Mercurial > repos > bgruening > deeptools_plot_heatmap

annotate plotHeatmap.xml @ 27:a4dfb122e52b draft

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"planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 7c89456b6a986259c96b8d280c53e4ab155696ef"
author bgruening
date Sat, 25 Jan 2020 05:15:40 -0500
parents 751adcc1ce82
children 42cb23d80271
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1 <tool id="deeptools_plot_heatmap" name="plotHeatmap" version="@WRAPPER_VERSION@.1" profile="18.01">
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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 --plotType '$advancedOpt.plotType'
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46
1
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47 #if str($advancedOpt.missingDataColor.value) != "None":
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48 --missingDataColor '$advancedOpt.missingDataColor'
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49 #end if
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51 #set colorMap = []
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52 #for $cmap in $advancedOpt.colorMapRepeat:
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53 #silent $colorMap.append(str($cmap.colorMap))
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54 #end for
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55 #if len($colorMap) > 0:
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56 --colorMap #echo " ".join($colorMap)#
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57 #end if
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58
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59 --alpha '$advancedOpt.alpha'
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60 #if str($advancedOpt.colorList).strip() != "":
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61 --colorList $advancedOpt.colorList
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62 #end if
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64 #if str($advancedOpt.zMin).strip() != "":
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65 --zMin $advancedOpt.zMin
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66 #end if
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67 #if str($advancedOpt.zMax).strip() != "":
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68 --zMax $advancedOpt.zMax
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69 #end if
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71 #if str($advancedOpt.yMin).strip() != "":
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72 --yMin $advancedOpt.yMin
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73 #end if
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74 #if $advancedOpt.yMax:
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75 --yMax $advancedOpt.yMax
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76 #end if
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78 --xAxisLabel '$advancedOpt.xAxisLabel'
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79 --yAxisLabel '$advancedOpt.yAxisLabel'
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81 --heatmapWidth $advancedOpt.heatmapWidth
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82 --heatmapHeight $advancedOpt.heatmapHeight
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84 --whatToShow '$advancedOpt.whatToShow'
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86 --startLabel '$advancedOpt.startLabel'
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87 --endLabel '$advancedOpt.endLabel'
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89 --refPointLabel '$advancedOpt.referencePointLabel'
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91 #if $advancedOpt.samplesLabel and str($advancedOpt.samplesLabel).strip() != "":
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92 --samplesLabel $advancedOpt.samplesLabel
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93 #end if
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94
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95 #if $advancedOpt.regionsLabel and str($advancedOpt.regionsLabel).strip() != "":
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96 --regionsLabel $advancedOpt.regionsLabel
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97 #end if
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98
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99 #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
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100 --plotTitle '$advancedOpt.plotTitle'
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101 #end if
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102
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103 --legendLocation '$advancedOpt.legendLocation'
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104
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105 --labelRotation '$advancedOpt.labelRotation'
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106
1
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107 $advancedOpt.perGroup
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108
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109 @KMEANS_CLUSTERING@
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110
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111 #end if
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112 ]]>
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113 </command>
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114 <inputs>
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115 <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data"
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116 label="Matrix file from the computeMatrix tool" help=""/>
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117
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118 <expand macro="input_graphic_output_settings">
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119 <expand macro="input_image_file_format" />
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120 <expand macro="output_dpi" />
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121 <expand macro="input_save_matrix_values" />
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122 </expand>
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123
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124 <conditional name="advancedOpt" >
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125 <param name="showAdvancedOpt" type="select" label="Show advanced options" >
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126 <option value="no" selected="true">no</option>
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127 <option value="yes">yes</option>
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128 </param>
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129 <when value="no" />
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130 <when value="yes">
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131 <expand macro="sortRegions" />
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132 <expand macro="sortUsing" />
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133 <param argument="--averageTypeSummaryPlot" type="select"
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134 label="Type of statistic that should be plotted in the summary image above the heatmap"
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135 help="">
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136 <option value="mean" selected="true">mean</option>
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137 <option value="median">median</option>
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138 <option value="min">min</option>
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139 <option value="max">max</option>
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140 <option value="sum">sum</option>
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141 <option value="std">std</option>
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142 </param>
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143 <param argument="--plotType" type="select" label="Type of summary plot">
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144 <option value="lines">plot the profile line based on the statistic selected above.</option>
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145 <option value="fill">fills the region between zero and the profile.</option>
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146 <option value="se">color the region between the profile and the standard error.</option>
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147 <option value="std">color the region between the profile and the standard deviation.</option>
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148 </param>
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149 <param argument="--missingDataColor" type="text" value="black" optional="true" label="Missing data color"
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150 help="If 'Represent missing data as zero' is not set, such cases will be colored in black by default.
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151 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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152 Also color names can be used, see a list here: http://packages.python.org/ete2/reference/reference_svgcolors.html.
