GUIplottingControls

Panel	Name	Type	Function.for.profile.plot	Function.for.heatmap	Description.Docs	Default.value
Title and axis	Title	text	Main title (topmost)	Main title (topmost), common for heatmaps	The main title of the plot, shown in top-center part of the figure; default empty	empty
Title and axis	X-axis label	text	Label below x-axis	Label below x-axis, repeated for each heatmap	Label shown below horizontal axis; default empty	empty
Title and axis	Y-axis label	text	Label left to y-axis, vertical text	Label left to y-axis, vertical text, repeated for each heatmap	Label shown below vertical axis; default empty	empty
Title and axis	Title font size	slider [1-48]	Main title font size	Main title font size	Font size of the title in points (point = ~1/72 an inch for standard A4 output); default 20 points	20pt
Title and axis	Labels font size	slider [1-48]	Labels below x-axis and y-axis font size	Labels below x-axis and y-axis font size	Font size of axis labels in points; default 16 points	16pt
Title and axis	Axis font size	slider [1-48]	x-axis and y-axis numbers font size	x-axis and y-axis numbers font size	Controls axis ticks font size, that is size of the numbers indicating position in base pairs on X-axis and means signal value on X-axis; default 14 points	14pt
Title and axis	Set X-axis limits	checkbox, numeric x2	Limits x-axis, e.g. plot only +/-1kb from original 10kb selection	Limits x-axis, e.g. plot 0nly +/-1kb rom original 10kb selection, apply to all	Set hard plotting limits for X-axis; default values are whole range chosen during plot set calculation	F, auto
Title and axis	Set Y-axis limits	checkbox, numeric x2	Limits y-axis, e.g. limit signal from 1 to 10	NO FUNCTION, possibly limiting genes/clusters	Set hard plotting limits for Y-axis; default values are a range between lowest and highest mean signal extended by error estimate	F, auto
Guide lines and data scaling	Transform signal	dropdown	Transform all signal with binary logarithm	Transform all signal with binary logarithm	if set to Log2 transform performs log2 transformation of the signal prior to plotting; default setting is Do not transform	Do not transform
Guide lines and data scaling	Show vertical guide line	checkbox	Show vertical line at 0 and end of anchored range for AF	Show vertical line at 0 and end of anchored range for AF, apply to all	show the vertical line at point 0 - beginning of the feature or midpoint and end of the pseudo-length scaled features (only for anchored plots); turn on by default	T
Guide lines and data scaling	Show horizontal guide line	checkbox, numeric	Shows horizontal guide line, users decides where	NO FUNCTION, possibly controlling cluster indicates and labels	show the horizontal line at user determined height; turn off by default	F,0
Guide lines and data scaling	Show error estimates	checkbox	Show SE and 95%CI as fields	NO FUNCTION	show error standard error and 95% confidence interval as fields, if turned off only the line representing the mean signal is shown; turn on by default	F
Keys, labels and colours panel	Colors	checkbox	Reveals color selection in grid, affects singe profiles	Reveals color selection in grid, affects singe heatmaps	checkboxes revealing a color picker on plot set grid. This input allows to control the colors of specific feature-track pair average plots or sub-heatmaps. In browser supporting the color picker 'e.g. Chrome' the system dialog will show up. In other browsers (e.g. Firefox) the JavaScript color picker will be initialized	F
Keys, labels and colors panel	Label	checkbox	Reveals label selection in grid, labels go into key/legend	Reveals label selection in grid, labels go above heatmaps, below main title	checkboxes revealing a label text input plot set grid. This controls the names shown on the key with average plots or the heatmap top labels.	F
Keys, labels and colors panel	Priority/Order	checkbox	Reveals priority selection in grid, affects order in key/legend (top to bottom)	Reveals priority selection in grid, affects order of heatmaps (left to right)	checkboxes revealing numeric input on plot set grid. These number determine the order of average plots and heatmaps. Feature-track pair with the highest priority will be listed on the top of key for average plots and left-most for heatmaps.	F
Keys, labels and colors panel	Show plot key	checkbox	Controls visibility and position of main key/legend	NO FUNCTION, possibly controls visibility of color key	shows the key giving the color to feature-track pair label mapping. If turned on the additional drop-down allows to choose the position on the plot, top-right by default	T,topright
