code.utf8.md

Load packages

library(readxl)
library(tidyverse)
library(ggthemes)
library(janitor)
library(patchwork)

Customize ggplot themes

my_theme <- theme_bw() +
  theme(
    legend.position = "none",
    axis.line.x = element_line(color = "black", size = 0.5),
    axis.line.y = element_line(color = "white", size = 1),
    axis.text.y = element_blank(),
    axis.ticks = element_blank(),
    panel.border = element_blank(),
    panel.grid.major.x = element_blank(),
    panel.grid.minor.x = element_blank(),
    panel.grid.major.y = element_blank())

my_theme2 <- theme_bw() +
  theme(
    legend.position = "none",
    axis.line.x = element_line(color = "black", size = 0.5),
    axis.line.y = element_line(color = "white", size = 1),
    panel.border = element_blank(),
    panel.grid.major.y = element_blank(),
    panel.grid.minor.y = element_blank(),
  axis.text.y = element_text(face = "italic"))
  
my_theme3 <- theme_bw() +
  theme(
    legend.position = "none",
   axis.line.x = element_line(color = "black", size = 0.5),
    axis.line.y = element_line(color = "white", size = 1),
    panel.border = element_blank(),
    panel.grid.major.x = element_blank(),
    panel.grid.minor.y = element_blank(),
   legend.text = element_text(face = "italic"))

Read data from XLSX

fus <- read_excel("data/fusarium-parana.xlsx")
# using read_excel to deal better with encoding format

Summary and visualization

All isolates per host

fus %>% 
  tabyl(Host)

All strains per year

fus %>% 
  tabyl(Host)

Fig1A <- fus %>% 
  tabyl(Host) %>% 
    ggplot(aes(reorder(Host, n), n, label = n))+
     geom_col(fill = "#ffcc99", color = "black", size = 0.5)+
  theme(axis.text.x=element_text(face="italic"))+
      geom_text(position = position_dodge(width = 1),
            hjust = 0.5, vjust = -0.2) +
  labs(x = "", y = "Number of strains")+
  scale_y_continuous(expand = c(0, 0), limits = c(0, 600)) +
  my_theme

All strains per year

fus %>% 
  tabyl(Year)

Fig1B <- fus %>% 
  tabyl(Year) %>% 
    ggplot(aes(Year,n, label = n))+
    geom_col(fill = "#ffcc99", color = "black", size = 0.5)+
  theme_light()+
    geom_text(hjust = 0.5, vjust = -0.2) +
  labs(x = "", y = "Number of strains")+
    scale_y_continuous(expand = c(0, 0), limits = c(0, 350)) +
  my_theme

All strains per complexes

fus %>% 
  tabyl(Complexes)

Fig1C <- fus %>% 
  tabyl(Complexes) %>% 
    ggplot(aes(reorder(Complexes, n),n, label = n))+
    geom_col(fill = "#ffcc99", color = "black", size = 0.5)+
   coord_flip()+
  theme(axis.text.x=element_text(face="italic"))+
      geom_text(position = position_dodge(width = 1),
            hjust = 0) +
  labs(x = "", y = "Number of strains")+
  scale_y_continuous( limits = c(0, 650)) +
  my_theme2

Figure 1

fig1 <- ((Fig1A / Fig1B) | Fig1C) + plot_annotation(tag_levels = 'A')
ggsave("figs/fig1.png", width =6, height =4)
fig1

All species by host

Wheat

fus %>% 
  filter(Host == "Wheat") %>% 
  tabyl(Complex2,  Year)

Fig2A <- fus %>% 
  filter(Host == "Wheat") %>% 
  tabyl(Complex2,  Year) %>% 
  gather(year, n, 2:6) %>% 
  ggplot(aes(year, n, fill = Complex2))+
    geom_col()+
scale_fill_brewer(palette = "Paired")+
 theme_light()+
  labs(x = "Year", y = "Number of strains", fill = "", title = "Wheat (n = 366)")+
   scale_y_continuous(expand = c(0, 0), limits = c(0, 180)) +
  my_theme3

Barley

fus %>% 
  filter(Host == "Barley") %>% 
  tabyl(Complex2,  Year)

Fig2B <- fus %>% 
   filter(Host == "Barley") %>% 
  tabyl(Complex2,  Year) %>% 
  gather(year, n, 2:6) %>% 
  ggplot(aes(year, n, fill = Complex2))+
    geom_col()+
  scale_fill_brewer(palette = "Paired")+
   theme_light()+
  labs(x = "Year", y = "Number of strains", fill = "", title = "Barley (n = 421)")+
       scale_y_continuous(expand = c(0, 0), limits = c(0, 180)) +
  my_theme3

Figure 2

patch <- Fig2A + Fig2B & theme(legend.position = "right") 
p1 <- patch + plot_layout(guides = "collect")+ plot_annotation(tag_levels = 'A')
ggsave("figs/fig2.png", width =7, height =4)
p1

