6 Appendix

Some tables and graphs for the supplementary material.

load(file='metadag_work_space.RData')

Table MBB sizes

write_delim=write_delim(table_MBB_size,
                        file="data_appendix/table_MBB_size.csv",
                        delim=",")

clust4_MSA2=tibble(mDAG_Id=names(clust4_MSA),
                      clust4_MSA=as.integer(clust4_MSA))
clust4_Mun2=tibble(mDAG_Id=names(clust4_Mun),
                      clust4_Mun=as.integer(clust4_Mun))

clust4_MSA_Eukaryotes_taxo= meta_taxo %>% filter(!is.na(Kingdom))%>%
  select(-c(Freq_Kingdom,Freq_Phylum,Freq_Class)) %>%
  left_join(clust4_MSA2,by="mDAG_Id")
  
clust4_Mun_Eukaryotes_taxo= meta_taxo %>% filter(!is.na(Kingdom))%>%
  select(-c(Freq_Kingdom,Freq_Phylum,Freq_Class)) %>%
  left_join(clust4_Mun2,by="mDAG_Id")
  



write_delim(clust4_MSA_Eukaryotes_taxo,
                        file="data_appendix/clust4_MSA_Eukaryotes_taxo.csv",
                        delim=",")
write_delim(clust4_Mun_Eukaryotes_taxo,
                        file="data_appendix/clust4_Mun_Eukaryotes_taxo.csv",
                        delim=",")

Heatmaps by Kingdom MSA y Mun: Animals, Fungi, Plants ans Protists.

Animals

##  Animals by phylum
meta_animals= meta_taxo %>% filter(Kingdom=="Animals")
namesP=names(rev(sort(table(meta_animals$Phylum))))
namesP

 [1] "Vertebrates"      "Arthropods"       "Mollusks"         "Cnidarians"      
 [5] "Nematodes"        "Flatworms"        "Echinoderms"      "Tunicates"       
 [9] "Cephalochordates" "Poriferans"       "Placozoans"       "Hemichordates"   
[13] "Brachiopodas"     "Annelids"

dff=data.frame(Phylum=meta_animals$Phylum)
Phylum=ordered(meta_animals$Phylum,levels=namesP)
numbersP=paste(c(paste0(0,1:9),10:14),namesP,sep="-")
levels(Phylum)=numbersP
dff$Phylum=Phylum
col=rainbow(length(namesP))

colorsP=list(Phylum=col)
names(colorsP$Phylum)=numbersP

annot <- HeatmapAnnotation(df = dff, 
                               col = colorsP,
                               annotation_name_side = "left",
                               show_annotation_name=TRUE )

MSA_heat_2 <-  Heatmap(
  matrix = Sim_MSA_mDAG[meta_animals$mDAG_Id,
                        meta_animals$mDAG_Id],
  name = "MSA similarity",
  column_title = "m-DAGs MSA-similarity  Animals by Phyla",
  col = rev(viridis(256)),
  cluster_rows = FALSE,
  show_heatmap_legend = FALSE,
  cluster_columns = FALSE,
  top_annotation = annot,
  show_column_names = FALSE,
  show_row_names = FALSE,
  left_annotation =
    rowAnnotation(
      df = dff,
      col = colorsP,
      show_annotation_name = FALSE
    )
)




Mun_heat_2 <- Heatmap(
  matrix = Sim_Mun_mDAG[meta_animals$mDAG_Id,
                        meta_animals$mDAG_Id],
  column_title = "m-DAGs Munkres-similarity  Animals by Phyla",
 col = rev(viridis(256)),
  cluster_rows = FALSE,
  show_heatmap_legend = FALSE,
  cluster_columns = FALSE,
  top_annotation = annot,
  show_column_names = FALSE,
  show_row_names = FALSE,
  left_annotation =
    rowAnnotation(
      df = dff,
      col = colorsP,
      show_annotation_name = FALSE
    )
)

Save graphics

png 
  2

png 
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Plants

meta_plants= meta_taxo[1:884,] %>% filter(Kingdom=="Plants")
namesP=names(rev(sort(table(meta_plants$Phylum))))
namesP

[1] "Eudicots" "Monocots" "Green"    "Red"      "Basal"    "Mosses"   "Ferns"

dff=data.frame(Phylum=meta_plants$Phylum)
Phylum=ordered(meta_plants$Phylum,levels=namesP)
numbersP=paste(c(paste0(0,1:7)),namesP,sep="-")
levels(Phylum)=numbersP
dff$Phylum=Phylum
col=rainbow(length(namesP))

colorsP=list(Phylum=col)
names(colorsP$Phylum)=numbersP

annot <- HeatmapAnnotation(df = dff, 
                               col = colorsP,
                               annotation_name_side = "left",
                               show_annotation_name=TRUE )

