Mercurial > repos > bgruening > deeptools_plot_heatmap

annotate plotHeatmap.xml @ 1:6a247ae015cc draft

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planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit fef8b344925620444d93d8159c0b2731a5777920
author bgruening
date Mon, 15 Feb 2016 10:26:54 -0500
parents e1bb51933e7f
children ca218dae7902
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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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13
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14 #if $output.showOutputSettings == "yes"
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15 --plotFileFormat "$output.outFileFormat"
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16
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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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24 #else
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25 --plotFileFormat 'png'
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26 #end if
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28 #if $advancedOpt.showAdvancedOpt == "yes"
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29 #if $advancedOpt.sortRegions:
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30 --sortRegions '$advancedOpt.sortRegions'
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31 #end if
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32
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33 #if $advancedOpt.sortUsing:
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34 --sortUsing '$advancedOpt.sortUsing'
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35 #end if
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37 #if $advancedOpt.averageTypeSummaryPlot:
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38 --averageTypeSummaryPlot '$advancedOpt.averageTypeSummaryPlot'
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39 #end if
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41 #if str($advancedOpt.missingDataColor.value) != "None":
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42 --missingDataColor '$advancedOpt.missingDataColor'
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43 #end if
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45 --colorMap '$advancedOpt.colorMap'
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46
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47 #if str($advancedOpt.zMin).strip() != "":
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48 --zMin $advancedOpt.zMin
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49 #end if
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50 #if $advancedOpt.zMax:
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51 --zMax $advancedOpt.zMax
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52 #end if
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53
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54 #if str($advancedOpt.yMin).strip() != "":
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55 --yMin $advancedOpt.yMin
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56 #end if
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57 #if $advancedOpt.yMax:
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58 --yMax $advancedOpt.yMax
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59 #end if
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61 --xAxisLabel '$advancedOpt.xAxisLabel'
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62 --yAxisLabel '$advancedOpt.yAxisLabel'
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64 --heatmapWidth $advancedOpt.heatmapWidth
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65 --heatmapHeight $advancedOpt.heatmapHeight
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66
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67 --whatToShow '$advancedOpt.whatToShow'
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68
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69 --startLabel '$advancedOpt.startLabel'
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70 --endLabel '$advancedOpt.endLabel'
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71
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72 --refPointLabel '$advancedOpt.referencePointLabel'
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73
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74 #if $advancedOpt.samplesLabel and str($advancedOpt.samplesLabel).strip() != "":
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75 --samplesLabel $advancedOpt.samplesLabel
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76 #end if
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78 #if $advancedOpt.regionsLabel and str($advancedOpt.regionsLabel).strip() != "":
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79 --regionsLabel $advancedOpt.regionsLabel
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80 #end if
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81
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82 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
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83 --plotTitle '$advancedOpt.plotTitle'
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84 #end if
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85
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86 $advancedOpt.perGroup
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87
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88 @KMEANS_CLUSTERING@
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89
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90 #end if
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91 ]]>
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92 </command>
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93 <inputs>
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94 <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data" label="Matrix file from the computeMatrix tool" help=""/>
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95
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96 <expand macro="input_graphic_output_settings">
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97 <expand macro="input_image_file_format" />
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98 <expand macro="input_save_matrix_values" />
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99 </expand>
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100
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101 <conditional name="advancedOpt" >
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102 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
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103 <option value="no" selected="true">no</option>
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104 <option value="yes">yes</option>
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105 </param>
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106 <when value="no" />
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107 <when value="yes">
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108 <expand macro="sortRegions" />
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109 <expand macro="sortUsing" />
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110 <param argument="--averageTypeSummaryPlot" type="select"
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111 label="Type of statistic that should be plotted in the summary image above the heatmap"
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112 help="">
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113 <option value="mean" selected="true">mean</option>
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114 <option value="median">median</option>
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115 <option value="min">min</option>
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116 <option value="max">max</option>
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117 <option value="sum">sum</option>
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118 <option value="std">std</option>
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119 </param>
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120
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121 <param argument="--missingDataColor" type="text" value="black" optional="true" label="Missing data color"
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122 help="If 'Represent missing data as zero' is not set, such cases will be colored in black by default.
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123 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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124 Also color names can be used, see a list here: http://packages.python.org/ete2/reference/reference_svgcolors.html.
