“Â briennakh
1 hour ago

I just noticed that this non-pictorial expression would not work with overlapping segments, but your answer below does. @kglr
â€“Â briennakh
55 mins ago

add a commentÂ |Â

up vote
3
down vote

favorite

I need to visualize a sequence, with the ability to emphasize certain segments.

For example, take this sequence seq:

seq = -----------------DTLCIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDKHNGKLCK
LRGVAPLHLGKCNIAGWILGNPECESLSTASSWSYIVETPSSDNGTCYPGDFIDYEELREQLSSVSSFER
FEIFPKTSSWPNHDSNKGVTAACPHAGAKSFYKNLIWLVKKGNSYPKLSKSYINDKGKEVLVLWGIHHPS
TSADQQSLYQNADTYVFVGSSRYSKKFKPEIAIRPKVRDQEGRMNYYWTLVEPGDKITFEATGNLVVPRY
AFAMERNAGSGIIISDTPVHDCNTTCQTPKGAINTSLPFQNIHPITIGKCPKYVKSTKLRLATGLRNIPS
G----LFGAIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADLKSTQNAIDEITNKVNSVIEKMNTQFTAV
GKEFNHLEKRIENLNKKVDDGFLDIWTYNAELLVLLENERTLDYHDSNVKNLYEKVRSQLKNNAKEIGNG
CFEFYHKCDNTCMESVKNGTYDYPKYSEEAKLNREEIDS-------------------------------
--------------------------------------------------------------------

The list of segments I want to emphasize: segments = "AGSGIIISDTPVHDC", "AIDEITNKVNSVIEK", AKSFYKNLIWLVKKG.

I'm thinking that something that looks like this would work for the emphasis, where the black line is the length of the sequence, and the blue boxes are the segments:

enter image description here

To get start and ending positions of each segment, we can use StringPosition[seq, #] & /@ segments.

Now I'm not sure which visualization tool would help me visualize this sequence and emphasize the segment using these start and end positions.

edited 1 hour ago

J. M. is somewhat okay.â™¦

94.6k10293454

asked 2 hours ago

briennakh

3669

how about StringReplace[seq, s : Alternatives @@ segments :> ToString[Style[s, Red, Bold], StandardForm]]?
â€“Â kglr
1 hour ago

That's definitely good, and I actually already had something similar to that, but I need something that's more pictorial, thanks though! @kglr
â€“Â briennakh
1 hour ago

I just noticed that this non-pictorial expression would not work with overlapping segments, but your answer below does. @kglr
â€“Â briennakh
55 mins ago

add a commentÂ |Â

up vote
3
down vote

favorite

I need to visualize a sequence, with the ability to emphasize certain segments.

For example, take this sequence seq:

seq = -----------------DTLCIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDKHNGKLCK
LRGVAPLHLGKCNIAGWILGNPECESLSTASSWSYIVETPSSDNGTCYPGDFIDYEELREQLSSVSSFER
FEIFPKTSSWPNHDSNKGVTAACPHAGAKSFYKNLIWLVKKGNSYPKLSKSYINDKGKEVLVLWGIHHPS
TSADQQSLYQNADTYVFVGSSRYSKKFKPEIAIRPKVRDQEGRMNYYWTLVEPGDKITFEATGNLVVPRY
AFAMERNAGSGIIISDTPVHDCNTTCQTPKGAINTSLPFQNIHPITIGKCPKYVKSTKLRLATGLRNIPS
G----LFGAIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADLKSTQNAIDEITNKVNSVIEKMNTQFTAV
GKEFNHLEKRIENLNKKVDDGFLDIWTYNAELLVLLENERTLDYHDSNVKNLYEKVRSQLKNNAKEIGNG
CFEFYHKCDNTCMESVKNGTYDYPKYSEEAKLNREEIDS-------------------------------
--------------------------------------------------------------------

The list of segments I want to emphasize: segments = "AGSGIIISDTPVHDC", "AIDEITNKVNSVIEK", AKSFYKNLIWLVKKG.