MSA_heat_2 <-  Heatmap(
  matrix = Sim_MSA_mDAG[meta_plants$mDAG_Id,
                        meta_plants$mDAG_Id],
  name = "MSA similarity",
  column_title = "m-DAGs MSA-similarity  Plants by Phyla",
  col = rev(viridis(256)),
  cluster_rows = FALSE,
  show_heatmap_legend = FALSE,
  cluster_columns = FALSE,
  top_annotation = annot,
  show_column_names = FALSE,
  show_row_names = FALSE,
  left_annotation =
    rowAnnotation(
      df = dff,
      col = colorsP,
      show_annotation_name = FALSE
    )
)

Mun_heat_2 <- Heatmap(
  matrix = Sim_Mun_mDAG[meta_plants$mDAG_Id,
                        meta_plants$mDAG_Id],
    name = "Mun similarity",
  column_title = "m-DAGs Munkres-similarity  Plants by Phyla",
col = rev(viridis(256)),
  cluster_rows = FALSE,
  show_heatmap_legend = FALSE,
  cluster_columns = FALSE,
  top_annotation = annot,
  show_column_names = FALSE,
  show_row_names = FALSE,
  left_annotation =
    rowAnnotation(
      df = dff,
      col = colorsP,
      show_annotation_name = FALSE
    )
)

Save graphics

png 
  2

png 
  2

Fungi

meta_fungi= meta_taxo%>% filter(Kingdom=="Fungi")
namesP=names(rev(sort(table(meta_fungi$Phylum))))
namesP

[1] "Ascomycetes"     "Basidiomycetes"  "Microsporidians"

dff=data.frame(Phylum=meta_fungi$Phylum)
Phylum=ordered(meta_fungi$Phylum,levels=namesP)
n=length(namesP)

numbersP=paste(c(paste0(0,1:n)),namesP,sep="-")
levels(Phylum)=numbersP
dff$Phylum=Phylum
col=rainbow(length(namesP))

colorsP=list(Phylum=col)
names(colorsP$Phylum)=numbersP

annot <- HeatmapAnnotation(df = dff, 
                               col = colorsP,
                               annotation_name_side = "left",
                               show_annotation_name=TRUE )

MSA_heat_2 <-  Heatmap(
  matrix = Sim_MSA_mDAG[meta_fungi$mDAG_Id,
                        meta_fungi$mDAG_Id],
  name = "MSA similarity",
  column_title = "m-DAGs MSA-similarity  Fungi by Phyla",
  col = rev(viridis(256)),
  cluster_rows = FALSE,
  show_heatmap_legend = FALSE,
  cluster_columns = FALSE,
  top_annotation = annot,
  show_column_names = FALSE,
  show_row_names = FALSE,
  left_annotation =
    rowAnnotation(
      df = dff,
      col = colorsP,
      show_annotation_name = FALSE
    )
)

Mun_heat_2 <- Heatmap(
  matrix = Sim_Mun_mDAG[meta_fungi$mDAG_Id,
                        meta_fungi$mDAG_Id],
    name = "Mun similarity",
  column_title = "m-DAGs Munkres-similarity  Fungi by Phyla",
col = rev(viridis(256)),
  cluster_rows = FALSE,
  show_heatmap_legend = FALSE,
  cluster_columns = FALSE,
  top_annotation = annot,
  show_column_names = FALSE,
  show_row_names = FALSE,
  left_annotation =
    rowAnnotation(
      df = dff,
      col = colorsP,
      show_annotation_name = FALSE
    )
)

Save graphics

png 
  2

png 
  2

Protists

meta_protists= meta_taxo %>% filter(Kingdom=="Protists")

namesP=names(rev(sort(table(meta_protists$Phylum))))
namesP

[1] "Alveolates"        "Euglenozoa"        "Stramenopiles"    
[4] "Amoebozoa"         "Metamonada"        "Choanoflagellates"
[7] "Heterolobosea"     "Haptophyta"        "Cryptomonads"

dff=data.frame(Phylum=meta_protists$Phylum)
Phylum=ordered(meta_protists$Phylum,levels=namesP)
n=length(namesP)
numbersP=paste(c(paste0(0,1:n)),namesP,sep="-")
levels(Phylum)=numbersP
dff$Phylum=Phylum
col=rainbow(length(namesP))

colorsP=list(Phylum=col)
names(colorsP$Phylum)=numbersP

annot <- HeatmapAnnotation(df = dff, 
                               col = colorsP,
                               annotation_name_side = "left",
                               show_annotation_name=TRUE )

