DATASET_TANGLEGRAM #In tanglegrams, an additional tree is displayed next to the main tree. Matching leaf nodes (or nodes specified in the DATA section below) are connected with lines #lines starting with a hash are comments and ignored during parsing #=================================================================# # MANDATORY SETTINGS # #=================================================================# #select the separator which is used to delimit the data below (TAB or SPACE).This separator must be used throughout this file. COMMA cannot be used in this dataset, since it is used within the TANGLEGRAM_TREE SEPARATOR TAB #SEPARATOR SPACE #label is used in the legend table (can be changed later) DATASET_LABEL example_tanglegram #dataset color (can be changed later) COLOR #00ff00 #The tree which will be displayed next to the main tree. Put the complete tree text between the fields TANGLEGRAM_TREE and END_TANGLEGRAM_TREE. It can be in Newick, Nexus or phyloXML format, and can contain additional metadata as for standard iTOL trees. #Its IDs which exactly match the main tree IDs will be automatically connected. #Additional connections (between non-matching nodes) can be defined below in the DATA section TANGLEGRAM_TREE #((((((Thalassiosira_pseudonana:0.33483, #(Cryptosporidium_hominis:0.25048, #Plasmodium_falciparum:0.28267)Apicomplexa:0.14359[100])Eukaryota:0.03495[42], #((Cyanidioschyzon_merolae:0.38319)Eukaryota:0.08133[96], #(Dictyostelium_discoideum:0.34685,(((Eremothecium_gossypii:0.07298,Saccharomyces_cerevisiae:0.07619)Saccharomycetaceae:0.21170[100],Schizosaccharomyces_pombe:0.24665)Ascomycota:0.15370[100],(((Diptera:0.10724)Diptera:0.09870[100],((Takifugu_rubripes:0.03142)Actinopterygii:0.04335[100],(((Rattus_norvegicus:0.03107)Murinae:0.00398[91],(Homo_sapiens:0.00957,Pan_troglodytes:0.03864)Hominidae:0.01549[100])Euarchontoglires:0.01629[99],Gallus_gallus:0.04596)Gnathostomata:0.01859[100])Gnathostomata:0.09688[100])Metazoa:0.03693[95],(Caenorhabditis_elegans:0.01843,Caenorhabditis_briggsae:0.01896)Caenorhabditis:0.24324[100])Metazoa:0.09911[100])Eukaryota:0.04004[85])Eukaryota:0.02708[41])Eukaryota:0.02636[44])Eukaryota:0.06455[87], #Leishmania_major:0.45664)Eukaryota:0.10129[100],Giardia_lamblia:0.55482)Eukaryota:0.57543[100]):0.88776); END_TANGLEGRAM_TREE #=================================================================# # all other optional settings can be set or changed later # # in the web interface (under 'Datasets' tab) # #=================================================================# #Each dataset can have a legend, which is defined using LEGEND_XXX fields below #For each row in the legend, there should be one shape, color and label. #Optionally, you can define an exact legend position using LEGEND_POSITION_X and LEGEND_POSITION_Y. To use automatic legend positioning, do NOT define these values #Optionally, shape scaling can be present (LEGEND_SHAPE_SCALES). For each shape, you can define a scaling factor between 0 and 1. #To order legend entries horizontally instead of vertically, set LEGEND_HORIZONTAL to 1 #Shape should be a number between 1 and 12, or any protein domain shape definition. #1: square #2: circle #3: star #4: right pointing triangle #5: left pointing triangle #6: checkmark #7: solid line #8: dashed line #9: dotted line #10:arrow left #11:arrow right #12:bidirectional arrow #7: solid line #8: dashed line #9: dotted line #LEGEND_TITLE Dataset legend #LEGEND_SCALE 1 #LEGEND_POSITION_X 100 #LEGEND_POSITION_Y 100 #LEGEND_HORIZONTAL 0 #LEGEND_SHAPES 1 2 3 #LEGEND_COLORS #ff0000 #00ff00 #0000ff #LEGEND_LABELS value1 value2 value3 #LEGEND_SHAPE_SCALES 1 1 0.5 #style for the default connections between the leaves (normal, dashed or dotted) DEFAULT_CONNECTION_STYLE normal #default connection color (hex, RGB or RGBA notation) DEFAULT_CONNECTION_COLOR #888888 #default connection width in pixels DEFAULT_CONNECTION_WIDTH 1 #margins between the end of leaf labels/tree nodes and the start/end of the connection line CONNECTION_MARGIN_RIGHT 0 CONNECTION_MARGIN_LEFT 0 #starts and ends of the connections will have a straigt line of this length CONNECTION_TAIL 0 #connections will be curved CONNECTION_CURVE 1 #maximum connection width specified in the DATA section will be drawn with this value. All other widths will be scaled down proportionally MAXIMUM_LINE_WIDTH 1 #display the leaf labels on the tanglegram tree SHOW_LABELS 1 #leaf label size factor SIZE_FACTOR 1 #leaf label shift in pixels (positive or negative), relative to the tanglegram