DATASET_RANGE #Colored/labeled range datasets allow the highlighting of various clades or leaf ranges by using colored boxes or brackets. #lines starting with a hash sign are comments and ignored during parsing #=================================================================# # MANDATORY SETTINGS # #=================================================================# #select the separator which is used to delimit the data below (TAB,SPACE or COMMA).This separator must be used throughout this file. #SEPARATOR TAB #SEPARATOR SPACE SEPARATOR COMMA #label is used in the legend table (can be changed later) DATASET_LABEL,example range #dataset color in the legend table COLOR,#ffff00 #=================================================================# # OPTIONAL SETTINGS # #=================================================================# #=================================================================# # all optional settings can be set or changed later # # in the web interface (under 'Datasets' tab) # #=================================================================# #RANGE_TYPE defines how the rages will be visualized: #box: standard colored box/polygon. Various LINE_? fields in the range definition will be used for the border style. #bracket: a line or bracket outside the tree RANGE_TYPE,box # #Box/polygon specific options, used when RANGE_TYPE is 'box' # #specify what the range boxes will cover: 'label','clade' or 'tree' RANGE_COVER,clade #simplify or smooth polygons when in unrooted display mode: 'none', 'simplify' or 'smooth' UNROOTED_SMOOTH,simplify #when RANGE_COVER is set to 'clade' or 'tree', you can disable the covering of labels (ie. limiting the boxes to the tree structure only) COVER_LABELS,0 #if set to 1, ranges will cover any displayed extrernal datasets as well COVER_DATASETS,0 #if set to 1, size of the boxes will be extended to fit their labels FIT_LABELS,0 # #Bracket specific options, used when RANGE_TYPE is 'bracket' # #bracket style can be: 'none','square' or 'curved' BRACKET_STYLE,square #size of the bracket ends (for 'square' or 'curved' brackets) BRACKET_SIZE,20 #shift the bracket position horizontally BRACKET_SHIFT,50 #if set to 1, brackets will be displayed behind the last visible external dataset BRACKET_BEHIND_DATASETS,1 # #Options related to range labels # SHOW_LABELS,1 #the position of the label in the range box (or relative to the bracket): 'top-left','top-center','top-right', # 'center-left','center-center','center-right', # 'bottom-left','bottom-center','bottom-right' LABEL_POSITION,bottom-right #Display the labels vertically. In circular display mode (or with brackets in unrooted display mode), labels will be aligned to the circle LABELS_VERTICAL,0 #labels remain straight, regardless of the tree rotation or other rotation parameters STRAIGHT_LABELS,0 #rotate all labels by the specified angle LABEL_ROTATION,0 #shift all labels horizontally and/or vertically LABEL_SHIFT_X,0 LABEL_SHIFT_Y,0 #add a colored outline to the label font; useful when displaying labels over similarly colored boxes (e.g. black font on a dark box) LABEL_OUTLINE_WIDTH,0 LABEL_OUTLINE_COLOR,#ffffff #calculate the label color automatically (black or white), based on the darkness of the range color LABEL_AUTO_COLOR,0 #multiply the size of all labels by this factor LABEL_SIZE_FACTOR,1 #shrink range boxes or brackets vertically, to introduce spacing between neighbouring ranges VERTICAL_SHRINK,0 #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 6, or any protein domain shape definition. #1: square #2: circle #3: star #4: right pointing triangle #5: left pointing triangle #6: checkmark #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 #Internal tree nodes can be specified by using IDs directly, or by using the 'last common ancestor' method described in iTOL help pages #=================================================================# # Actual data follows after the "DATA" keyword # #=================================================================# #the following fields are available in each line: #START_NODE_ID,END_NODE_ID,FILL_COLOR,GRADIENT_COLOR,LINE_COLOR,LINE_STYLE,LINE_WIDTH,LABEL_TEXT,LABEL_COLOR,LABEL_SIZE_FACTOR,LABEL_STYLE #The range is defined through START_NODE_ID and END_NODE_ID. #If GRADIENT_FILL color is defined, the box will be filled with a gradient from FILL_COLOR to GRADIENT_COLOR. Brackets will also be visualized as gradients. #LINE_COLOR will be used for the box/polygon border, or for the brackets. If not specified, FILL_COLOR will be used instead #LINE_STYLE can be 'solid', 'dashed' or 'dotted' #LABEL_STYLE can be 'normal', 'bold', 'italic' or 'bold-italic' DATA #Examples #a range between leaves 9606 and 184922, filled with a gradient from white (#ffffff) to red (#ff0000), with a 2px dashed black (#000000) border and a blue (#0000ff) italic label #9606,184922,#ffffff,#ff0000,#000000,dashed,2,Example range,#0000ff,1,italic