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1 <?xml version="1.0" ?>
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2 <tool id="qiime_gneiss_dendrogram-heatmap" name="qiime gneiss dendrogram-heatmap" version="2018.4">
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3 <description> - Dendrogram heatmap.</description>
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4 <requirements>
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5 <requirement type="package" version="2018.4">qiime2</requirement>
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6 </requirements>
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7 <command>
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8 <![CDATA[
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9 qiime gneiss dendrogram-heatmap --i-table=$itable
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10 #def list_dict_to_string(list_dict):
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11 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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12 #for d in list_dict[1:]:
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13 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
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14 #end for
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15 #return $file_list
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16 #end def
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17 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) --m-metadata-column="$mmetadatacolumn" --i-tree=$itree
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18 #if str($cmdconfig) != 'None':
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19 --cmd-config=$cmdconfig
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20 #end if
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21
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22 #if $pndim:
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23 --p-ndim=$pndim
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24 #end if
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25
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26 #if str($pcolormap) != 'None':
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27 --p-color-map=$pcolormap
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28 #end if
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29 --o-visualization=ovisualization
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30 #if str($pmethod) != 'None':
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31 --p-method=$pmethod
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32 #end if
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33 ;
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34 qiime tools export ovisualization.qzv --output-dir out && mkdir -p '$ovisualization.files_path'
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35 && cp -r out/* '$ovisualization.files_path'
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36 && mv '$ovisualization.files_path/index.html' '$ovisualization'
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37 ]]>
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38 </command>
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39 <inputs>
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40 <param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Composition] The feature table that will be plotted as a heatmap. This table is assumed to have strictly positive values. [required]" name="itable" optional="False" type="data"/>
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41 <param format="qza,no_unzip.zip" label="--i-tree: Hierarchy A hierarchy of feature identifiers where each tipcorresponds to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree. [required]" name="itree" optional="False" type="data"/>
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42
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43 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
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44 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
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45 </repeat>
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46 <param label="--m-metadata-column: MetadataColumn[Categorical] Column from metadata file or artifact viewable as metadata. Categorical metadata column to group the samples. [required]" name="mmetadatacolumn" optional="False" type="text"/>
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47
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48 <param label="--p-ndim: Number of dimensions to highlight. [default: 10]" name="pndim" optional="True" type="integer" value="10"/>
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49
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50 <param label="--p-method: Specifies how the data should be normalized
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51 for display.Options include 'log' or 'clr'
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52 (default='clr'). [default: clr]" name="pmethod" optional="True" type="select">
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53 <option selected="True" value="None">Selection is Optional</option>
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54 <option value="log">log</option>
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55 <option value="clr">clr</option>
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56 </param>
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57
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58 <param label="--p-color-map: Specifies the color map for plotting the
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59 heatmap. See https://matplotlib.org/examples
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60 /color/colormaps_reference.html for more
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61 details. [default: viridis]" name="pcolormap" optional="True" type="select">
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62 <option selected="True" value="None">Selection is Optional</option>
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63 <option value="gist_heat">gist_heat</option>
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64 <option value="plasma">plasma</option>
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65 <option value="PiYG">PiYG</option>
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66 <option value="Pastel2">Pastel2</option>
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67 <option value="nipy_spectral">nipy_spectral</option>
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68 <option value="inferno">inferno</option>
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69 <option value="YlGn">YlGn</option>
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70 <option value="bone">bone</option>
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71 <option value="YlGnBu">YlGnBu</option>
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72 <option value="hsv">hsv</option>
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73 <option value="summer">summer</option>
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74 <option value="Set1">Set1</option>
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75 <option value="BrBG">BrBG</option>
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76 <option value="magma">magma</option>
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77 <option value="Paired">Paired</option>
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78 <option value="Vega10">Vega10</option>
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79 <option value="brg">brg</option>
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80 <option value="PuBu">PuBu</option>
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81 <option value="Spectral">Spectral</option>
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82 <option value="YlOrBr">YlOrBr</option>
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83 <option value="GnBu">GnBu</option>
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84 <option value="PuOr">PuOr</option>
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85 <option value="ocean">ocean</option>
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86 <option value="Reds">Reds</option>
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87 <option value="prism">prism</option>
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88 <option value="Vega20">Vega20</option>
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89 <option value="PuRd">PuRd</option>
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90 <option value="seismic">seismic</option>
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91 <option value="Dark2">Dark2</option>
