Mercurial > repos > bgruening > deeptools_plot_heatmap

annotate plotHeatmap.xml @ 36:1de3ede909ef draft

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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 5a01e3a370130f32a82d5436504371ed95be1754
author bgruening
date Thu, 05 Apr 2018 10:46:29 -0400
parents 6d5a88e9c5ae
children 7d1521817494
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1 <tool id="deeptools_plot_heatmap" name="plotHeatmap" version="@WRAPPER_VERSION@.0">
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2 <description>creates a heatmap for score distributions across genomic regions</description>
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3 <macros>
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4 <token name="@BINARY@">plotHeatmap</token>
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5 <import>deepTools_macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <command>
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9 <![CDATA[
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10 @BINARY@
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11 --matrixFile '$matrixFile'
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12 --outFileName '$outFileName'
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14 #if $output.showOutputSettings == "yes"
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15 --plotFileFormat '$output.outFileFormat'
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17 #if $outFileNameMatrix:
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18 --outFileNameMatrix '$outFileNameMatrix'
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19 #end if
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21 #if $outFileSortedRegions:
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22 --outFileSortedRegions '$outFileSortedRegions'
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23 #end if
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25 #if $output.dpi:
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26 --dpi '$output.dpi'
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27 #end if
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28 #else
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29 --plotFileFormat 'png'
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30 #end if
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32 #if $advancedOpt.showAdvancedOpt == "yes"
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33 #if $advancedOpt.sortRegions:
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34 --sortRegions '$advancedOpt.sortRegions'
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35 #end if
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37 #if $advancedOpt.sortUsing:
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38 --sortUsing '$advancedOpt.sortUsing'
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39 #end if
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41 #if $advancedOpt.averageTypeSummaryPlot:
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42 --averageTypeSummaryPlot '$advancedOpt.averageTypeSummaryPlot'
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43 #end if
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45 #if str($advancedOpt.missingDataColor.value) != "None":
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46 --missingDataColor '$advancedOpt.missingDataColor'
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47 #end if
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48
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49 #set colorMap = []
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50 #for $cmap in $advancedOpt.colorMapRepeat:
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51 #silent $colorMap.append(str($cmap.colorMap))
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52 #end for
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53 #if len($colorMap) > 0:
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54 --colorMap #echo " ".join($colorMap)#
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55 #end if
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56
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57 --alpha '$advancedOpt.alpha'
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58 #if str($advancedOpt.colorList).strip() != "":
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59 --colorList $advancedOpt.colorList
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60 #end if
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62 #if str($advancedOpt.zMin).strip() != "":
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63 --zMin $advancedOpt.zMin
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64 #end if
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65 #if str($advancedOpt.zMax).strip() != "":
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66 --zMax $advancedOpt.zMax
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67 #end if
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69 #if str($advancedOpt.yMin).strip() != "":
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70 --yMin $advancedOpt.yMin
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71 #end if
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72 #if $advancedOpt.yMax:
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73 --yMax $advancedOpt.yMax
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74 #end if
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76 --xAxisLabel '$advancedOpt.xAxisLabel'
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77 --yAxisLabel '$advancedOpt.yAxisLabel'
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79 --heatmapWidth $advancedOpt.heatmapWidth
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80 --heatmapHeight $advancedOpt.heatmapHeight
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82 --whatToShow '$advancedOpt.whatToShow'
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84 --startLabel '$advancedOpt.startLabel'
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85 --endLabel '$advancedOpt.endLabel'
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87 --refPointLabel '$advancedOpt.referencePointLabel'
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89 #if $advancedOpt.samplesLabel and str($advancedOpt.samplesLabel).strip() != "":
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90 --samplesLabel $advancedOpt.samplesLabel
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91 #end if
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92
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93 #if $advancedOpt.regionsLabel and str($advancedOpt.regionsLabel).strip() != "":
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94 --regionsLabel $advancedOpt.regionsLabel
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95 #end if
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96
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97 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
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98 --plotTitle '$advancedOpt.plotTitle'
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99 #end if
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100
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101 --labelRotation '$advancedOpt.labelRotation'
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102
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103 $advancedOpt.perGroup
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104
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105 @KMEANS_CLUSTERING@
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106
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107 #end if
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108 ]]>
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109 </command>
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110 <inputs>
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111 <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data"
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112 label="Matrix file from the computeMatrix tool" help=""/>
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113
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114 <expand macro="input_graphic_output_settings">
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115 <expand macro="input_image_file_format" />
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116 <expand macro="output_dpi" />
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117 <expand macro="input_save_matrix_values" />
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118 </expand>
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119
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120 <conditional name="advancedOpt" >
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121 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
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122 <option value="no" selected="true">no</option>
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123 <option value="yes">yes</option>
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124 </param>
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125 <when value="no" />
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126 <when value="yes">
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127 <expand macro="sortRegions" />
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128 <expand macro="sortUsing" />
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129 <param argument="--averageTypeSummaryPlot" type="select"
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130 label="Type of statistic that should be plotted in the summary image above the heatmap"
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131 help="">
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132 <option value="mean" selected="true">mean</option>
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133 <option value="median">median</option>
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134 <option value="min">min</option>
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135 <option value="max">max</option>
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136 <option value="sum">sum</option>
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137 <option value="std">std</option>
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138 </param>
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139
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140 <param argument="--missingDataColor" type="text" value="black" optional="true" label="Missing data color"
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141 help="If 'Represent missing data as zero' is not set, such cases will be colored in black by default.
