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1 library('getopt')
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2 library('ape')
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3 suppressPackageStartupMessages(library('phyloseq'))
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4 library(biomformat)
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5 library(plyr)
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6 Sys.setenv("DISPLAY"=":1")
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7 library("ggplot2")
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8 suppressPackageStartupMessages(library("doParallel"))
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9 ncores = ceiling(detectCores() * 0.8)
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10 registerDoParallel(cores=ncores)
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11
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12 options(warn=-1)
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13
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14 theme_set(theme_bw())
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15
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16 #http://saml.rilspace.com/creating-a-galaxy-tool-for-r-scripts-that-output-images-and-pdfs
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17 #http://joey711.github.io/phyloseq-demo/phyloseq-demo.html
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18 option_specification = matrix(c(
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19 'otu_table','o',2,'character',
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20 'tax_table','t',2,'character',
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21 'meta_table','m',2,'character',
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22 'biom','b',2,'character',
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23 'subset','s',2,'character',
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24 'method','n',2,'character',
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25 'distance','d',2,'character',
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26 'kingdom','k',2,'character',
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27 'plottype','e',2,'numeric',
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28 'category','g',2,'numeric',
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29 'outdir','r',2,'character',
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30 'htmlfile','h',2,'character'
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31 ),byrow=TRUE,ncol=4);
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32
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33
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34 options <- getopt(option_specification);
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35 options(bitmapType="cairo")
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36
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37 if (!is.null(options$outdir)) {
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38 # Create the directory
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39 dir.create(options$outdir,FALSE)
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40 }
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41
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42
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43
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44 method<-options$method
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45 ### select a kingdom for phyloseq plot (e.g., "phylum")
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46 #kingdom_str<-colnames(tax_table)[options$kingdom]
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47 kingdom_str<-options$kingdom
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48 distance<-options$distance
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49 plottype<-options$plottype
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50
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51 ### prepare the directory and file name
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52 pdffile <- gsub("[ ]+", "", paste(options$outdir,"/pdffile.pdf"))
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53 pngfile_nmds <- gsub("[ ]+", "", paste(options$outdir,"/nmds.png"))
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54 pngfile_nmds_facet <- gsub("[ ]+", "", paste(options$outdir,"/nmds_facet.png"))
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55 htmlfile <- gsub("[ ]+", "", paste(options$htmlfile))
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56
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57
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58 ### This function accepts different two different type of BIOM file format
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59 readBIOM<-function(inBiom){
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60 tryCatch({
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61 phyloseq_obj<-import_biom(inBiom,parallel=TRUE)
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62 return(phyloseq_obj)
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63 },
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64 error=function(e){
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65 biom_obj<-read_biom(inBiom)
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66
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67 otu_matrix = as(biom_data(biom_obj), "matrix")
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68 OTU_TABLE = otu_table(otu_matrix, taxa_are_rows=TRUE)
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69
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70 taxonomy_matrix = as.matrix(observation_metadata(biom_obj), rownames.force=TRUE)
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71 TAXONOMY_TABLE = tax_table(taxonomy_matrix)
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72
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73 metadata.temp<-sample_metadata(biom_obj)
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74 METADATA_TABLE<-plyr::ldply(metadata.temp, rbind)
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75 rownames(METADATA_TABLE)<-as.character(METADATA_TABLE$.id)
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76
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77 phyloseq_obj = phyloseq(OTU_TABLE, TAXONOMY_TABLE,sample_data(METADATA_TABLE))
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78 return(phyloseq_obj)
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79 }
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80 )
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81 }
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82
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83
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84 create_OTU_PDF<-function(pdf_file,phyloseq_obj,phyloseq_ord,kingdom_str,htmlfile,pngfile_nmds,pngfile_nmds_facet){
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85 pdf(pdf_file);
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86 p1<-plot_ordination(phyloseq_obj,phyloseq_ord,type="taxa",color="Phylum",title="taxa")
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87 print(p1)
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88 p2<-plot_ordination(phyloseq_obj,phyloseq_ord,type="taxa",color="Phylum",title="taxa") + facet_wrap(formula(paste('~',kingdom_str)),3)
