Suppl. Figure 1. Bacterial abundance across datasets

##################
# LOAD LIBRARIES #
##################
suppressWarnings({suppressMessages({suppressPackageStartupMessages({
  #remotes::install_github("czarnewski/niceRplots",force=T)
  library(niceRplots)
  library(tidyverse)
})  })  })

#############
# LODA DATA #
#############
datasets_all_samples <- readRDS("/Users/vilkal/work/Brolidens_work/Projects/Gabriella_repo/results/datasets_all_samples.RDS")
datasets_all_samples_ <- readRDS("../../results/03_normalize_data_output/datasets_all_samples.RDS")

#################
# COLOR PALETTS #
#################
Set1 <- c("#4DAF4A", "#E41A1C", "#984EA3", "#377EB8","#A6D854", "#FFFF33", "#FF7F00", "#A65628", "#F781BF", "#999999")
pal <- c(Set1,RColorBrewer::brewer.pal(8,"Set2"),
         RColorBrewer::brewer.pal(9,"Pastel1"),RColorBrewer::brewer.pal(8,"Pastel2")) #color pallete for plots

Violin plot

x <- datasets_all_samples_[[1]]
top <- t(t(2^x-1)/colSums(2^x-1)) %>%
  as_tibble(., rownames ="tax") %>%
  pivot_longer(cols = -tax, names_to = 'ID') %>%
  group_by(tax) %>%
  summarise(mean = mean(value)) %>% 
  arrange(desc(mean)) %>%
  filter(!(tax == "Not assigned")) %>%
  pluck(., "tax") %>%
  .[1:30]

Lum <- datasets_all_samples_[[1]][rownames(datasets_all_samples_[[1]])%in%top,]
Tis <- datasets_all_samples_[[2]][rownames(datasets_all_samples_[[1]])%in%top,]

x_Lum <- Lum %>% as_tibble(., rownames ="tax") %>%
  pivot_longer(cols = -tax, names_to = 'ID') #%>% 
  #pivot_wider(names_from = tax, values_from = value)

x_Tis <- Tis %>% as_tibble(., rownames ="tax") %>%
  pivot_longer(cols = -tax, names_to = 'ID') #%>% 
  #pivot_wider(names_from = tax, values_from = value)

xx <- x_Lum %>% left_join(x_Tis, by=c("tax","ID")) %>% select(-ID)
xx_ <- xx %>% filter(!(is.na(.$value.y))) # filter out NA from Tissue

Luminal <- set_names(xx$value.x, xx$tax)
Tissue <- set_names(xx_$value.y, xx_$tax) 

t <- rbind(Tissue, Luminal)

## Warning in rbind(Tissue, Luminal): number of columns of result is not a multiple
## of vector length (arg 1)

###################################
# BACTERIAL ABUNDANCE IN DATASETS #
###################################
par(mar=c(6.5,2.5,0,0)) #b,l,t,r
violist(data = t, smooth = .1,
        genes = c("Tissue", "Luminal"),
        clustering = factor( colnames(t),levels = top),
        srt=45, cex.axis=0.7, pt.cex=0.2,
        transparency = 50,col = pal)

Supplementary Figure 1. Abundance distribution of individual taxa in the luminal and tissue microbiome data sets. Violin plots showing the distribution of relative abundance of the top 30 most abundant taxa in the luminal and tissue-adherent data sets.