Introduction of Circos Yunyun Zhou 03/11/2014
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Introduction of Circos
Yunyun Zhou
03112014
Introduction
PRETTY Circular visualization
POPULAR --- APPEARED IN A VARIETY OF PUBLICATIONS
Overview
CIRCOS Features
Methods
Applications
Questions
httpcircosca
Features
CIRCOS is only a circular visualization tool no analysis
Creation of images is controlled through a plain-text configuration file
Circos can be used to display any kind of information
---initially design specific to genomics
---currently any relationship among data
ie chemical reactivity tracking transactionshellip
visualizing tables
Typical Circos Image
(A) histogram (B) ideograms (C) histogram (D) heatmap (E) links (F) highlights (G) grid (H) ticks
CIRCOS installation
1 System requirement UnixLinuxMac
2 Download amp Install circos software
3 Install Required Perl modules
4 Download Tutorial (Best practice examples)
Plain Text Input Files
gt circos -conf etccircosconf
Configuration file (circosconf)
ltticksgt ltltinclude etcticksconfgtgt ltticksgt
ticksconf
Genome to Genome link
Clickable image
bull Associate areas of the image with web links bull Any element in the image (ideogram tick band highlight ribobn etc) can
have an associated URL
FEATURES
MAKING IDEOGRAMS CLICKABLE
ltideogramgt
ideogram_url = httpwwwgooglecomsearchq=[chr]
helliphellip
ltideogramgt
chr - hs1 1 0 247249719 chr1 url=special_scriptchr=[chr]
chr - hs2 2 0 242951149 chr2 url=another_special_scriptchr=[chr]
chr - hs3 3 0 199501827 chr3
DEFINING URLS SPECIFIC TO INDIVIDUAL IDEOGRAMS
METHODS
Image map
1 Microbial Genome 2 Link Geometry - Detailed Bezier Control 3 Labeling Karyotype Bands 4 Image Maps 5 Image Transparency and Background 6 Manipulating Histograms 7 Variable Radius Link Ends 8 Stacked Histograms 9 Transparent Links 10 ID Fields 11 Heat Map Links 12 Inverted Links 13 Copy Number Data 14 Directed Links 15 Pattern Fills 16 Automating Tracks 17 Automating Heatmaps 18 Circular Stacked Bar Plots 19 Cortical Maps mdash Connectograms 20 Cell Cycle mdash Part 1 21 Cell Cycle mdash Part 2 22 Nature Cover Encode Diagram 23 Naming Names
Recipes
bull Configuration files bull Input data file bull Output images
Provided files
Copy number variation scatter plot
chrom start end logFC
hs3 7683536 8465787 143
hs11 465784 756867 -065
gctxt
track for [03]
CNV data range [-33]
Different background for the positive and negative CNV values
ltplotgt type = scatter file = data813datacnvtxt r0 = 06r r1 = 075r min = -3 max = 0 glyph = circle glyph_size = 8 color = red ltaxesgt ltaxisgt color = lred thickness = 2 spacing = 01r ltaxisgt ltaxesgt ltbackgroundsgt ltbackgroundgt color = vlred_a5 ltbackgroundgt ltbackgroundsgt hellip
track for [-30] ltplotgt type = scatter file = data813datacnvtxt r0 = 075r r1 = 09r min = 0 max = 3 glyph = circle glyph_size = 8 color = green ltaxesgt ltaxisgt color = lgreen thickness = 2 spacing = 01r ltaxisgt ltaxesgt ltbackgroundsgt ltbackgroundgt color = vlred_a5 ltbackgroundgt ltbackgroundsgt hellip
Visualizing Biological Data
httpvizbiorg
Genomic alignments
Phylogenies
macromolecular structures
system biology
Introduction
PRETTY Circular visualization
POPULAR --- APPEARED IN A VARIETY OF PUBLICATIONS
Overview
CIRCOS Features
Methods
Applications
Questions
httpcircosca
Features
CIRCOS is only a circular visualization tool no analysis
Creation of images is controlled through a plain-text configuration file
Circos can be used to display any kind of information
---initially design specific to genomics
---currently any relationship among data
ie chemical reactivity tracking transactionshellip
visualizing tables
Typical Circos Image
(A) histogram (B) ideograms (C) histogram (D) heatmap (E) links (F) highlights (G) grid (H) ticks
CIRCOS installation