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142 By using this parameter a different color can be set. A value between 0 and 1 will be used for a gray scale (black is 0).
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143 Also color names can be used, see a list here: http://packages.python.org/ete2/reference/reference_svgcolors.html.
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144 Alternatively colors can be specified using the #rrggbb notation." />
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145
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146 <repeat name="colorMapRepeat" title="Colormap to use for each sample"
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147 help="A different colormap can be applied to each column of the heatmap. If you select fewer colormaps than you have samples in your matrix, then the select colormap(s) will be repeated (e.g., if you select one colormap then it will be applied to all samples).">
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148 <expand macro="colorMap" />
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149 </repeat>
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150 <param argument="--alpha" type="float" value="1.0" min="0.0"
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151 max="1.0" optional="True"
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152 label="Alpha channel (transparency)"
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153 help="The alpha channel (transparency) to use for the heatmaps. The default is 1.0 and values must
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154 be between 0 and 1. A value of 0.0 would be fully transparent." />
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155
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156 <param argument="--colorList" type="text" value="" size="50" optional="True"
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157 label="List of colors for each heatmap. Separate lists by spaces and the colors in the list by comas"
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158 help="The color of the heatmaps can be specified as a list of colors separated by comas with
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159 not space in between. For example: white,blue white,green will set a color map from white
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160 to blue for the first heatmap and for white to green for the next heatmap."/>
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161 <expand macro="zMin_zMax" />
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162 <param argument="--yMin" type="float" value="" size="3" optional="True"
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163 label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values" help=""/>
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164 <param argument="--yMax" type="float" value="" size="3" optional="True"
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165 label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values" help=""/>
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166 <param argument="--xAxisLabel" type="text" value="distance from TSS (bp)" size="200"
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167 label="The x-axis label" help="" />
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168 <param argument="--yAxisLabel" type="text" value="genes" size="30"
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169 label="The y-axis label for the top panel" help="" />
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170
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171 <param argument="--heatmapWidth" type="float" value="7.5" min="1" max="100"
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172 label="Heatmap width in cm" help="The minimum value is 1 and the maximum is 100."/>
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173 <param argument="--heatmapHeight" type="float" value="25" min="3" max="100"
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174 label="Heatmap height in cm" help="The minimum value is 3 and the maximum is 100."/>
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175
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176 <param argument="--whatToShow" type="select" label="What to show"
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177 help ="The default is to include a summary or profile plot on top of the heatmap and a heatmap colorbar.">
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178 <option value="plot, heatmap and colorbar" selected="true">summary plot, heatmap and colorbar</option>
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179 <option value="plot and heatmap">summary plot and heatmap (no colorbar)</option>
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180 <option value="heatmap and colorbar">heatmap and colorbar</option>
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181 </param>
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182
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183 <param argument="--startLabel" type="text" value="TSS" size="10"
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184 label="Label for the region start"
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185 help ="Only for scale-regions mode. Label shown in the plot for the start of the region. Default is TSS (transcription start site), but could be changed to anything, e.g. &quot;peak start&quot;." />
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186 <param argument="--endLabel" type="text" value="TES" size="10"
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187 label="Label for the region end"
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188 help="Only for scale-regions mode. Label shown in the plot for the region end. Default is TES (transcription end site)."/>
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189
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190 <param argument="--referencePointLabel" type="text" value="TSS" size="10"
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191 label="Reference point label"
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192 help ="Label shown in the plot for the reference-point. Default is the same as the reference point selected (e.g. TSS), but could be anything, e.g. &quot;peak start&quot; etc." />
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193 <param argument="--samplesLabel" type="text" size="30"
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194 label="Labels for the samples (each bigwig) plotted"
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195 help="The default is to use the file name of the sample. The sample labels should be separated by
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196 spaces and quoted if a label itself contains a space E.g. label-1 &quot;label 2&quot;">
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197 <sanitizer>
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198 <valid initial="string.printable">
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199 </valid>
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200 </sanitizer>
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201 </param>
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202 <param argument="--regionsLabel" type="text" size="30"
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203 label="Labels for the regions plotted in the heatmap"
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204 help="If more than one region is being plotted a list of labels separated by space is required.
