library(readr)

library(dplyr)

library(reshape2)

library(stringr)

library(ggplot2)

library(RColorBrewer)

table <- read_tsv("mluteus_accessory_core_BGCs.txt")

hm.palette <- colorRampPalette(rev(brewer.pal(11, 'RdYlBu')), space='Lab')

library(tidyverse)

library(grid)

hacky_df <- data.frame(

var = c("Core", "Global BE", "HK BE", "NCBI"),

var_color = c("#e41a1c", "#377eb8","#4daf4a", "#984ea3")

)

plot_new <-

ggplot(df) + # don't specify x and y here. Otherwise geom_rect will complain.

geom_rect(

data=hacky_df,

aes(xmin=-Inf, xmax=Inf, fill=var_color, alpha=0.4)) +

geom_point(aes(x = Genome, y = Gene_cluster_type)) +

coord_cartesian(clip="off") +

facet_wrap(~ Source, scales = "free") +

scale_fill_manual(values = c("Core" = "#e41a1c", "Global BE" = "#377eb8", "HK BE" = "#4daf4a", "NCBI" = "#984ea3")) +

theme_bw() +

theme(

strip.background = element_rect(fill=NA),

strip.text = element_text(face="bold")

)

table2 <- read_tsv("mluteus_accessory_core_BGCs.txt")

Plot <- ggplot(table2,aes(x=Genome, y=Gene_cluster_type))

Plot <- Plot + facet_grid(~Source, scales = "free",space="free") #+ scale_y_continuous(expand = c(0,0))

Plot <- Plot + geom_point(aes(fill=Gene_cluster_type,size=3),pch=21,alpha = 0.8)

Plot <- Plot + scale_fill_manual(values = c("Core" = "#e41a1c", "Global BE" = "#377eb8", "HK BE" = "#4daf4a", "NCBI" = "#984ea3"))

Plot <- Plot + theme(strip.background = element_rect(fill = "Dark2"))

Plot <- Plot + theme(axis.text.x = element_blank())

Plot <- Plot + theme(axis.ticks.x = element_blank())

Plot <- Plot + scale_fill_brewer(palette = "Set1")

Plot <- Plot + xlab(paste0("M.luteus genomes")) + ylab(paste0("Type of BGCs"))

Plot <- Plot + theme(legend.position = "bottom")

table <- read_tsv("identical_MAGs_summary_meta.txt") %>%

select(Genotype,Taxonomy,Type, Location)

table$count <- 1

table <- table %>%

group_by(Genotype,Taxonomy,Type, Location) %>%

mutate(sum=sum(count)) %>%

ungroup() %>%

select(-count) %>%

unique()

Plot <- ggplot(table,aes(x=Location, y=Taxonomy, shape=Genotype))

Plot <- Plot + facet_wrap(~Type)

Plot <- Plot + geom_point(aes(color=Location,size=sum),alpha = 0.7)

Plot <- Plot + theme_bw()

Plot <- Plot + theme(axis.text.x = element_text(angle = 90, hjust = 0))

Plot <- Plot + scale_color_brewer(palette = "Set2")

Plot <- Plot + ylab(paste0("Taxonomy of representative MAG"))+xlab(paste0("Residence"))