The function gg_Marker_Box() 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 RedSingle 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_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 )
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_Box(
xG = myG,
xY = myY,
traits = "DTF_Sask_2017",
markers = markers,
marker.colors = gwaspr_Colors,
remove.hets = F,
remove.N = T,
plot.violin = T,
plot.box = T,
plot.points = T,
box.width = 0.1,
point.size = 1,
point.beeswarm = F,
ncol = NULL,
legend.rows = 1,
title = NULL,
subtitle = paste(markers, collapse = "\n"),
cv.source = "xG",
cv.name = NULL,
cv.colors = NULL,
cv.label = cv.name,
groupByCV = F )
# Save
ggsave("figures/gg_Marker_Box_02.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"),
# Remove heterozygotic markers
remove.hets = T )
# Save
ggsave("figures/gg_Marker_Box_03.png",
mp, width = 8, height = 4 )
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", "darkblue"),
# Choose what should be plotted
plot.violin = F,
plot.box = T,
plot.points = F,
# Change the width of the boxplots
box.width = 0.3 )
# Save
ggsave("figures/gg_Marker_Box_04.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", "darkblue"),
# Choose what should be plotted
plot.violin = T,
plot.box = F,
plot.points = T,
# Set the point size
point.size = 2)
# Save
ggsave("figures/gg_Marker_Box_05.png",
mp, width = 6, height = 4 )
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("burlywood4", "maroon3", "purple3"),
# 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("darkorange3", "steelblue", "darkblue") )
# Save
ggsave("figures/gg_Marker_Box_06.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", "darkblue"),
# 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_07.png",
mp, width = 6, height = 4 )
Grouped by 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", "darkblue"),
# 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",
# Plot CV on x-axis instead of marker
groupByCV = T)
# Save
ggsave("figures/gg_Marker_Box_08.png",
mp, width = 6, height = 4 )