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205 If a label itself contains a space, then quotes are needed.
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206 For example, label_1 &quot;label 2&quot;" />
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207
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208 <expand macro="plotTitle" />
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209 <expand macro="labelRotation" />
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210 <param argument="--perGroup" type="boolean" truevalue="--perGroup" falsevalue=""
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211 label="Make one plot per group of regions"
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212 help="The default is to make one plot per bigWig file, i.e., all samples next to each other. Choosing this option will make one plot per group of regions."/>
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213
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214 <expand macro="kmeans_clustering" />
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215 </when>
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216 </conditional>
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217 </inputs>
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218 <outputs>
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219 <expand macro="output_image_file_format" />
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220 <expand macro="output_graphic_outputs" />
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221 <expand macro="output_save_matrix_values" />
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222 </outputs>
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223 <tests>
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224 <test>
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225 <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
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226 <output name="outFileName" file="heatmapper_result1.png" ftype="png" compare="sim_size" delta="4000" />
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227 </test>
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228 <test>
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229 <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
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230 <param name="showAdvancedOpt" value="yes" />
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231 <param name="whatToShow" value="heatmap and colorbar" />
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232 <output name="outFileName" file="heatmapper_result2.png" ftype="png" compare="sim_size" delta="4000" />
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233 </test>
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234 </tests>
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235 <help>
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236 <![CDATA[
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237
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238 What it does
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239 --------------
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240
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241 ``plotHeatmap`` visualizes scores associated with genomic regions, for example ChIP enrichment values around the TSS of genes.
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242 Like ``plotProfile``, it requires that computeMatrix was run first to calculate the values.
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243
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244 We have implemented a number of optional parameters to optimize the visual output and we encourage you to play around with the min/max values
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245 displayed in the heatmap as well as with the different coloring options.
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246
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247 **TIP:** *If your data is rather sparse and the resulting heatmap is too black, change the "Missing data color" to white (via "Advanced options").*
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248
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249 The most powerful option is probably the **k-means/hierarchical clustering** where you can sort your regions into groups of regions with similar score distributions.
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250
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251 **NOTE:** *The clustering will only work if you supplied a single BED file to computeMatrix. plotHeatmap cannot cluster regions within pre-defined groups. Moreover, k-means will be much faster than hierarchical clustering.*
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252
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253 Output
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254 --------------
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255
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256 This is a heatmap based on two bigWig files generated with default settings and k-means clustering.
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257
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258 .. image:: $PATH_TO_IMAGES/plotHeatmap_example.png
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259 :width: 600
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260 :height: 694
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261
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262 .. image:: $PATH_TO_IMAGES/plotHeatmap_example02.png
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263 :width: 600
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264 :height: 694
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265
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266 In addition to the image, ``plotHeatmap`` can also generate the values underlying both the heatmap.
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267
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268 See the following table for the optional output options:
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269
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270 +-----------------------------------+--------------------+-----------------+-----------------+
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271 | **optional output type** | **computeMatrix** | **plotHeatmap** | **plotProfile** |
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272 +-----------------------------------+--------------------+-----------------+-----------------+
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273 | values underlying the heatmap | yes | yes | no |
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274 +-----------------------------------+--------------------+-----------------+-----------------+
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275 | values underlying the profile | no | no | yes |
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276 +-----------------------------------+--------------------+-----------------+-----------------+
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277 | sorted and/or filtered regions | yes | yes | yes |
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278 +-----------------------------------+--------------------+-----------------+-----------------+
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279
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280 **More examples** can be found in our `Gallery <http://deeptools.readthedocs.org/en/latest/content/example_gallery.html#normalized-chip-seq-signals-and-peak-regions>`_.
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281
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282 -----
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283
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284 @REFERENCES@
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285 ]]>
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286 </help>
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287 <expand macro="citations" />
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288 </tool>