tree LABEL_SHIFT 0 #alignment of the tanglegram leaf labels (left or right), relative to the tanglegram tree LABEL_ALIGN right #pan the tanglegram tree horizontally and/or vertically TREE_PAN_H 0 TREE_PAN_V 0 #tanglegram tree scaling factors, horizontal and vertical TREE_SCALE_H 1 TREE_SCALE_V 1 #===============================================================================================# # parameters related to any 'colorstrip' or 'symbol' datasets defined in the DATA section below # #===============================================================================================# #define the labels for any colored strips or external symbols below. Label order should match the COLUMN_INDEX (or negative position index for symbols), #ie. the first value will be used for COLUMN_INDEX 1 and so on. COLUMN_LABELS label_for_column_index_1 label_for_column_index_2 label_for_column_index_3 #margin between the tanglegram tree and its external datasets, in pixels TANGLEGRAM_EXTERNAL_MARGIN 0 #display or hide the columns labels above the colored strips/external symbols SHOW_COLUMN_LABELS 0 #column label size factor COLUMN_LABEL_SIZE_FACTOR 1 #column label shift in pixels (positive or negative), horizontal and vertical COLUMN_LABEL_SHIFT_X 0 COLUMN_LABEL_SHIFT_Y 0 #column label rotation COLUMN_LABEL_ROTATION 0 #==================================# # 'colorstrip' specific parameters # #==================================# #display or hide any colored strips defined in the DATA section SHOW_STRIPS 1 #width of the colored strips #STRIP_WIDTH 25 #always show internal values; if set, values associated to internal nodes will be displayed even if these nodes are not collapsed. SHOW_INTERNAL 0 #When multiple colored strips are present on the tanglegram, they will be separated by this amount of pixels #STRIP_SPACING 0 #border width; if set above 0, a border of specified width (in pixels) will be drawn around the color strip #STRIP_BORDER_WIDTH 0 #border color; used when STRIP_BORDER_WIDTH is above 0 #STRIP_BORDER_COLOR #0000ff #if set to 1, border will be drawn completely around each colored strip box separately #COMPLETE_BORDER 0 #display or hide the individual label inside each colored strip (when defined in the data below) #SHOW_STRIP_LABELS 1 #position of the strip label within the box; 'top', 'center' or 'bottom' #STRIP_LABEL_POSITION center #strip label size factor (relative to the tree leaf labels) #STRIP_LABEL_SIZE_FACTOR 1 #rotation of the strip labels; used only in rectangular tree display mode #STRIP_LABEL_ROTATION 0 #strip label shift in pixels (positive or negative) #STRIP_LABEL_SHIFT 0 #STRIP_LABEL_COLOR #000000 #calculate the strip label color automatically (black or white), based on the darkness of the color strip #STRIP_LABEL_AUTO_COLOR 0 #==============================# # 'symbol' specific parameters # #==============================# #display or hide any symbols defined in the DATA section SHOW_SYMBOLS 1 #largest symbol will be displayed with this size, others will be proportionally smaller. MAXIMUM_SYMBOL_SIZE 25 #When multiple external symbol columns are present on the tanglegram, they will be separated by this amount of pixels #SYMBOL_SPACING 0 #border width; if set above 0, a border of specified width (in pixels) will be drawn around each symbol #SYMBOL_BORDER_WIDTH 0 #border color; used when SYMBOL_BORDER_WIDTH is above 0, and for filled symbols only #SYMBOL_BORDER_COLOR #0000ff #================================================================# # end of parameters related to 'colorstrip' or 'symbol' datasets # #================================================================# #=================================================================# # Actual data follows after the "DATA" keyword # #=================================================================# DATA #In the DATA section, several types of annotations can be specified. The type is defined in the first field, and can be 'connect', 'style' or 'colorstrip'. #Information below is split into sections based on the annotation types #========================== #'connect' type annotations #========================== #By using the 'connect' annotation, you can define additional connections between non-matching leaves, or set non-default styles for matching leaf connections #Each line defines a single connection between 2 leaves and consists of the following fields: #connect MAIN_TREE_NODE_ID TANGLEGRAM_TREE_NODE_ID WIDTH COLOR STYLE LABEL #Only the leaf IDs are required. You can also specify the same