FGSC by host within year

Wheat

Fig3A <- fus %>% 
  filter(Complex2 == "FGSC") %>% 
  filter(Host == "Wheat") %>% 
  tabyl(Species,  Year) %>% 
  gather(year, n, 2:6) %>% 
  ggplot(aes(year, n, fill = Species, label = n))+
    geom_col()+
  scale_fill_brewer(palette = "Dark2")+
 theme_light()+
  labs(x = "", y = "Number of strains", fill = "FGSC", title = "Wheat (n = 266)")+
         scale_y_continuous(expand = c(0, 0), limits = c(0,130)) +
  my_theme3

Barley

Fig3B <- fus %>% 
    filter(Complex2 == "FGSC") %>% 
   filter(Host == "Barley") %>% 
  tabyl(Species,  Year) %>% 
  gather(year, n, 2:6) %>% 
  ggplot(aes(year, n, fill = Species))+
    geom_col()+
  scale_fill_brewer(palette = "Dark2")+
   theme_light()+
  labs(x = "", y = "Number of strains", fill = "FGSC", title = "Barley (n = 305)")+
       scale_y_continuous(expand = c(0, 0)) +
  my_theme3

Figure 3

patch1 <- Fig3A + Fig3B + theme(legend.position = "right") 
Fig3AB <- patch1 + plot_layout(guides = "collect")+ plot_annotation(tag_levels = 'A')  
ggsave("figs/fig3.png", width =8, height =4)
Fig3AB

FTSC by host within year

Wheat

Fig3C <- fus %>% 
    filter(Complex2 == "FTSC") %>%
   filter(Host == "Wheat") %>% 
  filter(Species != "F. acuminatum") %>% 
  tabyl(Species,  Year) %>% 
  gather(year, n, 2:6) %>% 
  ggplot(aes(year, n, fill = Species))+
    geom_col()+
    scale_fill_brewer(palette = "Set2")+
   theme_light()+
 
  labs(x = "Year", y = "Number of strains", fill = "FTSC", title = "Wheat (n = 25)")+
   scale_y_continuous(expand = c(0, 0), limits = c(0,12)) +
  my_theme3

Barley

Fig3D <- fus %>% 
    filter(Complex2 == "FTSC") %>% 
   filter(Host == "Barley") %>% 
  tabyl(Species,  Year) %>% 
  gather(year, n, 2:6) %>% 
  ggplot(aes(year, n, fill = Species))+
    geom_col()+
  scale_fill_brewer(palette = "Set2")+
   theme_light()+
  labs(x = "Year", y = "Number of strains", fill = "FTSC", title = "Barley (n = 36)")+
     scale_y_continuous(expand = c(0, 0), limits = c(0,12)) +
  my_theme3

Figure 4

patch2 <- Fig3C + Fig3D + theme(legend.position = "right") 
Fig3CD <- patch2 + plot_layout(guides = "collect")+ plot_annotation(tag_levels = 'A') 
ggsave("figs/fig4.png", width =8, height =4)
Fig3CD

Independence tests

Host vs. complexes

host_complexes <- fus %>% 
  tabyl(Complexes, Host)

chisq.test(host_complexes)

## Warning in stats::chisq.test(., ...): Chi-squared approximation may be incorrect

## 
##  Pearson's Chi-squared test
## 
## data:  host_complexes
## X-squared = 12.159, df = 8, p-value = 0.1443

fisher.test(host_complexes)

## 
##  Fisher's Exact Test for Count Data
## 
## data:  host_complexes
## p-value = 0.07159
## alternative hypothesis: two.sided

year vs. complexes

year_complex2 <- fus %>% 
  tabyl(Complex2, Year)

fisher.test(year_complex2, simulate.p.value = TRUE)

## 
##  Fisher's Exact Test for Count Data with simulated p-value (based on
##  2000 replicates)
## 
## data:  year_complex2
## p-value = 0.0004998
## alternative hypothesis: two.sided

FGSC vs. host

host_fgsc <- fus %>% 
  filter(Complex2 == "FGSC") %>% 
  tabyl(Species, Host)
chisq.test(host_fgsc)

## 
##  Pearson's Chi-squared test
## 
## data:  host_fgsc
## X-squared = 7.3975, df = 3, p-value = 0.06025

FGSC vs. year

year_fgsc <- fus %>% 
  filter(Complex2 == "FGSC") %>% 
  tabyl(Species, Year)
fisher.test(year_fgsc, simulate.p.value = T)

## 
##  Fisher's Exact Test for Count Data with simulated p-value (based on
##  2000 replicates)
## 
## data:  year_fgsc
## p-value = 0.0004998
## alternative hypothesis: two.sided

Toxin data

tox <- read_excel("data/toxin-ftsc.xlsx",1) %>% 
  gather(toxin, value, 3:7 )
tox

Code

Load packages

Customize ggplot themes

Read data from XLSX

Summary and visualization

All isolates per host

All strains per year

All strains per year

All strains per complexes

Figure 1

All species by host

Wheat

Barley

Figure 2

FGSC by host within year

Wheat

Barley

Figure 3

FTSC by host within year

Wheat

Barley

Figure 4

Independence tests

Host vs. complexes

year vs. complexes

FGSC vs. host

FGSC vs. year

Toxin data