MSA_heat_2 <-  Heatmap(
  matrix = Sim_MSA_mDAG[meta_protists$mDAG_Id,
                        meta_protists$mDAG_Id],
  name = "MSA similarity",
  column_title = "m-DAGs MSA-similarity  Protist by Phyla",
  col = rev(viridis(256)),
  cluster_rows = FALSE,
  show_heatmap_legend = FALSE,
  cluster_columns = FALSE,
  top_annotation = annot,
  show_column_names = FALSE,
  show_row_names = FALSE,
  left_annotation =
    rowAnnotation(
      df = dff,
      col = colorsP,
      show_annotation_name = FALSE
    )
)

Mun_heat_2 <- Heatmap(
  matrix = Sim_Mun_mDAG[meta_protists$mDAG_Id,
                        meta_protists$mDAG_Id],
    name = "Mun similarity",
  column_title = "m-DAGs Munkres-similarity  Protist by Phyla",
col = rev(viridis(256)),
  cluster_rows = FALSE,
  show_heatmap_legend = FALSE,
  cluster_columns = FALSE,
  top_annotation = annot,
  show_column_names = FALSE,
  show_row_names = FALSE,
  left_annotation =
    rowAnnotation(
      df = dff,
      col = colorsP,
      show_annotation_name = FALSE
    )
)

Save graphics

draw(MSA_heat_2,merge_legend=TRUE)

draw(Mun_heat_2,merge_legend=TRUE)