1 System requirement UnixLinuxMac
2 Download amp Install circos software
3 Install Required Perl modules
4 Download Tutorial (Best practice examples)
Plain Text Input Files
gt circos -conf etccircosconf
Configuration file (circosconf)
ltticksgt ltltinclude etcticksconfgtgt ltticksgt
ticksconf
Genome to Genome link
Clickable image
bull Associate areas of the image with web links bull Any element in the image (ideogram tick band highlight ribobn etc) can
have an associated URL
FEATURES
MAKING IDEOGRAMS CLICKABLE
ltideogramgt
ideogram_url = httpwwwgooglecomsearchq=[chr]
helliphellip
ltideogramgt
chr - hs1 1 0 247249719 chr1 url=special_scriptchr=[chr]
chr - hs2 2 0 242951149 chr2 url=another_special_scriptchr=[chr]
chr - hs3 3 0 199501827 chr3
DEFINING URLS SPECIFIC TO INDIVIDUAL IDEOGRAMS
METHODS
Image map
1 Microbial Genome 2 Link Geometry - Detailed Bezier Control 3 Labeling Karyotype Bands 4 Image Maps 5 Image Transparency and Background 6 Manipulating Histograms 7 Variable Radius Link Ends 8 Stacked Histograms 9 Transparent Links 10 ID Fields 11 Heat Map Links 12 Inverted Links 13 Copy Number Data 14 Directed Links 15 Pattern Fills 16 Automating Tracks 17 Automating Heatmaps 18 Circular Stacked Bar Plots 19 Cortical Maps mdash Connectograms 20 Cell Cycle mdash Part 1 21 Cell Cycle mdash Part 2 22 Nature Cover Encode Diagram 23 Naming Names
Recipes
bull Configuration files bull Input data file bull Output images
Provided files
Copy number variation scatter plot
chrom start end logFC
hs3 7683536 8465787 143
hs11 465784 756867 -065
gctxt
track for [03]
CNV data range [-33]
Different background for the positive and negative CNV values
ltplotgt type = scatter file = data813datacnvtxt r0 = 06r r1 = 075r min = -3 max = 0 glyph = circle glyph_size = 8 color = red ltaxesgt ltaxisgt color = lred thickness = 2 spacing = 01r ltaxisgt ltaxesgt ltbackgroundsgt ltbackgroundgt color = vlred_a5 ltbackgroundgt ltbackgroundsgt hellip
track for [-30] ltplotgt type = scatter file = data813datacnvtxt r0 = 075r r1 = 09r min = 0 max = 3 glyph = circle glyph_size = 8 color = green ltaxesgt ltaxisgt color = lgreen thickness = 2 spacing = 01r ltaxisgt ltaxesgt ltbackgroundsgt ltbackgroundgt color = vlred_a5 ltbackgroundgt ltbackgroundsgt hellip
Visualizing Biological Data
httpvizbiorg
Genomic alignments
Phylogenies
macromolecular structures
system biology
Overview
CIRCOS Features
Methods
Applications
Questions
httpcircosca
Features
CIRCOS is only a circular visualization tool no analysis
Creation of images is controlled through a plain-text configuration file
Circos can be used to display any kind of information
---initially design specific to genomics
---currently any relationship among data
ie chemical reactivity tracking transactionshellip
visualizing tables
Typical Circos Image
(A) histogram (B) ideograms (C) histogram (D) heatmap (E) links (F) highlights (G) grid (H) ticks
CIRCOS installation
1 System requirement UnixLinuxMac
2 Download amp Install circos software
3 Install Required Perl modules
4 Download Tutorial (Best practice examples)
Plain Text Input Files
gt circos -conf etccircosconf
Configuration file (circosconf)
ltticksgt ltltinclude etcticksconfgtgt ltticksgt
ticksconf
Genome to Genome link
Clickable image
bull Associate areas of the image with web links bull Any element in the image (ideogram tick band highlight ribobn etc) can
have an associated URL
FEATURES
MAKING IDEOGRAMS CLICKABLE
ltideogramgt
ideogram_url = httpwwwgooglecomsearchq=[chr]
helliphellip
ltideogramgt
chr - hs1 1 0 247249719 chr1 url=special_scriptchr=[chr]
chr - hs2 2 0 242951149 chr2 url=another_special_scriptchr=[chr]
chr - hs3 3 0 199501827 chr3
DEFINING URLS SPECIFIC TO INDIVIDUAL IDEOGRAMS
METHODS
Image map