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153 Alternatively colors can be specified using the #rrggbb notation." />
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154
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155 <repeat name="colorMapRepeat" title="Colormap to use for each sample"
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156 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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157 <expand macro="colorMap" />
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158 </repeat>
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159 <param argument="--alpha" type="float" value="1.0" min="0.0"
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160 max="1.0" optional="True"
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161 label="Alpha channel (transparency)"
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162 help="The alpha channel (transparency) to use for the heatmaps. The default is 1.0 and values must
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163 be between 0 and 1. A value of 0.0 would be fully transparent." />
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164
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165 <param argument="--colorList" type="text" value="" size="50" optional="True"
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166 label="List of colors for each heatmap. Separate lists by spaces and the colors in the list by comas"
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167 help="The color of the heatmaps can be specified as a list of colors separated by comas with
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168 not space in between. For example: white,blue white,green will set a color map from white
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169 to blue for the first heatmap and for white to green for the next heatmap."/>
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170 <expand macro="zMin_zMax" />
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171 <param argument="--yMin" type="float" value="" size="3" optional="True"
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172 label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values" help=""/>
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173 <param argument="--yMax" type="float" value="" size="3" optional="True"
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174 label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values" help=""/>
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175 <param argument="--xAxisLabel" type="text" value="distance from TSS (bp)" size="200"
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176 label="The x-axis label" help="" />
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177 <param argument="--yAxisLabel" type="text" value="genes" size="30"
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178 label="The y-axis label for the top panel" help="" />
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179
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180 <param argument="--heatmapWidth" type="float" value="7.5" min="1" max="100"
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181 label="Heatmap width in cm" help="The minimum value is 1 and the maximum is 100."/>
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182 <param argument="--heatmapHeight" type="float" value="25" min="3" max="100"
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183 label="Heatmap height in cm" help="The minimum value is 3 and the maximum is 100."/>
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184
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185 <param argument="--whatToShow" type="select" label="What to show"
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186 help ="The default is to include a summary or profile plot on top of the heatmap and a heatmap colorbar.">
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187 <option value="plot, heatmap and colorbar" selected="true">summary plot, heatmap and colorbar</option>
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188 <option value="plot and heatmap">summary plot and heatmap (no colorbar)</option>
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189 <option value="heatmap and colorbar">heatmap and colorbar</option>
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190 </param>
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191
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192 <param argument="--startLabel" type="text" value="TSS" size="10"
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193 label="Label for the region start"
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194 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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195 <param argument="--endLabel" type="text" value="TES" size="10"
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196 label="Label for the region end"
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197 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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198
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199 <param argument="--referencePointLabel" type="text" value="TSS" size="10"
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200 label="Reference point label"
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201 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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202 <param argument="--samplesLabel" type="text" size="30"
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203 label="Labels for the samples (each bigwig) plotted"
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204 help="The default is to use the file name of the sample. The sample labels should be separated by
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205 spaces and quoted if a label itself contains a space E.g. label-1 &quot;label 2&quot;">
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206 <sanitizer>
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207 <valid initial="string.printable">
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208 </valid>
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209 </sanitizer>
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210 </param>
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211 <param argument="--regionsLabel" type="text" size="30"
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212 label="Labels for the regions plotted in the heatmap"
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213 help="If more than one region is being plotted a list of labels separated by space is required.
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214 If a label itself contains a space, then quotes are needed.
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215 For example, label_1 &quot;label 2&quot;" />
1
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216
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217 <expand macro="plotTitle" />
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218 <expand macro="legendLocation" />
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219 <expand macro="labelRotation" />
1
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220 <param argument="--perGroup" type="boolean" truevalue="--perGroup" falsevalue=""
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221 label="Make one plot per group of regions"
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222 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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223
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224 <expand macro="kmeans_clustering" />
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225 </when>
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226 </conditional>
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227 </inputs>
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228 <outputs>
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229 <expand macro="output_image_file_format" />
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230 <expand macro="output_graphic_outputs" />
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231 <expand macro="output_save_matrix_values" />
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232 </outputs>
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233 <tests>
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234 <test>
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235 <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
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236 <output name="outFileName" file="heatmapper_result1.png" ftype="png" compare="sim_size" delta="4000" />
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237 </test>
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238 <test>
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239 <param name="matrixFile" value="computeMatrix_result1.gz" ftype="deeptools_compute_matrix_archive" />
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240 <param name="showAdvancedOpt" value="yes" />
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241 <param name="whatToShow" value="heatmap and colorbar" />
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242 <output name="outFileName" file="heatmapper_result2.png" ftype="png" compare="sim_size" delta="4000" />
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243 </test>
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244 </tests>
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245 <help>
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246 <![CDATA[
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247
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248 What it does
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249 --------------
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250
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251 ``plotHeatmap`` visualizes scores associated with genomic regions, for example ChIP enrichment values around the TSS of genes.
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252 Like ``plotProfile``, it requires that computeMatrix was run first to calculate the values.
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253
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254 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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255 displayed in the heatmap as well as with the different coloring options.
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256
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257 **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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258
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259 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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260
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261 **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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262
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263 Output
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264 --------------
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265
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266 This is a heatmap based on two bigWig files generated with default settings and k-means clustering.
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267
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268 .. image:: $PATH_TO_IMAGES/plotHeatmap_example.png
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269 :width: 600
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270 :height: 694
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271
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272 .. image:: $PATH_TO_IMAGES/plotHeatmap_example02.png
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273 :width: 600
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274 :height: 694
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275
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276 In addition to the image, ``plotHeatmap`` can also generate the values underlying both the heatmap.
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277
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278 See the following table for the optional output options:
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279
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280 +-----------------------------------+--------------------+-----------------+-----------------+
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281 | **optional output type** | **computeMatrix** | **plotHeatmap** | **plotProfile** |
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282 +-----------------------------------+--------------------+-----------------+-----------------+
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283 | values underlying the heatmap | yes | yes | no |
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284 +-----------------------------------+--------------------+-----------------+-----------------+
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285 | values underlying the profile | no | no | yes |
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286 +-----------------------------------+--------------------+-----------------+-----------------+
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287 | sorted and/or filtered regions | yes | yes | yes |
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288 +-----------------------------------+--------------------+-----------------+-----------------+
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289
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290 **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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291
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292 -----
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293
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294 @REFERENCES@
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295 ]]>
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296 </help>
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297 <expand macro="citations" />
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298 </tool>