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appendix.qmd
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## 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)
```