1 Microbial Genome 2 Link Geometry - Detailed Bezier Control 3 Labeling Karyotype Bands 4 Image Maps 5 Image Transparency and Background 6 Manipulating Histograms 7 Variable Radius Link Ends 8 Stacked Histograms 9 Transparent Links 10 ID Fields 11 Heat Map Links 12 Inverted Links 13 Copy Number Data 14 Directed Links 15 Pattern Fills 16 Automating Tracks 17 Automating Heatmaps 18 Circular Stacked Bar Plots 19 Cortical Maps mdash Connectograms 20 Cell Cycle mdash Part 1 21 Cell Cycle mdash Part 2 22 Nature Cover Encode Diagram 23 Naming Names
Recipes
bull Configuration files bull Input data file bull Output images
Provided files
Copy number variation scatter plot
chrom start end logFC
hs3 7683536 8465787 143
hs11 465784 756867 -065
gctxt
track for [03]
CNV data range [-33]
Different background for the positive and negative CNV values
ltplotgt type = scatter file = data813datacnvtxt r0 = 06r r1 = 075r min = -3 max = 0 glyph = circle glyph_size = 8 color = red ltaxesgt ltaxisgt color = lred thickness = 2 spacing = 01r ltaxisgt ltaxesgt ltbackgroundsgt ltbackgroundgt color = vlred_a5 ltbackgroundgt ltbackgroundsgt hellip
track for [-30] ltplotgt type = scatter file = data813datacnvtxt r0 = 075r r1 = 09r min = 0 max = 3 glyph = circle glyph_size = 8 color = green ltaxesgt ltaxisgt color = lgreen thickness = 2 spacing = 01r ltaxisgt ltaxesgt ltbackgroundsgt ltbackgroundgt color = vlred_a5 ltbackgroundgt ltbackgroundsgt hellip
Visualizing Biological Data
httpvizbiorg
Genomic alignments
Phylogenies
macromolecular structures
system biology
Features
CIRCOS is only a circular visualization tool no analysis
Creation of images is controlled through a plain-text configuration file
Circos can be used to display any kind of information
---initially design specific to genomics
---currently any relationship among data
ie chemical reactivity tracking transactionshellip
visualizing tables
Typical Circos Image
(A) histogram (B) ideograms (C) histogram (D) heatmap (E) links (F) highlights (G) grid (H) ticks
CIRCOS installation
1 System requirement UnixLinuxMac
2 Download amp Install circos software
3 Install Required Perl modules
4 Download Tutorial (Best practice examples)
Plain Text Input Files
gt circos -conf etccircosconf
Configuration file (circosconf)
ltticksgt ltltinclude etcticksconfgtgt ltticksgt
ticksconf
Genome to Genome link
Clickable image
bull Associate areas of the image with web links bull Any element in the image (ideogram tick band highlight ribobn etc) can
have an associated URL
FEATURES
MAKING IDEOGRAMS CLICKABLE
ltideogramgt
ideogram_url = httpwwwgooglecomsearchq=[chr]
helliphellip
ltideogramgt
chr - hs1 1 0 247249719 chr1 url=special_scriptchr=[chr]
chr - hs2 2 0 242951149 chr2 url=another_special_scriptchr=[chr]
chr - hs3 3 0 199501827 chr3
DEFINING URLS SPECIFIC TO INDIVIDUAL IDEOGRAMS
METHODS
Image map
1 Microbial Genome 2 Link Geometry - Detailed Bezier Control 3 Labeling Karyotype Bands 4 Image Maps 5 Image Transparency and Background 6 Manipulating Histograms 7 Variable Radius Link Ends 8 Stacked Histograms 9 Transparent Links 10 ID Fields 11 Heat Map Links 12 Inverted Links 13 Copy Number Data 14 Directed Links 15 Pattern Fills 16 Automating Tracks 17 Automating Heatmaps 18 Circular Stacked Bar Plots 19 Cortical Maps mdash Connectograms 20 Cell Cycle mdash Part 1 21 Cell Cycle mdash Part 2 22 Nature Cover Encode Diagram 23 Naming Names
Recipes
bull Configuration files bull Input data file bull Output images
Provided files
Copy number variation scatter plot
chrom start end logFC
hs3 7683536 8465787 143
hs11 465784 756867 -065
gctxt
track for [03]
CNV data range [-33]
Different background for the positive and negative CNV values
ltplotgt type = scatter file = data813datacnvtxt r0 = 06r r1 = 075r min = -3 max = 0 glyph = circle glyph_size = 8 color = red ltaxesgt ltaxisgt color = lred thickness = 2 spacing = 01r ltaxisgt ltaxesgt ltbackgroundsgt ltbackgroundgt color = vlred_a5 ltbackgroundgt ltbackgroundsgt hellip
