######################################## # # # startup.config # # # ######################################## # # This protocol-script will be run automatically when MotifLab is started in # GUI mode # # It can be used to provide defaults for various display settings, # such as default color-palettes for certain region types. # Note, however, that display settings are also saved together with a session, # so if you load a session, the settings specified in that session will # replace the ones listed here. # # The configuration script can also be used to preload data objects, # for instance motif collections that you use all the time. # Be aware, however, that data which relies on the presence of other data # should not be preloaded # (for instance feature data that require a set of sequences to be specified), # since this can lead to MotifLab not being able to execute the protocol # successfully and will thus not be able to start correctly. # # You can edit the startup protocol for MotifLab by selecting "Options..." # from the "Configure" menu and then press the "Edit GUI Startup Script" button # under the "Other" tab. # Example: If you uncomment the next line (remove # in front), # the JASPAR Core motifs will be automatically loaded on startup. #Jaspar_Core = new Motif Collection(Collection:Jaspar Core) # The following lines describe the color-scheme used for the # "ENCODE ChromatinState Segmentation by HMM" [wgEncodeBroadHmm] track described in the paper # # Ernst J, et al. (2011) "Mapping and analysis of chromatin state dynamics in nine human cell types", Nature, 473(7345):43-49 # # The light gray color #D0D0D0 used here for 13,14,15 is a little bit darker # than the light gray at #F5F5F5 used by UCSC Genome Browser # $regionColor(1 Active Promoter)=#FF0000 $regionColor(2 Weak Promoter)=#FF6969 $regionColor(3 Poised Promoter)=#CF0BC6 $regionColor(4 Strong Enhancer)=#FACA00 $regionColor(5 Strong Enhancer)=#FACA00 $regionColor(6 Weak Enhancer)=#FFFC04 $regionColor(7 Weak Enhancer)=#FFFC04 $regionColor(8 Insulator)=#0ABEFE $regionColor(9 Txn Transition)=#00B050 $regionColor(10 Txn Elongation)=#00B050 $regionColor(11 Weak Txn)=#99FF66 $regionColor(12 Repressed)=#7F7F7F $regionColor(13 Heterochrom/lo)=#D0D0D0 $regionColor(14 Repetitive/CNV)=#D0D0D0 $regionColor(15 Repetitive/CNV)=#D0D0D0 $regionColor(1_Active_Promoter)=#FF0000 $regionColor(2_Weak_Promoter)=#FF6969 $regionColor(3_Poised_Promoter)=#CF0BC6 $regionColor(4_Strong_Enhancer)=#FACA00 $regionColor(5_Strong_Enhancer)=#FACA00 $regionColor(6_Weak_Enhancer)=#FFFC04 $regionColor(7_Weak_Enhancer)=#FFFC04 $regionColor(8_Insulator)=#0ABEFE $regionColor(9_Txn_Transition)=#00B050 $regionColor(10_Txn_Elongation)=#00B050 $regionColor(11_Weak_Txn)=#99FF66 $regionColor(12_Repressed)=#7F7F7F $regionColor(13_Heterochrom/lo)=#D0D0D0 $regionColor(14_Repetitive/CNV)=#D0D0D0 $regionColor(15_Repetitive/CNV)=#D0D0D0 $regionColor(Tss)=#FF0000 $regionColor(TssF)=#FF0000 $regionColor(PromF)=#FF6969 $regionColor(PromP)=#CF0BC6 $regionColor(Enh)=#FACA00 $regionColor(EnhF)=#FACA00 $regionColor(EnhWF)=#FFFC04 $regionColor(EnhW)=#FFFC04 $regionColor(DNaseU)=#FFFC04 $regionColor(DNaseD)=#FFFC04 $regionColor(FaireW)=#FFFC04 $regionColor(CtrcfO)=#0ABEFE $regionColor(Ctcf)=#0ABEFE $regionColor(Gen5')=#00B050 $regionColor(Elon)=#00B050 $regionColor(ElonW)=#00B050 $regionColor(Gen3')=#00B050 $regionColor(Pol2)=#00B050 $regionColor(H4K20)=#00B050 $regionColor(Low)=#99FF66 $regionColor(ReprD)=#7F7F7F $regionColor(Repr)=#7F7F7F $regionColor(ReprW)=#7F7F7F $regionColor(Quies)=#D0D0D0 $regionColor(Art)=#D0D0D0 # Draw "ChromatinState" tracks in multi-color mode (as long as default names are used) !multicolor(ChromatinState_Gm12878,ChromatinState_H1,ChromatinState_HepG2,ChromatinState_HMEC,ChromatinState_HSMM,ChromatinState_HUVEC,ChromatinState_K562,ChromatinState_NHLF,ChromatinState_NHEK)=TRUE # Draw "RepeatMasker" tracks in multi-color mode also !multicolor(RepeatMasker,RepeatMasker327)=TRUE # Clustal color scheme for amino acid regions !regioncolor(A)=#80a0f0 !regioncolor(R)=#f01505 !regioncolor(N)=#00ff00 !regioncolor(D)=#c048c0 !regioncolor(C)=#f08080 !regioncolor(Q)=#00ff00 !regioncolor(E)=#c048c0 !regioncolor(G)=#f09048 !regioncolor(H)=#15a4a4 !regioncolor(I)=#80a0f0 !regioncolor(L)=#80a0f0 !regioncolor(K)=#f01505 !regioncolor(M)=#80a0f0 !regioncolor(F)=#80a0f0 !regioncolor(P)=#ffff00 !regioncolor(S)=#00ff00 !regioncolor(T)=#00ff00 !regioncolor(W)=#80a0f0 !regioncolor(Y)=#15a4a4 !regioncolor(V)=#80a0f0 !regioncolor(Stop)=#000000 # Some default settings for drawing barcharts (used by e.g. "Benchmark" analysis). # The following three settings affect the widths of the bars and the distances between them. # Note that "bardistance" is the distance from the start of one bar to the start of the next (not the spacing between), # so if "bardistance" is set to a value smaller than the "barwidth" the bars will overlap $setting(barchart.barwidth)=8 $setting(barchart.bardistance)=12 $setting(barchart.bargroupspacing)=28 # Draw bars using flat fill or gradient fill (so they look like tubes). # Recognized values are "ON/YES/TRUE" or "OFF/NO/FALSE" $setting(barchart.gradientfill)=OFF # Draw borders around the bars. # The values "OFF","FALSE" or "NONE" turns off borders. # If the value is the name or code for a color (e.g. "BLACK", "255,0,0" or # "#FF8800") borders will be drawn in that color. # Any other value will result in a border which is the same color as the bar # itself but drawn slightly darker $setting(barchart.border)=DARKER # Offset for drop-shadow (0 is no shadow) $setting(barchart.shadow)=2 # Draw a black box around the whole barchart, and draw grid-lines in X and Y direction # Recognized values are "ON/YES/TRUE" or "OFF/NO/FALSE" $setting(barchart.box)=OFF $setting(barchart.gridX)=ON $setting(barchart.gridY)=ON # Colors for benchmark statistics $setting("systemColor.Sensitivity")=RED $setting("systemColor.Specificity")=GREEN $setting("systemColor.Positive Predictive Value")=BLUE $setting("systemColor.Negative Predictive Value")=YELLOW $setting("systemColor.Performance Coefficient")=MAGENTA $setting("systemColor.Average Site Performance")=CYAN $setting("systemColor.F-measure")=ORANGE $setting("systemColor.Accuracy")=LIGHT_GRAY $setting("systemColor.Correlation Coefficient")=BLACK $setting("systemColor.Sensitivity (site)")=255,140,140 $setting("systemColor.Positive Predictive Value (site)")=96,173,255 $setting("systemColor.Average Site Performance (site)")=0,150,150 $setting("systemColor.Performance Coefficient (site)")=153,51,255 $setting("systemColor.F-measure (site)")=180,90,30 # Standard system colors palette (used e.g. when drawing graphs) $setting("systemColor.color1")=RED $setting("systemColor.color2")=BLUE $setting("systemColor.color3")=GREEN $setting("systemColor.color4")=MAGENTA $setting("systemColor.color5")=CYAN $setting("systemColor.color6")=YELLOW # Colors used for small inline histograms in tables $setting("systemColor.histogram")=100,100,255 $setting("systemColor.histogramSelected")=200,200,255 # Additional settings for drawing graphs $setting("graph.tickFont")=Dialog $setting("graph.tickFontSize")=12 $setting("graph.legendFont")=Dialog $setting("graph.legendFontSize")=12 $setting("graph.labelFont")=Dialog $setting("graph.labelFontSize")=12 $setting("graph.labelFontStyle")=bold $setting("graph.titleFont")=Dialog $setting("graph.titleFontSize")=14 $setting("graph.titleFontStyle")=bold # 'graph.dotStyle' is the glyph used to plot data points in e.g. regression graphs. The available styles are: 0=circle, 1=filled circle, 2=box, 3=filled box, 4=x, 5=+, 6=*, 7=. $setting("graph.dotStyle")=0 $setting("graph.dotSize")=2 # Settings for drawing motif and module images $setting("motif.border")=ON $setting("motif.height")=19 $setting("motif.imageFormat")=gif $setting("module.border")=ON $setting("module.height")=28 $setting("module.imageFormat")=png # Default TAB-spacing used in Output panels (changes to this setting only applies to new Output panels not existing ones) $setting(systemSetting.tab)=8