Keys, labels and colors panel	Show error estimate key	checkbox	Controls visibility and position of error estimate key/legend	NO FUNCTION	shows the key explaining the meaning of error fields. If turned-on the additional drop-down allows to choose the position on the plot, top-left by default	F,topleft
Keys, labels and colors panel	Legend font size	slider [1-48]	Controls font size for keys/legends	NO FUNCTION, possibly controls font size of color key	set the size of font used to plot the keys; 12 default	12pt
Heatmap setup	Sort heatmap rows by mean signal	dropdown	NO FUNCTION	Sort heatmap rows by mean signal in increasing or decreasing order	sorts the heatmap rows based on the mean value of each row across all sub-heatmaps. Can be set to increasing or decreasing order. Turned off by default.	do not sort
Heatmap setup	Clustering algorithm	dropdown, numeric	NO FUNCTION	Select clustering algorithm and set up number of clusters	choose clustering algorithm (k-means, hierarchical or Suppressor). If clustering is not desired, choose do not cluster, which uses the feature file in the uploaded order . K-means by default.	K-means,5
Heatmap setup	Make cluster calculation repeatable	checkbox	NO FUNCTION	Make clustering with non-deterministic algorithms repeatable	enforces, that clustering with non deterministic algorithms, like k means or Suppressor will generate the same results as most recently plotted heatmap. This is achieved by re using R random number generator seed.	F
Heatmap setup	Plot cluster only selected	dropdown	NO FUNCTION	Zoom selected cluster to whole plot height	this option is available only if Make cluster calculation repeatable is turned on. Allows to select one of the clusters zoom it to whole plot height. Plot all clusters by default.	All clusters
Heatmap setup	Choose individual heatmaps for sorting/clustering	checkbox	NO FUNCTION	Reveals include/exclude in clustering/sorting selection UI in grid	this option determines if each sub-heatmap should have a separate color key (plotted below the heatmap) or a single, common key should be calculated for all sub-plots (plotted rightmost). By default all sub-heatmap have their own color keys. The example below show the difference between separate (left) and common (right) color keys:	F
Heatmap setup	Heatmaps have individual color keys	checkbox	NO FUNCTION	If selected each heatmap have a separate colour key	this option determines if each sub-heatmap should have a separate color key (plotted below the heatmap) or a single, common key should be calculated for all sub-plots (plotted rightmost). By default all sub-heatmap have their own color keys. The example below show the difference between separate (left) and common (right) color keys:	T
Heatmap setup	Set default color key limits	checkbox	NO FUNCTION	If selected color key limits are selected by user	this option determines the limits in mapping the numerical values to the colors. The range of colors generated is dependent on these options. Values lower or higher than the given limits will be plotted in the limit value color. If this checkbox is not selected, limits are auto-generated using Color key scaling parameter. If this option it turned off two numerical fields, min and max, are shown to manually set the limits.	F
Heatmap setup	Color key scaling	slider [0-0.1]	NO FUNCTION	Coefficient for auto-calculating key limits, hidden if above is unchecked	this slider influences how color key limits are generated. For example, 0.01 (default value) calculates limits using data ranging from 1-99 percentile of available data points. 0.1 uses data ranging from 10-90 percentile. The general formula for limit is: [quantile(data, Color key scaling); quantile(data, 1-Color key scaling)]	0.01
Heatmap setup	min and max color key values	numeric	NO FUNCTION	Set color key limits, visible if "Color key scaling" is selected	enter values to manually specify color key limits as numeric values.	[-1,10]
Heatmap setup	Set individual color key limits	checkbox	NO FUNCTION	Reveals individual min/max color key controls in grid	this option is similar to manual set up of color key limits, but this allows one to specify different values for individual sub-heatmaps. When this checkbox is selected min and max numeric input menu is shown on the plot set grid	F
Heatmap setup	Set default colorspace	checkbox	NO FUNCTION	Allows to change the default heatmap color mapping	When this option is selected three color pickers are shown to set up custom color mappings for heatmaps. The following example below shows standard jet colors (left), default blue color mapping after selecting the checkbox (middle) and custom color selection (right):	F
Heatmap setup	min/mid/max color pickers	color	NO FUNCTION	Creates a color key palette by mapping 3 colours for min, medium and max values	[see above]	[while,lightblue,navyblue]