track for [-30] ltplotgt type = scatter file = data813datacnvtxt r0 = 075r r1 = 09r min = 0 max = 3 glyph = circle glyph_size = 8 color = green ltaxesgt ltaxisgt color = lgreen thickness = 2 spacing = 01r ltaxisgt ltaxesgt ltbackgroundsgt ltbackgroundgt color = vlred_a5 ltbackgroundgt ltbackgroundsgt hellip
Visualizing Biological Data
httpvizbiorg
Genomic alignments
Phylogenies
macromolecular structures
system biology
Typical Circos Image
(A) histogram (B) ideograms (C) histogram (D) heatmap (E) links (F) highlights (G) grid (H) ticks
CIRCOS installation
1 System requirement UnixLinuxMac
2 Download amp Install circos software
3 Install Required Perl modules
4 Download Tutorial (Best practice examples)
Plain Text Input Files
gt circos -conf etccircosconf
Configuration file (circosconf)
ltticksgt ltltinclude etcticksconfgtgt ltticksgt
ticksconf
Genome to Genome link
Clickable image
bull Associate areas of the image with web links bull Any element in the image (ideogram tick band highlight ribobn etc) can
have an associated URL
FEATURES
MAKING IDEOGRAMS CLICKABLE
ltideogramgt
ideogram_url = httpwwwgooglecomsearchq=[chr]
helliphellip
ltideogramgt
chr - hs1 1 0 247249719 chr1 url=special_scriptchr=[chr]
chr - hs2 2 0 242951149 chr2 url=another_special_scriptchr=[chr]
chr - hs3 3 0 199501827 chr3
DEFINING URLS SPECIFIC TO INDIVIDUAL IDEOGRAMS
METHODS
Image map
1 Microbial Genome 2 Link Geometry - Detailed Bezier Control 3 Labeling Karyotype Bands 4 Image Maps 5 Image Transparency and Background 6 Manipulating Histograms 7 Variable Radius Link Ends 8 Stacked Histograms 9 Transparent Links 10 ID Fields 11 Heat Map Links 12 Inverted Links 13 Copy Number Data 14 Directed Links 15 Pattern Fills 16 Automating Tracks 17 Automating Heatmaps 18 Circular Stacked Bar Plots 19 Cortical Maps mdash Connectograms 20 Cell Cycle mdash Part 1 21 Cell Cycle mdash Part 2 22 Nature Cover Encode Diagram 23 Naming Names
Recipes
bull Configuration files bull Input data file bull Output images
Provided files
Copy number variation scatter plot
chrom start end logFC
hs3 7683536 8465787 143
hs11 465784 756867 -065
gctxt
track for [03]
CNV data range [-33]
Different background for the positive and negative CNV values
ltplotgt type = scatter file = data813datacnvtxt r0 = 06r r1 = 075r min = -3 max = 0 glyph = circle glyph_size = 8 color = red ltaxesgt ltaxisgt color = lred thickness = 2 spacing = 01r ltaxisgt ltaxesgt ltbackgroundsgt ltbackgroundgt color = vlred_a5 ltbackgroundgt ltbackgroundsgt hellip
track for [-30] ltplotgt type = scatter file = data813datacnvtxt r0 = 075r r1 = 09r min = 0 max = 3 glyph = circle glyph_size = 8 color = green ltaxesgt ltaxisgt color = lgreen thickness = 2 spacing = 01r ltaxisgt ltaxesgt ltbackgroundsgt ltbackgroundgt color = vlred_a5 ltbackgroundgt ltbackgroundsgt hellip
Visualizing Biological Data
httpvizbiorg
Genomic alignments
Phylogenies
macromolecular structures
system biology
CIRCOS installation
1 System requirement UnixLinuxMac
2 Download amp Install circos software
3 Install Required Perl modules
4 Download Tutorial (Best practice examples)
Plain Text Input Files
gt circos -conf etccircosconf
Configuration file (circosconf)
ltticksgt ltltinclude etcticksconfgtgt ltticksgt
ticksconf
Genome to Genome link
Clickable image
bull Associate areas of the image with web links bull Any element in the image (ideogram tick band highlight ribobn etc) can
have an associated URL
FEATURES
MAKING IDEOGRAMS CLICKABLE
ltideogramgt
ideogram_url = httpwwwgooglecomsearchq=[chr]
helliphellip
ltideogramgt
chr - hs1 1 0 247249719 chr1 url=special_scriptchr=[chr]
chr - hs2 2 0 242951149 chr2 url=another_special_scriptchr=[chr]