ID in both trees, when a specific, non-default style should be used for that particular connection #All connection widths will be normalized based on the MAXIMUM_LINE_WIDTH specified for the whole dataset #STYLE defines the connection line style, and can be one of 'normal', 'dashed' or 'dotted'. #color can be specified in hexadecimal, RGB or RGBA notation #label will be shown in the mouseover info popup, if defined #Examples: #connect Giardia_lamblia Giardia_lamblia 4 #ff0000 dotted test label #connect Homo_sapiens Homo_sapiens 2 #0000ff normal Human label #connect Drosophila_melanogaster Diptera 1 #00ff00 dashed Diptera links #connect Anopheles_gambiae Diptera 1 #00ff00 dashed Diptera links #========================= #'style' type annotations #========================= #By using the 'style' keyword in the first field, you can define branch/label styles for the tanglegram tree. #The format is identical to the main "Branch and label styles" dataset, check the 'dataset_styles_template.txt' file for complete details #Note that you can use the last common ancestor method to define internal tanglegram tree nodes as well (check the help page for details) #Each line defines a style to be applied, and consists of the following fields: #style TANGLEGRAM_TREE_NODE_ID TYPE WHAT COLOR WIDTH_OR_SIZE_FACTOR STYLE BACKGROUND_COLOR #Examples: #Homo sapiens node will have its label displayed in blue with bold italic font, and with yellow background #style Homo_sapiens label node #0000ff 1 bold-italic #ffff00 #Metazoa clade starting at the last common ancestor of Caenorhabditis_elegans and Homo_sapiens will have all its branches colored green #style Caenorhabditis_elegans|Homo_sapiens branch clade #00ff00 1 normal #============================= #'colorstrip' type annotations #============================= #By using the 'colorstrip' keyword in the first field, you can define one or more colored strips for the tanglegram tree. #You can define multiple separate colored strips by using different COLUMN_INDEX values. COLUMN_INDEX is any positive integer value, and #the strips will be rendered next to the tree in ascending COLUMN_INDEX order (ie. colored strip 1 will be first, followed by colored strip 2 and so on). #note that the COLUMN_INDEX is shared with the 'symbol' type annotations, so that multiple colored strips and external symbol columns datasets can be mixed #Note that you can use the last common ancestor method to define internal tanglegram tree nodes as well (check the help page for details) #Each line defines a colored box for a node, and consists of the following fields: #colorstrip COLUMN_INDEX TANGLEGRAM_TREE_NODE_ID COLOR LABEL #Examples: #Homo sapiens node will have a red box as colored strip 1, and a green box as colored strip 2 #colorstrip 1 Homo_sapiens #ff0000 red_box #colorstrip 2 Homo_sapiens #00ff00 green_box #Metazoa clade (the last common ancestor of Caenorhabditis_elegans and Homo_sapiens) will have a blue box as colored strip 1 #colorstrip 1 Caenorhabditis_elegans|Homo_sapiens #0000ff blue_box #============================= #'symbol' type annotations #============================= #By using the 'symbol' keyword in the first field, you can define one or more symbol annotations for the tanglegram tree. #The format is identical to the main "Branch / external symbols" dataset, check the 'dataset_symbols_template.txt' file for complete details. #Note that you can use the last common ancestor method to define internal tanglegram tree nodes as well (check the help page for details) #Each line defines a symbol to be displayed, and consists of the following fields: #symbol TANGLEGRAM_TREE_NODE_ID SYMBOL SIZE COLOR FILL POSITION LABEL #Clarification about the position of external symbols: # when using negative values for the POSITION field, these are shared with the COLUMN_INDEX values used in the 'colorstrip' annotations # For example, symbol POSITION value -2 corresponds to the second column, ie. COLUMN_INDEX 2 # By using different values of COLUMN_INDEX and POSITION, there can be multiple colored strips and external symbol columns in any order you wish #Examples: #Homo sapiens node will have a filled red rectangle in external column 1, and an outline blue circle internally in the middle of its branch. #symbol Homo_sapiens 1 10 #ff0000 1 -1 external_square #symbol Homo_sapiens 2 10 #0000ff 0 0.5 internal_blue_circle #Mus musculus node will have an outline green star in external column 1, and a filled red in column 3. #symbol Mus_musculus 0 #symbol Mus_musculus 1