I'm thinking that something that looks like this would work for the emphasis, where the black line is the length of the sequence, and the blue boxes are the segments:

enter image description here

To get start and ending positions of each segment, we can use StringPosition[seq, #] & /@ segments.

Now I'm not sure which visualization tool would help me visualize this sequence and emphasize the segment using these start and end positions.

edited 1 hour ago

J. M. is somewhat okay.â™¦

94.6k10293454

asked 2 hours ago

briennakh

3669

I need to visualize a sequence, with the ability to emphasize certain segments.

For example, take this sequence seq:

seq = -----------------DTLCIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDKHNGKLCK
LRGVAPLHLGKCNIAGWILGNPECESLSTASSWSYIVETPSSDNGTCYPGDFIDYEELREQLSSVSSFER
FEIFPKTSSWPNHDSNKGVTAACPHAGAKSFYKNLIWLVKKGNSYPKLSKSYINDKGKEVLVLWGIHHPS
TSADQQSLYQNADTYVFVGSSRYSKKFKPEIAIRPKVRDQEGRMNYYWTLVEPGDKITFEATGNLVVPRY
AFAMERNAGSGIIISDTPVHDCNTTCQTPKGAINTSLPFQNIHPITIGKCPKYVKSTKLRLATGLRNIPS
G----LFGAIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADLKSTQNAIDEITNKVNSVIEKMNTQFTAV
GKEFNHLEKRIENLNKKVDDGFLDIWTYNAELLVLLENERTLDYHDSNVKNLYEKVRSQLKNNAKEIGNG
CFEFYHKCDNTCMESVKNGTYDYPKYSEEAKLNREEIDS-------------------------------
--------------------------------------------------------------------

The list of segments I want to emphasize: segments = "AGSGIIISDTPVHDC", "AIDEITNKVNSVIEK", AKSFYKNLIWLVKKG.

I'm thinking that something that looks like this would work for the emphasis, where the black line is the length of the sequence, and the blue boxes are the segments:

enter image description here

To get start and ending positions of each segment, we can use StringPosition[seq, #] & /@ segments.

Now I'm not sure which visualization tool would help me visualize this sequence and emphasize the segment using these start and end positions.

list-manipulation visualization segmentation

edited 1 hour ago

J. M. is somewhat okay.â™¦

94.6k10293454

asked 2 hours ago

briennakh

3669

edited 1 hour ago

J. M. is somewhat okay.â™¦

94.6k10293454

asked 2 hours ago

briennakh

3669

edited 1 hour ago

J. M. is somewhat okay.â™¦

94.6k10293454

edited 1 hour ago

J. M. is somewhat okay.â™¦

94.6k10293454

edited 1 hour ago

J. M. is somewhat okay.â™¦

94.6k10293454

asked 2 hours ago

briennakh

3669

asked 2 hours ago

briennakh

3669

asked 2 hours ago

briennakh

3669

how about StringReplace[seq, s : Alternatives @@ segments :> ToString[Style[s, Red, Bold], StandardForm]]?
â€“Â kglr
1 hour ago

That's definitely good, and I actually already had something similar to that, but I need something that's more pictorial, thanks though! @kglr
â€“Â briennakh
1 hour ago

I just noticed that this non-pictorial expression would not work with overlapping segments, but your answer below does. @kglr
â€“Â briennakh
55 mins ago

add a commentÂ |Â

how about StringReplace[seq, s : Alternatives @@ segments :> ToString[Style[s, Red, Bold], StandardForm]]?
â€“Â kglr
1 hour ago

That's definitely good, and I actually already had something similar to that, but I need something that's more pictorial, thanks though! @kglr
â€“Â briennakh
1 hour ago

I just noticed that this non-pictorial expression would not work with overlapping segments, but your answer below does. @kglr
â€“Â briennakh
55 mins ago

how about StringReplace[seq, s : Alternatives @@ segments :> ToString[Style[s, Red, Bold], StandardForm]]?
â€“Â kglr
1 hour ago

That's definitely good, and I actually already had something similar to that, but I need something that's more pictorial, thanks though! @kglr
â€“Â briennakh
1 hour ago