chr - hs3 3 0 199501827 chr3
DEFINING URLS SPECIFIC TO INDIVIDUAL IDEOGRAMS
METHODS
Image map
1 Microbial Genome 2 Link Geometry - Detailed Bezier Control 3 Labeling Karyotype Bands 4 Image Maps 5 Image Transparency and Background 6 Manipulating Histograms 7 Variable Radius Link Ends 8 Stacked Histograms 9 Transparent Links 10 ID Fields 11 Heat Map Links 12 Inverted Links 13 Copy Number Data 14 Directed Links 15 Pattern Fills 16 Automating Tracks 17 Automating Heatmaps 18 Circular Stacked Bar Plots 19 Cortical Maps mdash Connectograms 20 Cell Cycle mdash Part 1 21 Cell Cycle mdash Part 2 22 Nature Cover Encode Diagram 23 Naming Names
Recipes
bull Configuration files bull Input data file bull Output images
Provided files
Copy number variation scatter plot
chrom start end logFC
hs3 7683536 8465787 143
hs11 465784 756867 -065
gctxt
track for [03]
CNV data range [-33]
Different background for the positive and negative CNV values
ltplotgt type = scatter file = data813datacnvtxt r0 = 06r r1 = 075r min = -3 max = 0 glyph = circle glyph_size = 8 color = red ltaxesgt ltaxisgt color = lred thickness = 2 spacing = 01r ltaxisgt ltaxesgt ltbackgroundsgt ltbackgroundgt color = vlred_a5 ltbackgroundgt ltbackgroundsgt hellip
track for [-30] ltplotgt type = scatter file = data813datacnvtxt r0 = 075r r1 = 09r min = 0 max = 3 glyph = circle glyph_size = 8 color = green ltaxesgt ltaxisgt color = lgreen thickness = 2 spacing = 01r ltaxisgt ltaxesgt ltbackgroundsgt ltbackgroundgt color = vlred_a5 ltbackgroundgt ltbackgroundsgt hellip
Visualizing Biological Data
httpvizbiorg
Genomic alignments
Phylogenies
macromolecular structures
system biology
Plain Text Input Files
gt circos -conf etccircosconf
Configuration file (circosconf)
ltticksgt ltltinclude etcticksconfgtgt ltticksgt
ticksconf
Genome to Genome link
Clickable image
bull Associate areas of the image with web links bull Any element in the image (ideogram tick band highlight ribobn etc) can
have an associated URL
FEATURES
MAKING IDEOGRAMS CLICKABLE
ltideogramgt
ideogram_url = httpwwwgooglecomsearchq=[chr]
helliphellip
ltideogramgt
chr - hs1 1 0 247249719 chr1 url=special_scriptchr=[chr]
chr - hs2 2 0 242951149 chr2 url=another_special_scriptchr=[chr]
chr - hs3 3 0 199501827 chr3
DEFINING URLS SPECIFIC TO INDIVIDUAL IDEOGRAMS
METHODS
Image map
1 Microbial Genome 2 Link Geometry - Detailed Bezier Control 3 Labeling Karyotype Bands 4 Image Maps 5 Image Transparency and Background 6 Manipulating Histograms 7 Variable Radius Link Ends 8 Stacked Histograms 9 Transparent Links 10 ID Fields 11 Heat Map Links 12 Inverted Links 13 Copy Number Data 14 Directed Links 15 Pattern Fills 16 Automating Tracks 17 Automating Heatmaps 18 Circular Stacked Bar Plots 19 Cortical Maps mdash Connectograms 20 Cell Cycle mdash Part 1 21 Cell Cycle mdash Part 2 22 Nature Cover Encode Diagram 23 Naming Names
Recipes
bull Configuration files bull Input data file bull Output images
Provided files
Copy number variation scatter plot
chrom start end logFC
hs3 7683536 8465787 143
hs11 465784 756867 -065
gctxt
track for [03]
CNV data range [-33]
Different background for the positive and negative CNV values
ltplotgt type = scatter file = data813datacnvtxt r0 = 06r r1 = 075r min = -3 max = 0 glyph = circle glyph_size = 8 color = red ltaxesgt ltaxisgt color = lred thickness = 2 spacing = 01r ltaxisgt ltaxesgt ltbackgroundsgt ltbackgroundgt color = vlred_a5 ltbackgroundgt ltbackgroundsgt hellip
track for [-30] ltplotgt type = scatter file = data813datacnvtxt r0 = 075r r1 = 09r min = 0 max = 3 glyph = circle glyph_size = 8 color = green ltaxesgt ltaxisgt color = lgreen thickness = 2 spacing = 01r ltaxisgt ltaxesgt ltbackgroundsgt ltbackgroundgt color = vlred_a5 ltbackgroundgt ltbackgroundsgt hellip
Visualizing Biological Data