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89 print(p2)
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90 garbage<-dev.off();
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91
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92 #png('nmds.png')
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93 bitmap(pngfile_nmds,"png16m")
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94 p3<-plot_ordination(phyloseq_obj,phyloseq_ord,type="taxa",color="Phylum",title="taxa")
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95 print(p3)
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96 garbage<-dev.off()
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97
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98 #png('nmds_facet.png')
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99 bitmap(pngfile_nmds_facet,"png16m")
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100 p4<-plot_ordination(phyloseq_obj,phyloseq_ord,type="taxa",color="Phylum",title="taxa") + facet_wrap(formula(paste('~',kingdom_str)),3)
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101 print(p4)
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102 garbage<-dev.off()
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103
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104 create_HTML_1(htmlfile)
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105 }
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106
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107 create_SAMPLE_PDF<-function(pdf_file,phyloseq_obj,phyloseq_ord,htmlfile,pngfile_nmds,category_type){
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108 pdf(pdf_file);
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109 p <- plot_ordination(phyloseq_obj, phyloseq_ord, type="samples", color=category_type)
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110 p <- p + geom_point(aes(fill=category_type)) + geom_point(size=5) + ggtitle("samples")
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111 print(p)
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112 garbage<-dev.off();
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113
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114 #png('nmds.png')
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115 bitmap(pngfile_nmds,"png16m")
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116 p1 <- plot_ordination(phyloseq_obj, phyloseq_ord, type="samples", color=category_type)
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117 p1 <- p1 + geom_point(aes(fill=category_type)) + geom_point(size=5) + ggtitle("samples")
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118 print(p1)
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119 garbage<-dev.off();
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120
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121 create_HTML_2(htmlfile)
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122 }
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123
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124 create_BIPLOT_PDF<-function(pdf_file,phyloseq_obj,phyloseq_ord,kingdom_str,htmlfile,pngfile_nmds,category_type){
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125 pdf(pdf_file);
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126 print(category_type)
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127 p_biplot <- plot_ordination(phyloseq_obj, phyloseq_ord, type="biplot", color=category_type, shape=kingdom_str,title="BIPLOT")
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128 print(p_biplot)
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129 garbage<-dev.off();
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130
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131 bitmap(pngfile_nmds,"png16m")
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132 p_biplot_png <- plot_ordination(phyloseq_obj, phyloseq_ord, type="biplot", color=category_type, shape=kingdom_str,title="BIPLOT")
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133 print(p_biplot_png)
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134 garbage<-dev.off();
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135
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136 create_HTML_2(htmlfile)
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137 }
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138
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139 create_SPLITPLOT_PDF<-function(pdf_file,phyloseq_obj,phyloseq_ord,kingdom_str,htmlfile,pngfile_nmds,category_type){
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140 pdf(pdf_file,width=10, height=6);
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141 split_plot <- plot_ordination(phyloseq_obj, phyloseq_ord, type="split", color=kingdom_str, shape=kingdom_str, label=category_type, title="SPLIT PLOT")
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142 split_plot <- split_plot + theme(plot.margin = unit(c(12,18,12,18),"pt"))
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143 print(split_plot)
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144 garbage<-dev.off();
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145
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146 bitmap(pngfile_nmds,"png16m", width=6, height=4, units="in",res=200)
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147 split_plot <- plot_ordination(phyloseq_obj, phyloseq_ord, type="split", color=kingdom_str, shape=kingdom_str, label=category_type, title="SPLIT PLOT")
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148 split_plot <- split_plot + theme(plot.margin = unit(c(12,18,12,18),"pt"))
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149 print(split_plot)
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150 garbage<-dev.off();
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151 create_HTML_2(htmlfile)
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152 }
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153
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154 create_HTML_1<-function(htmlfile){
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155 htmlfile_handle <- file(htmlfile)
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156 html_output = c('<html><body>',
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157 '<table align="center>',
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158 '<tr>',
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159 '<td valign="middle" style="vertical-align:middle;">',
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160 '<a href="pdffile.pdf"><img src="nmds.png"/></a>',
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161 '</td>',
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162 '</tr>',
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163 '<tr>',
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164 '<td valign="middle" style="vertical-align:middle;">',
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165 '<a href="pdffile.pdf"><img src="nmds_facet.png"/></a>',
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166 '</td>',
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167 '</tr>',
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168 '</table>',
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169 '</html></body>');
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170 writeLines(html_output, htmlfile_handle);