I just noticed that this non-pictorial expression would not work with overlapping segments, but your answer below does. @kglr
â€“Â briennakh
55 mins ago

add a commentÂ |Â

2 Answers
2

active

oldest

votes

up vote
2
down vote

accepted

Graphics[Gray, EdgeForm[Gray], FaceForm[LightBlue], 
 SequenceReplace[Flatten[Join[1, #[[1]] - 1, 
 Rectangle[#[[1]], -5, #[[2]], 5], #[[2]] + 1 & /@ 
 StringPosition[seq, s : Alternatives @@ segments], StringLength @ seq]],
 a_Integer, b_Integer :> Line[a, 0, b, 0]], ImageSize -> 80]

enter image description here

Alternatively, use NumberLinePlot:

NumberLinePlot[Interval/@StringPosition[seq, Alternatives @@ segments], 
 Spacings -> 0, Ticks -> None, ImageSize -> 600, 
 PlotStyle -> Directive[Opacity[1], PointSize[0], CapForm["Butt"], Thickness[.02]], 
 PlotRange->0, StringLength @ seq, Automatic]

enter image description here

edited 23 mins ago

answered 1 hour ago

kglr

165k8188388

Just had to adjust image size. This answer is amazing because it works for the rest of my segments, as well, which overlap... And it works.
â€“Â briennakh
1 hour ago

add a commentÂ |Â

up vote
1
down vote

seq must be a string

Graphics[Blue, Line[0, 15, StringLength@seq, 15], 
Rectangle[#, 0, #2, 30] & @@@ StringPosition[seq, segments]]

enter image description here

answered 1 hour ago

J42161217

1,706216

add a commentÂ |Â

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2 Answers
2

active

oldest

votes

2 Answers
2

active

oldest

votes

up vote
2
down vote

accepted

Graphics[Gray, EdgeForm[Gray], FaceForm[LightBlue], 
 SequenceReplace[Flatten[Join[1, #[[1]] - 1, 
 Rectangle[#[[1]], -5, #[[2]], 5], #[[2]] + 1 & /@ 
 StringPosition[seq, s : Alternatives @@ segments], StringLength @ seq]],
 a_Integer, b_Integer :> Line[a, 0, b, 0]], ImageSize -> 80]

enter image description here

Alternatively, use NumberLinePlot:

NumberLinePlot[Interval/@StringPosition[seq, Alternatives @@ segments], 
 Spacings -> 0, Ticks -> None, ImageSize -> 600, 
 PlotStyle -> Directive[Opacity[1], PointSize[0], CapForm["Butt"], Thickness[.02]], 
 PlotRange->0, StringLength @ seq, Automatic]

enter image description here

edited 23 mins ago

answered 1 hour ago

kglr

165k8188388

Just had to adjust image size. This answer is amazing because it works for the rest of my segments, as well, which overlap... And it works.
â€“Â briennakh
1 hour ago

add a commentÂ |Â

up vote
2
down vote

accepted

Graphics[Gray, EdgeForm[Gray], FaceForm[LightBlue], 
 SequenceReplace[Flatten[Join[1, #[[1]] - 1, 
 Rectangle[#[[1]], -5, #[[2]], 5], #[[2]] + 1 & /@ 
 StringPosition[seq, s : Alternatives @@ segments], StringLength @ seq]],
 a_Integer, b_Integer :> Line[a, 0, b, 0]], ImageSize -> 80]

enter image description here

Alternatively, use NumberLinePlot:

NumberLinePlot[Interval/@StringPosition[seq, Alternatives @@ segments], 
 Spacings -> 0, Ticks -> None, ImageSize -> 600, 
 PlotStyle -> Directive[Opacity[1], PointSize[0], CapForm["Butt"], Thickness[.02]], 
 PlotRange->0, StringLength @ seq, Automatic]

enter image description here

edited 23 mins ago

answered 1 hour ago

kglr

165k8188388

Just had to adjust image size. This answer is amazing because it works for the rest of my segments, as well, which overlap... And it works.
â€“Â briennakh
1 hour ago

add a commentÂ |Â

up vote
2
down vote

accepted

Graphics[Gray, EdgeForm[Gray], FaceForm[LightBlue], 
 SequenceReplace[Flatten[Join[1, #[[1]] - 1, 
 Rectangle[#[[1]], -5, #[[2]], 5], #[[2]] + 1 & /@ 
 StringPosition[seq, s : Alternatives @@ segments], StringLength @ seq]],
 a_Integer, b_Integer :> Line[a, 0, b, 0]], ImageSize -> 80]

enter image description here

Alternatively, use NumberLinePlot:

NumberLinePlot[Interval/@StringPosition[seq, Alternatives @@ segments], 
 Spacings -> 0, Ticks -> None, ImageSize -> 600, 
 PlotStyle -> Directive[Opacity[1], PointSize[0], CapForm["Butt"], Thickness[.02]], 
 PlotRange->0, StringLength @ seq, Automatic]

enter image description here

edited 23 mins ago

answered 1 hour ago

kglr

165k8188388

Graphics[Gray, EdgeForm[Gray], FaceForm[LightBlue], 
 SequenceReplace[Flatten[Join[1, #[[1]] - 1, 
 Rectangle[#[[1]], -5, #[[2]], 5], #[[2]] + 1 & /@ 
 StringPosition[seq, s : Alternatives @@ segments], StringLength @ seq]],
 a_Integer, b_Integer :> Line[a, 0, b, 0]], ImageSize -> 80]

enter image description here

Alternatively, use NumberLinePlot:

NumberLinePlot[Interval/@StringPosition[seq, Alternatives @@ segments], 
 Spacings -> 0, Ticks -> None, ImageSize -> 600, 
 PlotStyle -> Directive[Opacity[1], PointSize[0], CapForm["Butt"], Thickness[.02]], 
 PlotRange->0, StringLength @ seq, Automatic]

enter image description here

edited 23 mins ago

answered 1 hour ago

kglr

165k8188388

edited 23 mins ago

answered 1 hour ago

kglr

165k8188388

answered 1 hour ago

kglr

165k8188388

answered 1 hour ago

kglr

165k8188388

Just had to adjust image size. This answer is amazing because it works for the rest of my segments, as well, which overlap... And it works.
â€“Â briennakh
1 hour ago

add a commentÂ |Â

Just had to adjust image size. This answer is amazing because it works for the rest of my segments, as well, which overlap... And it works.
â€“Â briennakh
1 hour ago

Just had to adjust image size. This answer is amazing because it works for the rest of my segments, as well, which overlap... And it works.
â€“Â briennakh
1 hour ago

add a commentÂ |Â

up vote
1
down vote

seq must be a string

Graphics[Blue, Line[0, 15, StringLength@seq, 15], 
Rectangle[#, 0, #2, 30] & @@@ StringPosition[seq, segments]]

enter image description here

answered 1 hour ago

J42161217

1,706216

add a commentÂ |Â

up vote
1
down vote

seq must be a string

Graphics[Blue, Line[0, 15, StringLength@seq, 15], 
Rectangle[#, 0, #2, 30] & @@@ StringPosition[seq, segments]]

enter image description here

answered 1 hour ago

J42161217

1,706216

add a commentÂ |Â

up vote
1
down vote

seq must be a string

Graphics[Blue, Line[0, 15, StringLength@seq, 15], 
Rectangle[#, 0, #2, 30] & @@@ StringPosition[seq, segments]]

enter image description here

answered 1 hour ago

J42161217

1,706216

seq must be a string

Graphics[Blue, Line[0, 15, StringLength@seq, 15], 
Rectangle[#, 0, #2, 30] & @@@ StringPosition[seq, segments]]

enter image description here

answered 1 hour ago

J42161217

1,706216

answered 1 hour ago

J42161217

1,706216

answered 1 hour ago

J42161217

1,706216

answered 1 hour ago

J42161217

1,706216

add a commentÂ |Â

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