httpvizbiorg
Genomic alignments
Phylogenies
macromolecular structures
system biology
Configuration file (circosconf)
ltticksgt ltltinclude etcticksconfgtgt ltticksgt
ticksconf
Genome to Genome link
Clickable image
bull Associate areas of the image with web links bull Any element in the image (ideogram tick band highlight ribobn etc) can
have an associated URL
FEATURES
MAKING IDEOGRAMS CLICKABLE
ltideogramgt
ideogram_url = httpwwwgooglecomsearchq=[chr]
helliphellip
ltideogramgt
chr - hs1 1 0 247249719 chr1 url=special_scriptchr=[chr]
chr - hs2 2 0 242951149 chr2 url=another_special_scriptchr=[chr]
chr - hs3 3 0 199501827 chr3
DEFINING URLS SPECIFIC TO INDIVIDUAL IDEOGRAMS
METHODS
Image map
1 Microbial Genome 2 Link Geometry - Detailed Bezier Control 3 Labeling Karyotype Bands 4 Image Maps 5 Image Transparency and Background 6 Manipulating Histograms 7 Variable Radius Link Ends 8 Stacked Histograms 9 Transparent Links 10 ID Fields 11 Heat Map Links 12 Inverted Links 13 Copy Number Data 14 Directed Links 15 Pattern Fills 16 Automating Tracks 17 Automating Heatmaps 18 Circular Stacked Bar Plots 19 Cortical Maps mdash Connectograms 20 Cell Cycle mdash Part 1 21 Cell Cycle mdash Part 2 22 Nature Cover Encode Diagram 23 Naming Names
Recipes
bull Configuration files bull Input data file bull Output images
Provided files
Copy number variation scatter plot
chrom start end logFC
hs3 7683536 8465787 143
hs11 465784 756867 -065
gctxt
track for [03]
CNV data range [-33]
Different background for the positive and negative CNV values
ltplotgt type = scatter file = data813datacnvtxt r0 = 06r r1 = 075r min = -3 max = 0 glyph = circle glyph_size = 8 color = red ltaxesgt ltaxisgt color = lred thickness = 2 spacing = 01r ltaxisgt ltaxesgt ltbackgroundsgt ltbackgroundgt color = vlred_a5 ltbackgroundgt ltbackgroundsgt hellip
track for [-30] ltplotgt type = scatter file = data813datacnvtxt r0 = 075r r1 = 09r min = 0 max = 3 glyph = circle glyph_size = 8 color = green ltaxesgt ltaxisgt color = lgreen thickness = 2 spacing = 01r ltaxisgt ltaxesgt ltbackgroundsgt ltbackgroundgt color = vlred_a5 ltbackgroundgt ltbackgroundsgt hellip
Visualizing Biological Data
httpvizbiorg
Genomic alignments
Phylogenies
macromolecular structures
system biology
Genome to Genome link
Clickable image
bull Associate areas of the image with web links bull Any element in the image (ideogram tick band highlight ribobn etc) can
have an associated URL
FEATURES
MAKING IDEOGRAMS CLICKABLE
ltideogramgt
ideogram_url = httpwwwgooglecomsearchq=[chr]
helliphellip
ltideogramgt
chr - hs1 1 0 247249719 chr1 url=special_scriptchr=[chr]
chr - hs2 2 0 242951149 chr2 url=another_special_scriptchr=[chr]
chr - hs3 3 0 199501827 chr3
DEFINING URLS SPECIFIC TO INDIVIDUAL IDEOGRAMS
METHODS
Image map
1 Microbial Genome 2 Link Geometry - Detailed Bezier Control 3 Labeling Karyotype Bands 4 Image Maps 5 Image Transparency and Background 6 Manipulating Histograms 7 Variable Radius Link Ends 8 Stacked Histograms 9 Transparent Links 10 ID Fields 11 Heat Map Links 12 Inverted Links 13 Copy Number Data 14 Directed Links 15 Pattern Fills 16 Automating Tracks 17 Automating Heatmaps 18 Circular Stacked Bar Plots 19 Cortical Maps mdash Connectograms 20 Cell Cycle mdash Part 1 21 Cell Cycle mdash Part 2 22 Nature Cover Encode Diagram 23 Naming Names
Recipes
bull Configuration files bull Input data file bull Output images
Provided files
Copy number variation scatter plot
chrom start end logFC
hs3 7683536 8465787 143
hs11 465784 756867 -065
gctxt
track for [03]
CNV data range [-33]
Different background for the positive and negative CNV values
ltplotgt type = scatter file = data813datacnvtxt r0 = 06r r1 = 075r min = -3 max = 0 glyph = circle glyph_size = 8 color = red ltaxesgt ltaxisgt color = lred thickness = 2 spacing = 01r ltaxisgt ltaxesgt ltbackgroundsgt ltbackgroundgt color = vlred_a5 ltbackgroundgt ltbackgroundsgt hellip
