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gg_Marker_*()

Source: vignettes/gg_Marker.Rmd
gg_Marker.Rmd

The functions gg_Marker_Box(), gg_Marker_Bar(), and gg_Marker_Pie() create marker plots with your myY and myG GWAS input files.

Load data 

# 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")))
##                 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
## 11     CDC_LeMay_AGL          55.7          126.7                     0
## 12     CDC_Maxim_AGL          54.3          125.7                     1
## 13      CDC_QG.1_AGL          57.7          126.7                    NA
## 14 CDC_Red_Rider_AGL          57.0          123.5                     1
## 15   CDC_Redcoat_AGL          57.7          126.7                     1

gg_Marker_Box

Single marker, single trait

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

# Plot
mp <- gg_Marker_Box(
  # 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_Box_01.png", 
       mp, width = 6, height = 4 )

Customized Plots

Boxplots 

# Plot
mp <- gg_Marker_Box(
  # 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"),
  # Choose what should be plotted
  plot.violin = F,
  plot.box = T,
  plot.points = F,
  # Change the width of the boxplots
  box.width = 0.3,
  # Create a custom label for the y-axis
  yLab = "Days from sowing to flower" )
# Save
ggsave("figures/gg_Marker_Box_02.png", 
       mp, width = 6, height = 4 )

Violin + points 

# Plot
mp <- gg_Marker_Box(
  # 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"),
  # Choose what should be plotted
  plot.violin = T,
  plot.box = F,
  plot.points = T,
  # Set the point size
  point.size = 2,
  # Create a custom label for the y-axis
  yLab = "Days from sowing to flower" )
# Save
ggsave("figures/gg_Marker_Box_03.png", 
       mp, width = 6, height = 4 )

Covariable Point Color

myG covariable 
# Plot
mp <- gg_Marker_Box(
  # 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", "darkseagreen4", "steelblue", "burlywood4"),
  # Keep heterozygous markers
  remove.hets = F,
  # Choose what should be plotted
  plot.violin = T,
  plot.box = F,
  plot.points = T,
  # Set the point size
  point.size = 0.75,
  # Plot with geom_beeswarm instead of quasirandom
  point.beeswarm = T,
  # Select Covariable trait for points
  cv.name = "Lcu.1GRN.Chr2p44545877", 
  # Select colors for the covariable
  cv.colors = c("darkslategray4", "maroon3", "purple3"),
  # Set a custom label for the covariable legend
  cv.label = "Chr2p44545877" )
# Save
ggsave("figures/gg_Marker_Box_04.png", 
       mp, width = 6, height = 4 )

myY covariable 
# Plot
mp <- gg_Marker_Box(
  # 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"),
  # Choose what should be plotted
  plot.violin = T,
  plot.box = F,
  plot.points = T,
  # Set the point size
  point.size = 1.5,
  # Plot with geom_beeswarm instead of quasirandom
  point.beeswarm = T,
  # Select covariable source
  cv.source = "xY",
  # Select Covariable trait for points
  cv.name = "Cotyledon_Color", 
  # Select colors for the covariable
  cv.colors = c("darkred", "darkgoldenrod2", "darkgreen"),
  # Set a custom label for the covariable legend
  cv.label = "Cotyledon Color" )
# Save
ggsave("figures/gg_Marker_Box_05.png", 
       mp, width = 6, height = 4 )

Multiple markers, multiple traits 

# Plot
mp <- gg_Marker_Box(
  # 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.Chr5p1658484", "Lcu.1GRN.Chr2p44545877") )
# Save
ggsave("figures/gg_Marker_Box_06.png",
       mp, width = 8, height = 4 )

gg_Marker_Bar

Single marker, single trait 

# 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 )

Customized Plots

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"),
  # Choose what should be plotted
  plot.histogram = T,
  plot.density = F )
# Save
ggsave("figures/gg_Marker_Bar_02.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"),
  # Choose what should be plotted
  plot.histogram = F,
  plot.density = T )
# Save
ggsave("figures/gg_Marker_Bar_03.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_04.png", 
       mp, width = 8, 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("darkred", "darkgoldenrod2"),
  # Choose what should be plotted
  plot.histogram = T,
  plot.density = F )
# Save
ggsave("figures/gg_Marker_Bar_05.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("darkred", "darkgoldenrod2", "darkgreen"),
  # Choose what should be plotted
  plot.histogram = T,
  plot.density = F )
# Save
ggsave("figures/gg_Marker_Bar_06.png", 
       mp, width = 6, height = 4 )

gg_Marker_Pie 

# Plot 
mp <- gg_Marker_Pie(
  # Genotype data
  xG = myG, 
  # Phenotype data
  xY = myY,
  # Select traits to plot
  trait = "Cotyledon_Color",
  # Select markers to plot
  markers = "Lcu.1GRN.Chr1p365986872",
  # Select marker colors
  marker.colors = c("darkred", "darkgoldenrod2", "darkgreen") )
# Save
ggsave("figures/gg_Marker_Pie_01.png", 
       mp, width = 6, height = 4 )