## Appendix Some tables and graphs for the supplementary material. ```{r include=FALSE,message=FALSE} knitr::opts_chunk$set(echo = TRUE, cache=FALSE, warning = FALSE, message = FALSE, out.width = "100%",cache.lazy=FALSE) pdf="TRUE" library(tidyverse) library(igraph) library(ComplexHeatmap) library(viridis) library(circlize) library(plotly) library(randomcoloR) library(factoextra) library(RColorBrewer) library(kableExtra) library(igraph) library(GGally) ``` ```{r} load(file='metadag_work_space.RData') ``` Table MBB sizes ```{r} write_delim=write_delim(table_MBB_size, file="data_appendix/table_MBB_size.csv", delim=",") ``` ```{r} clust4_MSA2=tibble(mDAG_Id=names(clust4_MSA), clust4_MSA=as.integer(clust4_MSA)) clust4_Mun2=tibble(mDAG_Id=names(clust4_Mun), clust4_Mun=as.integer(clust4_Mun)) clust4_MSA_Eukaryotes_taxo= meta_taxo %>% filter(!is.na(Kingdom))%>% select(-c(Freq_Kingdom,Freq_Phylum,Freq_Class)) %>% left_join(clust4_MSA2,by="mDAG_Id") clust4_Mun_Eukaryotes_taxo= meta_taxo %>% filter(!is.na(Kingdom))%>% select(-c(Freq_Kingdom,Freq_Phylum,Freq_Class)) %>% left_join(clust4_Mun2,by="mDAG_Id") write_delim(clust4_MSA_Eukaryotes_taxo, file="data_appendix/clust4_MSA_Eukaryotes_taxo.csv", delim=",") write_delim(clust4_Mun_Eukaryotes_taxo, file="data_appendix/clust4_Mun_Eukaryotes_taxo.csv", delim=",") ``` Heatmaps by Kingdom MSA y Mun: Animals, Fungi, Plants ans Protists. **Animals** ```{r, fig.align='center', fig.height=5, cache=TRUE} ## Animals by phylum meta_animals= meta_taxo %>% filter(Kingdom=="Animals") namesP=names(rev(sort(table(meta_animals$Phylum)))) namesP dff=data.frame(Phylum=meta_animals$Phylum) Phylum=ordered(meta_animals$Phylum,levels=namesP) numbersP=paste(c(paste0(0,1:9),10:14),namesP,sep="-") levels(Phylum)=numbersP dff$Phylum=Phylum col=rainbow(length(namesP)) colorsP=list(Phylum=col) names(colorsP$Phylum)=numbersP annot <- HeatmapAnnotation(df = dff, col = colorsP, annotation_name_side = "left", show_annotation_name=TRUE ) MSA_heat_2 <- Heatmap( matrix = Sim_MSA_mDAG[meta_animals$mDAG_Id, meta_animals$mDAG_Id], name = "MSA similarity", column_title = "m-DAGs MSA-similarity Animals by Phyla", col = rev(viridis(256)), cluster_rows = FALSE, show_heatmap_legend = FALSE, cluster_columns = FALSE, top_annotation = annot, show_column_names = FALSE, show_row_names = FALSE, left_annotation = rowAnnotation( df = dff, col = colorsP, show_annotation_name = FALSE ) ) Mun_heat_2 <- Heatmap( matrix = Sim_Mun_mDAG[meta_animals$mDAG_Id, meta_animals$mDAG_Id], column_title = "m-DAGs Munkres-similarity Animals by Phyla", col = rev(viridis(256)), cluster_rows = FALSE, show_heatmap_legend = FALSE, cluster_columns = FALSE, top_annotation = annot, show_column_names = FALSE, show_row_names = FALSE, left_annotation = rowAnnotation( df = dff, col = colorsP, show_annotation_name = FALSE ) ) ``` Save graphics ```{r echo=FALSE, include=TRUE} pdf("data_appendix/MSA_animals_phyla.pdf") draw(MSA_heat_2,merge_legend=TRUE) dev.off() pdf("data_appendix/Mun_animals_phyla.pdf") draw(Mun_heat_2,merge_legend=TRUE) dev.off() ``` ```{r echo=FALSE, include=TRUE} draw(MSA_heat_2,merge_legend=TRUE) draw(Mun_heat_2,merge_legend=TRUE) ``` **Plants** ```{r, fig.align='center', fig.height=5, cache=FALSE} meta_plants= meta_taxo[1:884,] %>% filter(Kingdom=="Plants") namesP=names(rev(sort(table(meta_plants$Phylum)))) namesP dff=data.frame(Phylum=meta_plants$Phylum) Phylum=ordered(meta_plants$Phylum,levels=namesP) numbersP=paste(c(paste0(0,1:7)),namesP,sep="-") levels(Phylum)=numbersP dff$Phylum=Phylum col=rainbow(length(namesP)) colorsP=list(Phylum=col) names(colorsP$Phylum)=numbersP annot <- HeatmapAnnotation(df = dff, col = colorsP, annotation_name_side = "left", show_annotation_name=TRUE ) MSA_heat_2 <- Heatmap( matrix = Sim_MSA_mDAG[meta_plants$mDAG_Id, meta_plants$mDAG_Id], name = "MSA similarity", column_title = "m-DAGs MSA-similarity Plants by Phyla", col = rev(viridis(256)), cluster_rows = FALSE, show_heatmap_legend = FALSE, cluster_columns = FALSE, top_annotation = annot, show_column_names = FALSE, show_row_names = FALSE, left_annotation = rowAnnotation( df = dff, col = colorsP, show_annotation_name = FALSE ) ) Mun_heat_2 <- Heatmap( matrix = Sim_Mun_mDAG[meta_plants$mDAG_Id, meta_plants$mDAG_Id], name = "Mun similarity", column_title = "m-DAGs Munkres-similarity Plants by Phyla", col = rev(viridis(256)), cluster_rows = FALSE, show_heatmap_legend = FALSE, cluster_columns = FALSE, top_annotation = annot, show_column_names = FALSE, show_row_names = FALSE, left_annotation = rowAnnotation( df = dff, col = colorsP, show_annotation_name = FALSE ) ) ``` Save graphics ```{r echo=FALSE, include=TRUE} pdf("data_appendix/MSA_plants_phyla.pdf") draw(MSA_heat_2,merge_legend=TRUE) dev.off() pdf("data_appendix/Mun_plants_phyla.pdf") draw(Mun_heat_2,merge_legend=TRUE) dev.off() ``` ```{r echo=FALSE, include=TRUE} draw(MSA_heat_2,merge_legend=TRUE) draw(Mun_heat_2,merge_legend=TRUE) ``` **Fungi** ```{r, fig.align='center', fig.height=5, cache=FALSE} meta_fungi= meta_taxo%>% filter(Kingdom=="Fungi") namesP=names(rev(sort(table(meta_fungi$Phylum)))) namesP dff=data.frame(Phylum=meta_fungi$Phylum) Phylum=ordered(meta_fungi$Phylum,levels=namesP) n=length(namesP) numbersP=paste(c(paste0(0,1:n)),namesP,sep="-") levels(Phylum)=numbersP dff$Phylum=Phylum col=rainbow(length(namesP)) colorsP=list(Phylum=col) names(colorsP$Phylum)=numbersP annot <- HeatmapAnnotation(df = dff, col = colorsP, annotation_name_side = "left", show_annotation_name=TRUE ) MSA_heat_2 <- Heatmap( matrix = Sim_MSA_mDAG[meta_fungi$mDAG_Id, meta_fungi$mDAG_Id], name = "MSA similarity", column_title = "m-DAGs MSA-similarity Fungi by Phyla", col = rev(viridis(256)), cluster_rows = FALSE, show_heatmap_legend = FALSE, cluster_columns = FALSE, top_annotation = annot, show_column_names = FALSE, show_row_names = FALSE, left_annotation = rowAnnotation( df = dff, col = colorsP, show_annotation_name = FALSE ) ) Mun_heat_2 <- Heatmap( matrix = Sim_Mun_mDAG[meta_fungi$mDAG_Id, meta_fungi$mDAG_Id], name = "Mun similarity", column_title = "m-DAGs Munkres-similarity Fungi by Phyla", col = rev(viridis(256)), cluster_rows = FALSE, show_heatmap_legend = FALSE, cluster_columns = FALSE, top_annotation = annot, show_column_names = FALSE, show_row_names = FALSE, left_annotation = rowAnnotation( df = dff, col = colorsP, show_annotation_name = FALSE ) ) ``` Save graphics ```{r echo=FALSE, include=TRUE} pdf("data_appendix/MSA_fungi_phyla.pdf") draw(MSA_heat_2,merge_legend=TRUE) dev.off() pdf("data_appendix/Mun_fungi_phyla.pdf") draw(Mun_heat_2,merge_legend=TRUE) dev.off() ``` ```{r echo=FALSE, include=TRUE} draw(MSA_heat_2,merge_legend=TRUE) draw(Mun_heat_2,merge_legend=TRUE) ``` **Protists** ```{r, fig.align='center', fig.height=5, cache=TRUE} meta_protists= meta_taxo %>% filter(Kingdom=="Protists") namesP=names(rev(sort(table(meta_protists$Phylum)))) namesP dff=data.frame(Phylum=meta_protists$Phylum) Phylum=ordered(meta_protists$Phylum,levels=namesP) n=length(namesP) numbersP=paste(c(paste0(0,1:n)),namesP,sep="-") levels(Phylum)=numbersP dff$Phylum=Phylum col=rainbow(length(namesP)) colorsP=list(Phylum=col) names(colorsP$Phylum)=numbersP annot <- HeatmapAnnotation(df = dff, col = colorsP, annotation_name_side = "left", show_annotation_name=TRUE ) MSA_heat_2 <- Heatmap( matrix = Sim_MSA_mDAG[meta_protists$mDAG_Id, meta_protists$mDAG_Id], name = "MSA similarity", column_title = "m-DAGs MSA-similarity Protist by Phyla", col = rev(viridis(256)), cluster_rows = FALSE, show_heatmap_legend = FALSE, cluster_columns = FALSE, top_annotation = annot, show_column_names = FALSE, show_row_names = FALSE, left_annotation = rowAnnotation( df = dff, col = colorsP, show_annotation_name = FALSE ) ) Mun_heat_2 <- Heatmap( matrix = Sim_Mun_mDAG[meta_protists$mDAG_Id, meta_protists$mDAG_Id], name = "Mun similarity", column_title = "m-DAGs Munkres-similarity Protist by Phyla", col = rev(viridis(256)), cluster_rows = FALSE, show_heatmap_legend = FALSE, cluster_columns = FALSE, top_annotation = annot, show_column_names = FALSE, show_row_names = FALSE, left_annotation = rowAnnotation( df = dff, col = colorsP, show_annotation_name = FALSE ) ) ``` Save graphics ```{r echo=FALSE, include=FALSE} pdf("data_appendix/MSA_protists_phyla.pdf") draw(MSA_heat_2,merge_legend=TRUE) dev.off() pdf("data_appendix/Mun_protists_phyla.pdf") draw(Mun_heat_2,merge_legend=TRUE) dev.off() ``` ```{r} draw(MSA_heat_2,merge_legend=TRUE) draw(Mun_heat_2,merge_legend=TRUE) ```