track for [-30] ltplotgt type = scatter file = data813datacnvtxt r0 = 075r r1 = 09r min = 0 max = 3 glyph = circle glyph_size = 8 color = green ltaxesgt ltaxisgt color = lgreen thickness = 2 spacing = 01r ltaxisgt ltaxesgt ltbackgroundsgt ltbackgroundgt color = vlred_a5 ltbackgroundgt ltbackgroundsgt hellip
Visualizing Biological Data
httpvizbiorg
Genomic alignments
Phylogenies
macromolecular structures
system biology
Clickable image
bull Associate areas of the image with web links bull Any element in the image (ideogram tick band highlight ribobn etc) can
have an associated URL
FEATURES
MAKING IDEOGRAMS CLICKABLE
ltideogramgt
ideogram_url = httpwwwgooglecomsearchq=[chr]
helliphellip
ltideogramgt
chr - hs1 1 0 247249719 chr1 url=special_scriptchr=[chr]
chr - hs2 2 0 242951149 chr2 url=another_special_scriptchr=[chr]
chr - hs3 3 0 199501827 chr3
DEFINING URLS SPECIFIC TO INDIVIDUAL IDEOGRAMS
METHODS
Image map
1 Microbial Genome 2 Link Geometry - Detailed Bezier Control 3 Labeling Karyotype Bands 4 Image Maps 5 Image Transparency and Background 6 Manipulating Histograms 7 Variable Radius Link Ends 8 Stacked Histograms 9 Transparent Links 10 ID Fields 11 Heat Map Links 12 Inverted Links 13 Copy Number Data 14 Directed Links 15 Pattern Fills 16 Automating Tracks 17 Automating Heatmaps 18 Circular Stacked Bar Plots 19 Cortical Maps mdash Connectograms 20 Cell Cycle mdash Part 1 21 Cell Cycle mdash Part 2 22 Nature Cover Encode Diagram 23 Naming Names
Recipes
bull Configuration files bull Input data file bull Output images
Provided files
Copy number variation scatter plot
chrom start end logFC
hs3 7683536 8465787 143
hs11 465784 756867 -065
gctxt
track for [03]
CNV data range [-33]
Different background for the positive and negative CNV values
ltplotgt type = scatter file = data813datacnvtxt r0 = 06r r1 = 075r min = -3 max = 0 glyph = circle glyph_size = 8 color = red ltaxesgt ltaxisgt color = lred thickness = 2 spacing = 01r ltaxisgt ltaxesgt ltbackgroundsgt ltbackgroundgt color = vlred_a5 ltbackgroundgt ltbackgroundsgt hellip
track for [-30] ltplotgt type = scatter file = data813datacnvtxt r0 = 075r r1 = 09r min = 0 max = 3 glyph = circle glyph_size = 8 color = green ltaxesgt ltaxisgt color = lgreen thickness = 2 spacing = 01r ltaxisgt ltaxesgt ltbackgroundsgt ltbackgroundgt color = vlred_a5 ltbackgroundgt ltbackgroundsgt hellip
Visualizing Biological Data
httpvizbiorg
Genomic alignments
Phylogenies
macromolecular structures
system biology
Image map
1 Microbial Genome 2 Link Geometry - Detailed Bezier Control 3 Labeling Karyotype Bands 4 Image Maps 5 Image Transparency and Background 6 Manipulating Histograms 7 Variable Radius Link Ends 8 Stacked Histograms 9 Transparent Links 10 ID Fields 11 Heat Map Links 12 Inverted Links 13 Copy Number Data 14 Directed Links 15 Pattern Fills 16 Automating Tracks 17 Automating Heatmaps 18 Circular Stacked Bar Plots 19 Cortical Maps mdash Connectograms 20 Cell Cycle mdash Part 1 21 Cell Cycle mdash Part 2 22 Nature Cover Encode Diagram 23 Naming Names
Recipes
bull Configuration files bull Input data file bull Output images
Provided files
Copy number variation scatter plot
chrom start end logFC
hs3 7683536 8465787 143
hs11 465784 756867 -065
gctxt
track for [03]
CNV data range [-33]
Different background for the positive and negative CNV values
ltplotgt type = scatter file = data813datacnvtxt r0 = 06r r1 = 075r min = -3 max = 0 glyph = circle glyph_size = 8 color = red ltaxesgt ltaxisgt color = lred thickness = 2 spacing = 01r ltaxisgt ltaxesgt ltbackgroundsgt ltbackgroundgt color = vlred_a5 ltbackgroundgt ltbackgroundsgt hellip
