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gg_Marker_Bar()

Source: vignettes/gg_Marker_Bar.Rmd
gg_Marker_Bar.Rmd

The function gg_Marker_Bar() creates marker plots with your myY and myG GWAS input files.

Load data

Note: header = T

# Load genotype file (note: header = T)
myG <- read.csv("gwaspr_myG_hmp.csv", header = T)
# Load phenotype file
myY <- read.csv("gwaspr_myY.csv")
# Convert our nominal trait from numeric to factor.
myY <- myY %>% 
  mutate(Cotyledon_Color = mv(Cotyledon_RedvsYellow, c(1, 0, NA), c("Red", "Yellow", "Green")),
         Cotyledon_Color = factor(Cotyledon_Color, levels = c("Red", "Yellow", "Green")))
myY[1:10,]
##                 Name DTF_Sask_2017 DTF_Nepal_2017 Cotyledon_RedvsYellow
## 1    CDC_Asterix_AGL          54.7          128.0                     0
## 2      CDC_Rosie_AGL          59.0          123.3                     1
## 3       X3156.11_AGL          60.7          125.3                     1
## 4  CDC_Greenstar_AGL          56.7          121.0                     0
## 5     CDC_Cherie_AGL          54.3          125.3                     1
## 6     CDC_Glamis_AGL          59.0          123.0                     0
## 7       CDC_Gold_AGL          54.0          125.3                     0
## 8       CDC_Imax_AGL          53.0          128.7                     1
## 9    CDC_Impower_AGL          57.0          123.3                     0
## 10      CDC_KR.1_AGL          57.0          121.7                     1
##    Cotyledon_Color
## 1           Yellow
## 2              Red
## 3              Red
## 4           Yellow
## 5              Red
## 6           Yellow
## 7           Yellow
## 8              Red
## 9           Yellow
## 10             Red

Single marker, single trait

Specifying traits and markers along with your genotype and phenotype data as xG and xY is needed to create marker plots.

# Plot
mp <- gg_Marker_Bar(
  # Genotype data
  xG = myG, 
  # Phenotype data
  xY = myY,
  # Select traits to plot
  traits = "DTF_Sask_2017",
  # Select markers to plot
  markers = "Lcu.1GRN.Chr6p3269280" )
# Save
ggsave("figures/gg_Marker_Bar_01.png", 
       mp, width = 6, height = 4 )

All options

gg_Marker_Bar() contains a number of different options for customizing the marker plots.

# Prep data
markers <- c("Lcu.1GRN.Chr6p3269280")
# Plot
mp <- gg_Marker_Bar(
  xG = myG, 
  xY = myY,
  traits = "DTF_Sask_2017",
  markers = markers,
  marker.colors = gwaspr_Colors,
  remove.hets = T,
  remove.N = T,
  plot.histogram = T,
  plot.density = T,
  plot.counts = T,
  ncol = NULL,
  line.color = F,
  title = NULL,
  subtitle = paste(markers, collapse = "\n"),
  asfactor = F)
# Save
ggsave("figures/gg_Marker_Bar_02.png", 
       mp, width = 6, height = 4 )

Multiple markers, multiple traits 

# Plot
mp <- gg_Marker_Bar(
  # Genotype data
  xG = myG, 
  # Phenotype data
  xY = myY,
  # Select traits to plot
  traits = c("DTF_Nepal_2017", "DTF_Sask_2017"),
  # Select markers to plot
  markers = c("Lcu.1GRN.Chr2p44545877", "Lcu.1GRN.Chr5p1658484") )
# Save
ggsave("figures/gg_Marker_Bar_03.png", 
       mp, width = 8, height = 4 )

Histogram 

# Plot
mp <- gg_Marker_Bar(
  # Genotype data
  xG = myG, 
  # Phenotype data
  xY = myY,
  # Select traits to plot
  traits = "DTF_Sask_2017",
  # Select markers to plot
  markers = "Lcu.1GRN.Chr6p3269280",
  # Select marker colors
  marker.colors = c("darkorange3", "steelblue", "darkblue"),
  # Choose what should be plotted
  plot.histogram = T,
  plot.density = F )
# Save
ggsave("figures/gg_Marker_Bar_04.png", 
       mp, width = 6, height = 4 )

Density 

# Plot
mp <- gg_Marker_Bar(
  # Genotype data
  xG = myG, 
  # Phenotype data
  xY = myY,
  # Select traits to plot
  traits = "DTF_Sask_2017",
  # Select markers to plot
  markers = "Lcu.1GRN.Chr6p3269280",
  # Select marker colors
  marker.colors = c("darkorange3", "steelblue", "darkblue"),
  # Choose what should be plotted
  plot.histogram = F,
  plot.density = T )
# Save
ggsave("figures/gg_Marker_Bar_05.png", 
       mp, width = 6, height = 4)

Factor data

Numeric format 

# Plot 
mp <- gg_Marker_Bar(
  # Genotype data
  xG = myG, 
  # Phenotype data
  xY = myY,
  # Select traits to plot
  traits = "Cotyledon_RedvsYellow",
  # Select markers to plot
  markers = "Lcu.1GRN.Chr1p365986872",
  # Select marker colors
  marker.colors = c("darkorange3", "steelblue", "darkblue"),
  # Choose what should be plotted
  plot.histogram = T,
  plot.density = F )
# Save
ggsave("figures/gg_Marker_Bar_06.png", 
       mp, width = 6, height = 4 )

Factor format 

# Plot 
mp <- gg_Marker_Bar(
  # Genotype data
  xG = myG, 
  # Phenotype data
  xY = myY,
  # Select traits to plot
  traits = "Cotyledon_Color",
  # Select markers to plot
  markers = "Lcu.1GRN.Chr1p365986872",
  # Select marker colors
  marker.colors = c("darkorange3", "steelblue", "darkblue"),
  # Choose what should be plotted
  plot.histogram = T,
  plot.density = F )
# Save
ggsave("figures/gg_Marker_Bar_07.png", 
       mp, width = 6, height = 4 )