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171 close(htmlfile_handle);
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172 }
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173
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174 create_HTML_2<-function(htmlfile){
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175 htmlfile_handle <- file(htmlfile)
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176 html_output = c('<html><body>',
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177 '<table align="center>',
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178 '<tr>',
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179 '<td valign="middle" style="vertical-align:middle;">',
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180 '<a href="pdffile.pdf"><img src="nmds.png"/></a>',
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181 '</td>',
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182 '</tr>',
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183 '</table>',
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184 '</html></body>');
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185 writeLines(html_output, htmlfile_handle);
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186 close(htmlfile_handle);
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187 }
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188
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189 if(!is.null(options$biom)){
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190
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191 #physeq<-import_biom(options$biom)
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192 physeq<-readBIOM(options$biom)
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193
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194 if(length(rank_names(physeq)) == 8){
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195 tax_table(physeq) <- tax_table(physeq)[,-1]
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196 colnames(tax_table(physeq)) <- c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species")
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197 } else {
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198 colnames(tax_table(physeq)) <- c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species")
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199 }
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200
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201 ### select column name from sample table for nmds plot
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202 ## which(colnames(sample_data(biom)) == "vegetation_type_id")
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203 #category_type<-colnames(sample_data(physeq))[options$subset]
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204 category_type <- options$subset
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205
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206 ### obtain the unique value in the selected column from sample table
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207 category_option<-unique(sample_data(physeq))[,options$subset]
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208
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209 }else{
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210
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211 ### read the data into correct data type to create phyloseq object
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212 otu_table<-as.matrix(read.table(options$otu_table,header=T,sep="\t"))
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213 tax_table<-as.matrix(read.table(options$tax_table,header=T,sep="\t"))
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214 sample_table<-read.table(options$meta_table,header=T,sep="\t",stringsAsFactors=F)
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215
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216
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217 ### select column name from sample table for nmds plot
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218 category_type<-colnames(sample_table)[options$category]
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219
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220 ### obtain the unique value in the selected column from sample table
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221 category_option<-unique(sample_table[,options$category])
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222
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223
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224 ### create a sample object for phyloseq
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225 sample_object<-sample_data(sample_table)
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226
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227 ### create otu object for phyloseq
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228 OTU<-otu_table(otu_table, taxa_are_rows = TRUE)
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229
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230 ### create tax object for phyloseq
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231 TAX<-tax_table(tax_table)
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232
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233 ### create a phyloseq object
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234 physeq = phyloseq(OTU,TAX,sample_object)
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235 }
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236 # sample_data(physeq_filter)$category_input <- factor(category_input)
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237 category_input = get_variable(physeq, category_type) %in% category_option
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238 sample_data(physeq)$category_input <- factor(category_input)
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239
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240 # physeq_ord<-ordinate(physeq_filter,method,distance)
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241 physeq_ord<-ordinate(physeq,method,distance)
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242
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243 if(plottype == 1){
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244 #kingdom_str = colnames(tax_table)[2]
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245 create_OTU_PDF(pdffile,physeq,physeq_ord,kingdom_str,htmlfile,pngfile_nmds,pngfile_nmds_facet)
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246 }else if(plottype == 2){
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247 create_SAMPLE_PDF(pdffile,physeq,physeq_ord,htmlfile,pngfile_nmds,category_type)
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248 }else if(plottype == 3){
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249 create_BIPLOT_PDF(pdffile,physeq,physeq_ord,kingdom_str,htmlfile,pngfile_nmds,category_type)
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250 }else{
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251 create_SPLITPLOT_PDF(pdffile,physeq,physeq_ord,kingdom_str,htmlfile,pngfile_nmds,category_type)
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252 }
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253
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