track for [-30] ltplotgt type = scatter file = data813datacnvtxt r0 = 075r r1 = 09r min = 0 max = 3 glyph = circle glyph_size = 8 color = green ltaxesgt ltaxisgt color = lgreen thickness = 2 spacing = 01r ltaxisgt ltaxesgt ltbackgroundsgt ltbackgroundgt color = vlred_a5 ltbackgroundgt ltbackgroundsgt hellip
Visualizing Biological Data
httpvizbiorg
Genomic alignments
Phylogenies
macromolecular structures
system biology
1 Microbial Genome 2 Link Geometry - Detailed Bezier Control 3 Labeling Karyotype Bands 4 Image Maps 5 Image Transparency and Background 6 Manipulating Histograms 7 Variable Radius Link Ends 8 Stacked Histograms 9 Transparent Links 10 ID Fields 11 Heat Map Links 12 Inverted Links 13 Copy Number Data 14 Directed Links 15 Pattern Fills 16 Automating Tracks 17 Automating Heatmaps 18 Circular Stacked Bar Plots 19 Cortical Maps mdash Connectograms 20 Cell Cycle mdash Part 1 21 Cell Cycle mdash Part 2 22 Nature Cover Encode Diagram 23 Naming Names
Recipes
bull Configuration files bull Input data file bull Output images
Provided files
Copy number variation scatter plot
chrom start end logFC
hs3 7683536 8465787 143
hs11 465784 756867 -065
gctxt
track for [03]
CNV data range [-33]
Different background for the positive and negative CNV values
ltplotgt type = scatter file = data813datacnvtxt r0 = 06r r1 = 075r min = -3 max = 0 glyph = circle glyph_size = 8 color = red ltaxesgt ltaxisgt color = lred thickness = 2 spacing = 01r ltaxisgt ltaxesgt ltbackgroundsgt ltbackgroundgt color = vlred_a5 ltbackgroundgt ltbackgroundsgt hellip
track for [-30] ltplotgt type = scatter file = data813datacnvtxt r0 = 075r r1 = 09r min = 0 max = 3 glyph = circle glyph_size = 8 color = green ltaxesgt ltaxisgt color = lgreen thickness = 2 spacing = 01r ltaxisgt ltaxesgt ltbackgroundsgt ltbackgroundgt color = vlred_a5 ltbackgroundgt ltbackgroundsgt hellip
Visualizing Biological Data
httpvizbiorg
Genomic alignments
Phylogenies
macromolecular structures
system biology
Copy number variation scatter plot
chrom start end logFC
hs3 7683536 8465787 143
hs11 465784 756867 -065
gctxt
track for [03]
CNV data range [-33]
Different background for the positive and negative CNV values
ltplotgt type = scatter file = data813datacnvtxt r0 = 06r r1 = 075r min = -3 max = 0 glyph = circle glyph_size = 8 color = red ltaxesgt ltaxisgt color = lred thickness = 2 spacing = 01r ltaxisgt ltaxesgt ltbackgroundsgt ltbackgroundgt color = vlred_a5 ltbackgroundgt ltbackgroundsgt hellip
track for [-30] ltplotgt type = scatter file = data813datacnvtxt r0 = 075r r1 = 09r min = 0 max = 3 glyph = circle glyph_size = 8 color = green ltaxesgt ltaxisgt color = lgreen thickness = 2 spacing = 01r ltaxisgt ltaxesgt ltbackgroundsgt ltbackgroundgt color = vlred_a5 ltbackgroundgt ltbackgroundsgt hellip
Visualizing Biological Data
httpvizbiorg
Genomic alignments
Phylogenies
macromolecular structures
system biology
track for [03]
CNV data range [-33]
Different background for the positive and negative CNV values
ltplotgt type = scatter file = data813datacnvtxt r0 = 06r r1 = 075r min = -3 max = 0 glyph = circle glyph_size = 8 color = red ltaxesgt ltaxisgt color = lred thickness = 2 spacing = 01r ltaxisgt ltaxesgt ltbackgroundsgt ltbackgroundgt color = vlred_a5 ltbackgroundgt ltbackgroundsgt hellip
track for [-30] ltplotgt type = scatter file = data813datacnvtxt r0 = 075r r1 = 09r min = 0 max = 3 glyph = circle glyph_size = 8 color = green ltaxesgt ltaxisgt color = lgreen thickness = 2 spacing = 01r ltaxisgt ltaxesgt ltbackgroundsgt ltbackgroundgt color = vlred_a5 ltbackgroundgt ltbackgroundsgt hellip
Visualizing Biological Data
httpvizbiorg
Genomic alignments
Phylogenies
macromolecular structures
system biology
Visualizing Biological Data
httpvizbiorg
Genomic alignments
Phylogenies
macromolecular structures
system biology
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