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92 <option value="RdBu">RdBu</option>
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93 <option value="Accent">Accent</option>
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94 <option value="Set2">Set2</option>
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95 <option value="terrain">terrain</option>
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96 <option value="coolwarm">coolwarm</option>
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97 <option value="gnuplot">gnuplot</option>
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98 <option value="CMRmap">CMRmap</option>
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99 <option value="gnuplot2">gnuplot2</option>
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100 <option value="gist_ncar">gist_ncar</option>
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101 <option value="flag">flag</option>
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102 <option value="OrRd">OrRd</option>
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103 <option value="RdYlGn">RdYlGn</option>
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104 <option value="rainbow">rainbow</option>
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105 <option value="gist_rainbow">gist_rainbow</option>
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106 <option value="RdGy">RdGy</option>
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107 <option value="Pastel1">Pastel1</option>
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108 <option value="gist_earth">gist_earth</option>
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109 <option value="Set3">Set3</option>
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110 <option value="BuPu">BuPu</option>
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111 <option value="PRGn">PRGn</option>
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112 <option value="pink">pink</option>
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113 <option value="Purples">Purples</option>
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114 <option value="PuBuGn">PuBuGn</option>
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115 <option value="Vega20c">Vega20c</option>
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116 <option value="winter">winter</option>
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117 <option value="bwr">bwr</option>
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118 <option value="Vega20b">Vega20b</option>
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119 <option value="hot">hot</option>
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120 <option value="afmhot">afmhot</option>
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121 <option value="viridis">viridis</option>
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122 <option value="RdPu">RdPu</option>
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123 <option value="spring">spring</option>
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124 <option value="RdYlBu">RdYlBu</option>
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125 <option value="Greens">Greens</option>
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126 <option value="autumn">autumn</option>
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127 <option value="cubehelix">cubehelix</option>
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128 <option value="cool">cool</option>
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129 <option value="Blues">Blues</option>
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130 <option value="BuGn">BuGn</option>
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131 <option value="Greys">Greys</option>
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132 <option value="YlOrRd">YlOrRd</option>
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133 <option value="Oranges">Oranges</option>
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134 <option value="gray">gray</option>
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135 <option value="jet">jet</option>
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136 <option value="gist_stern">gist_stern</option>
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137 <option value="copper">copper</option>
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138 </param>
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139
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140 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
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141 </inputs>
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142 <outputs>
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143 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
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144 </outputs>
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145 <help><![CDATA[
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146 Dendrogram heatmap.
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147 --------------------
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148
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149 Visualize the feature table as a heatmap, with samples sorted along a
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150 specified categorical metadata column and features clustered together
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151 specified by the tree.
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152
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153 Parameters
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154 ----------
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155 table : FeatureTable[Composition]
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156 The feature table that will be plotted as a heatmap. This table is
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157 assumed to have strictly positive values.
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158 tree : Hierarchy
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159 A hierarchy of feature identifiers where each tipcorresponds to the
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160 feature identifiers in the table. This tree can contain tip ids that
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161 are not present in the table, but all feature ids in the table must be
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162 present in this tree.
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163 metadata : MetadataColumn[Categorical]
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164 Categorical metadata column to group the samples.
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165 ndim : Int, optional
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166 Number of dimensions to highlight.
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167 method : Str % Choices({'clr', 'log'}), optional
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168 Specifies how the data should be normalized for display.Options include
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169 'log' or 'clr' (default='clr').
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170 color_map : Str % Choices({'Accent', 'Blues', 'BrBG', 'BuGn', 'BuPu', 'CMRmap', 'Dark2', 'GnBu', 'Greens', 'Greys', 'OrRd', 'Oranges', 'PRGn', 'Paired', 'Pastel1', 'Pastel2', 'PiYG', 'PuBu', 'PuBuGn', 'PuOr', 'PuRd', 'Purples', 'RdBu', 'RdGy', 'RdPu', 'RdYlBu', 'RdYlGn', 'Reds', 'Set1', 'Set2', 'Set3', 'Spectral', 'Vega10', 'Vega20', 'Vega20b', 'Vega20c', 'YlGn', 'YlGnBu', 'YlOrBr', 'YlOrRd', 'afmhot', 'autumn', 'bone', 'brg', 'bwr', 'cool', 'coolwarm', 'copper', 'cubehelix', 'flag', 'gist_earth', 'gist_heat', 'gist_ncar', 'gist_rainbow', 'gist_stern', 'gnuplot', 'gnuplot2', 'gray', 'hot', 'hsv', 'inferno', 'jet', 'magma', 'nipy_spectral', 'ocean', 'pink', 'plasma', 'prism', 'rainbow', 'seismic', 'spring', 'summer', 'terrain', 'viridis', 'winter'}), optional
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171 Specifies the color map for plotting the heatmap. See
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172 https://matplotlib.org/examples/color/colormaps_reference.html for more
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173 details.
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174
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175 Returns
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176 -------
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177 visualization : Visualization
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178 \
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179 ]]>
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180 </help>
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181 </tool>
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