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125 Alternatively colors can be specified using the #rrggbb notation." />
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126
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127 <expand macro="colorMap" />
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128
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129 <param argument="--zMin" type="float" value="" size="3" optional="True"
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130 label="Minimum value for the heatmap intensities. Leave empty for automatic values" help=""/>
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131 <param argument="--zMax" type="float" value="" size="3" optional="True"
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132 label="Maximum value for the heatmap intensities. Leave empty for automatic values" help=""/>
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133 <param argument="--yMin" type="float" value="" size="3" optional="True"
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134 label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values" help=""/>
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135 <param argument="--yMax" type="float" value="" size="3" optional="True"
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136 label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values" help=""/>
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137 <param argument="--xAxisLabel" type="text" value="distance from TSS (bp)" size="200"
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138 label="The x-axis label" help="" />
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139 <param argument="--yAxisLabel" type="text" value="genes" size="30"
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140 label="The y-axis label for the top panel" help="" />
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141
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142 <param argument="--heatmapWidth" type="float" value="7.5" min="1" max="100"
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143 label="Heatmap width in cm" help="The minimum value is 1 and the maximum is 100."/>
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144 <param argument="--heatmapHeight" type="float" value="25" min="3" max="100"
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145 label="Heatmap height in cm" help="The minimum value is 3 and the maximum is 100."/>
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146
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147 <param argument="--whatToShow" type="select" label="What to show"
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148 help ="The default is to include a summary or profile plot on top of the heatmap and a heatmap colorbar.">
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149 <option value="plot, heatmap and colorbar" selected="true">summary plot, heatmap and colorbar</option>
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150 <option value="plot and heatmap">summary plot and heatmap (no colorbar)</option>
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151 <option value="heatmap and colorbar">heatmap and colorbar</option>
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152 </param>
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153
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154 <param argument="--startLabel" type="text" value="TSS" size="10"
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155 label="Label for the region start"
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156 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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157 <param argument="--endLabel" type="text" value="TES" size="10"
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158 label="Label for the region end"
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159 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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160
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161 <param argument="--referencePointLabel" type="text" value="TSS" size="10"
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162 label="Reference point label"
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163 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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164 <param argument="--samplesLabel" type="text" size="30"
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165 label="Labels for the samples (each bigwig) plotted"
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166 help="The default is to use the file name of the sample. The sample labels should be separated by
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167 spaces and quoted if a label itself contains a space E.g. label-1 &quot;label 2&quot;">
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168 <sanitizer>
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169 <valid initial="string.printable">
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170 </valid>
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171 </sanitizer>
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172 </param>
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173 <param argument="--regionsLabel" type="text" size="30"
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174 label="Labels for the regions plotted in the heatmap"
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175 help="If more than one region is being plotted a list of labels separated by space is required.
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176 If a label itself contains a space, then quotes are needed.
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177 For example, label_1, &quot;label 2&quot;" />
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178
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179 <expand macro="plotTitle" />
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180 <param argument="--perGroup" type="boolean" truevalue="--perGroup" falsevalue=""
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181 label="Make one plot per group of regions"
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182 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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183
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184 <expand macro="kmeans_clustering" />
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185 </when>
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186 </conditional>
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187 </inputs>
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188 <outputs>
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189 <expand macro="output_image_file_format" />
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190 <expand macro="output_graphic_outputs" />
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191 <expand macro="output_save_matrix_values" />
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192 </outputs>
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193 <tests>
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194 <test>
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195 <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
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196 <output name="outFileName" file="heatmapper_result1.png" ftype="png" compare="sim_size" delta="4000" />
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197 </test>
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198 <test>
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199 <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
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200 <param name="showAdvancedOpt" value="yes" />
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201 <param name="whatToShow" value="heatmap and colorbar" />
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202 <output name="outFileName" file="heatmapper_result2.png" ftype="png" compare="sim_size" delta="4000" />
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203 </test>
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204 </tests>
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205 <help>
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206 <![CDATA[
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207
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208 What it does
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209 --------------
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210
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211 ``plotHeatmap`` visualizes scores associated with genomic regions, for example ChIP enrichment values around the TSS of genes.
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212 Like ``plotProfile``, it requires that computeMatrix was run first to calculate the values.
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213
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214 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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215 displayed in the heatmap as well as with the different coloring options.
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216
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217 **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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218
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219 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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220
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221 **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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222
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223 Output
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224 --------------
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225
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226 This is a heatmap based on two bigWig files generated with default settings and k-means clustering.
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227
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228 .. image:: $PATH_TO_IMAGES/plotHeatmap_example.png
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229 :width: 600
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230 :height: 694
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231
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232 .. image:: $PATH_TO_IMAGES/plotHeatmap_example02.png
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233 :width: 600
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234 :height: 694
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235
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236 In addition to the image, ``plotHeatmap`` can also generate the values underlying both the heatmap.
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237
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238 See the following table for the optional output options:
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239
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240 +-----------------------------------+--------------------+-----------------+-----------------+
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241 | **optional output type** | **computeMatrix** | **plotHeatmap** | **plotProfile** |
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242 +-----------------------------------+--------------------+-----------------+-----------------+
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243 | values underlying the heatmap | yes | yes | no |
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244 +-----------------------------------+--------------------+-----------------+-----------------+
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245 | values underlying the profile | no | no | yes |
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246 +-----------------------------------+--------------------+-----------------+-----------------+
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247 | sorted and/or filtered regions | yes | yes | yes |
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248 +-----------------------------------+--------------------+-----------------+-----------------+
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249
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250 **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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251
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252 -----
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253
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254 @REFERENCES@
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255 ]]>
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256 </help>
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257 <expand macro="citations" />
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258 </tool>