DATASET_HEATMAP #In heatmaps, each ID is associated to multiple numeric values, which are displayed as a set of colored boxes defined by a color gradient #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,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_heatmap #dataset color (can be changed later) COLOR #ff0000 #define labels for each individual field column FIELD_LABELS f1 f2 f3 f4 f5 f6 #=================================================================# # OPTIONAL SETTINGS # #=================================================================# #Heatmaps can have an optional Newick formatted tree assigned. Its leaf IDs must exactly match the dataset FIELD_LABELS. #The tree will be used to sort the dataset fields, and will be displayed above the dataset. It can have branch lengths defined. #All newlines and spaces should be stripped from the tree, and COMMA cannot be used as the dataset separator if a FIELD_TREE is provided. FIELD_TREE (((f1:0.2,f5:0.5):1,(f2:0.2,f3:0.3):1.2):0.5,(f4:0.1,f6:0.5):0.8):1; #=================================================================# # 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 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 #left margin, used to increase/decrease the spacing to the next dataset. Can be negative, causing datasets to overlap. #MARGIN 0 #width of the individual boxes #STRIP_WIDTH 25 #always show internal values; if set, values associated to internal nodes will be displayed even if these nodes are not collapsed. It could cause overlapping in the dataset display. #SHOW_INTERNAL 0 #show dashed lines between leaf labels and the dataset #DASHED_LINES 1 #if a FIELD_TREE is present, it can be hidden by setting this option to 0 #SHOW_TREE 1 #define the color for the NULL values in the dataset. Use the letter X in the data to define the NULL values #COLOR_NAN #000000 #automatically create and display a legend based on the color gradients and values defined below #AUTO_LEGEND 1 #define the heatmap gradient colors. Values in the dataset will be mapped onto the corresponding color gradient. #COLOR_MIN #ff0000 #COLOR_MAX #0000ff #you can specify a gradient with three colors (e.g red to yellow to green) by setting 'USE_MID_COLOR' to 1, and specifying the midpoint color #USE_MID_COLOR 1 #COLOR_MID #ffff00 #By default, color gradients will be calculated based on dataset values. You can force different values to use in the calculation by setting the values below: #USER_MIN_VALUE 0 #USER_MID_VALUE 500 #USER_MAX_VALUE 1000 #border width; if set above 0, a border of specified width (in pixels) will be drawn around individual cells #BORDER_WIDTH 0 #border color; used only when BORDER_WIDTH is above 0 #BORDER_COLOR #0000ff #display or hide the text labels above each field column #SHOW_LABELS 1 #text label size factor #SIZE_FACTOR 1 #text label rotation #LABEL_ROTATION 0 #text label shift in pixels (positive or negative) #LABEL_SHIFT 0 #normalize the data using the function specified in NORMALIZATION_TYPE. DATA_NORMALIZATION can be set to #'rows' (normalize data for each tree leaf) or 'columns' (normalize data for each heatmap field) #DATA_NORMALIZATION rows #type of normalization to apply. The following types are available: #normal: values will be normalized between values A and B (specified in NORMALIZATION_RANGE) using the formula A+(val-min)*(B-A)/(max-min) #mean: values will be normalized between -1 and 1 using the formula (val-mean)/(max-min) #scaling: values will be Z-score normalized using the formula (val-mean)/std.dev #NORMALIZATION_TYPE scaling #used to define the A-B range for standard normalization #NORMALIZATION_RANGE 0 3 #Display the actual values inside the heatmap boxes. Can be either 'original' or 'normalized'. If the data is not normalized, original values will be used in any case. #DISPLAY_VALUES normalized #round the display values to this number of decimal points #ROUND_VALUES 2 #if set to 1, display values using scientific notation (e.g. 1e3 is 1000). Can be combined with ROUND_VALUES #VALUES_SCI_NOTATION 1 #color of the value labels #VALUE_COLOR #0000ff #if set to 1, calculate the value label color automatically, based on the darkness of the heatmap box. Labels will be white or black. #VALUE_AUTO_COLOR 1 #shift the position of the value labels by the specified number of pixels (X and Y) #VALUE_SHIFT 0 0 #rotate the value labels by this angle #VALUE_ROTATION 0 #multiply the value label font size by this factor #VALUE_SIZE_FACTOR 1 #Internal tree nodes can be specified using IDs directly, or using the 'last common ancestor' method described in iTOL help pages #=================================================================# # Actual data follows after the "DATA" keyword # #=================================================================# DATA #ID1 value1 value2 value3 value4 value5 value6 #You can use the 'X' letter instead of the numeric value to denote the empty fields. These will be colored using 'COLOR_NAN' option set above. #9606 100 300 250 100 50 210 #15303 20 X 130 200 300 15