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app.R
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library(shiny)
library(readxl)
library(bslib)
library(DT)
library(leaflet)
library(shinythemes)
library(ggplot2)
library(plotly)
# Loading the accession metadata
accessions <- read_excel(file.path(getwd(), "data", "accessions.xlsx"))
# More current version of GPS coordinates
accessions_map <- read.table(file.path(getwd(), "data", "accession_coordinates.tsv"),
header = TRUE, sep = "\t")
# Fixing typo
accessions_map$longitude[accessions_map$accession_id == "CW0119"] <- -73.79167
accessions_map$longitude[accessions_map$accession_id == "CW0099"] <- -73.79167
# Loading the flower measurements for the flower plot
flower_measurements <- read.table(file.path(getwd(), "data", "flower_measurements.tsv"),
header = TRUE)
# Loading the pollen measurements
pollen_measurements <- read.table(file.path(getwd(), "data", "pollen_measurements.tsv"),
header = TRUE) %>%
rename(accession_id = accession)
# Subsetting the accessions table and the flower measurements to only include the ones
# with complete phenotypes:
accessions <- accessions[accessions$name_CW %in% pollen_measurements$accession_id, ]
flower_measurements <- flower_measurements[flower_measurements$accession_id %in% pollen_measurements$accession_id, ]
# Functions ---------------------------------------------------------------
make_flower_plot <- function(plot_type, flower_df, row_selection) {
# Current bug 2022-09-20: if you click on a row that has no anther/pistil
# lengths, then everything turns pink (e.g. CW1006).
if (plot_type == "ratio") {
if ((length(row_selection) && any(flower_df$accession_id %in% accessions$name_CW[row_selection]))) {
# Making new column for if it's selected or not
selected_accessions <- accessions$name_CW[row_selection]
flower_df$row_selected <- NA
flower_df$row_selected[flower_df$accession_id %in% selected_accessions] <- "selected"
flower_df$row_selected[is.na(flower_df$row_selected)] <- "not_selected"
# Making the plot
output_plot <- plot_ly(data = flower_df,
x = reorder(flower_df$accession_id, flower_df$anther_over_pistil, median),
y = ~anther_over_pistil,
color = ~row_selected,
colors = c("white", "magenta"),
type = "box",
line = list(width = 1),
marker = list(size = 3))
# Adding aesthetics
output_plot <- output_plot %>% layout(title = list(text = "Anther and pistil lengths by accession",
font = list(size = 22)),
shapes = list(
type = "line",
x0 = 0,
x1 = 1,
xref = "paper",
y0 = 1,
y1 = 1,
line = list(color = "white", dash = "dot"),
layer = "below"),
xaxis = list(title = F,
showline = T,
showticklabels = F,
linewidth = 1,
linecolor = "white"),
yaxis = list(title = list(text = "Ratio of AL / PL",
font = list(size = 16),
standoff = 0),
range = list(0.6, 1.4),
showline = T,
showgrid = F,
linewidth = 1,
linecolor = "white",
tickfont = list(size = 10)),
font = list(family = "Arial Black",
color = "white"),
paper_bgcolor = "#060606",
plot_bgcolor = "#060606",
margin = list(t = 50, r = 30),
showlegend = F)
} else {
# Making the plot
output_plot <- plot_ly(data = flower_df,
x = reorder(flower_df$accession_id, flower_df$anther_over_pistil, median),
y = ~anther_over_pistil,
type = "box",
fillcolor = "#838383",
line = list(width = 1,
color = "#ffffff"),
marker = list(size = 3,
color = "#ffffff"))
# Adding aesthetics
output_plot <- output_plot %>% layout(title = list(text = "Anther and pistil lengths by accession",
font = list(size = 22)),
shapes = list(
type = "line",
x0 = 0,
x1 = 1,
xref = "paper",
y0 = 1,
y1 = 1,
line = list(color = "white", dash = "dot"),
layer = "below"),
xaxis = list(title = F,
showline = T,
showticklabels = F,
linewidth = 1,
linecolor = "white"),
yaxis = list(title = list(text = "Ratio of AL / PL",
font = list(size = 16),
standoff = 0),
range = list(0.6, 1.4),
showline = T,
showgrid = F,
linewidth = 1,
linecolor = "white",
tickfont = list(size = 10)),
font = list(family = "Arial Black",
color = "white"),
paper_bgcolor = "#060606",
plot_bgcolor = "#060606",
margin = list(t = 50, r = 30))
}
} else if (plot_type == "anther") {
if ((length(row_selection) && any(flower_df$accession_id %in% accessions$name_CW[row_selection]))) {
# Making new column for if it's selected or not
selected_accessions <- accessions$name_CW[row_selection]
flower_df$row_selected <- NA
flower_df$row_selected[flower_df$accession_id %in% selected_accessions] <- "selected"
flower_df$row_selected[is.na(flower_df$row_selected)] <- "not_selected"
# Making the plot
output_plot <- plot_ly(data = flower_df,
x = reorder(flower_df$accession_id, flower_df$anther_length, median),
y = ~anther_length,
color = ~row_selected,
colors = c("white", "magenta"),
type = "box",
line = list(width = 1),
marker = list(size = 3))
# Adding aesthetics
output_plot <- output_plot %>% layout(title = list(text = "Anther lengths by accession",
font = list(size = 22)),
xaxis = list(title = F,
showline = T,
showticklabels = F,
linewidth = 1,
linecolor = "white"),
yaxis = list(title = list(text = "Anther length (mm)",
font = list(size = 16),
standoff = 0),
range = list(5, 13),
showline = T,
showgrid = F,
linewidth = 1,
linecolor = "white",
tickfont = list(size = 10)),
font = list(family = "Arial Black",
color = "white"),
paper_bgcolor = "#060606",
plot_bgcolor = "#060606",
margin = list(t = 50, r = 30),
showlegend = F)
} else {
# Making the plot
output_plot <- plot_ly(data = flower_df,
x = reorder(flower_df$accession_id, flower_df$anther_length, median),
y = ~anther_length,
type = "box",
fillcolor = "#838383",
line = list(width = 1,
color = "#ffffff"),
marker = list(size = 3,
color = "#ffffff"))
# Adding aesthetics
output_plot <- output_plot %>% layout(title = list(text = "Anther lengths by accession",
font = list(size = 22)),
xaxis = list(title = F,
showline = T,
showticklabels = F,
linewidth = 1,
linecolor = "white"),
yaxis = list(title = list(text = "Anther length (mm)",
font = list(size = 16),
standoff = 0),
range = list(5, 13),
showline = T,
showgrid = F,
linewidth = 1,
linecolor = "white",
tickfont = list(size = 10)),
font = list(family = "Arial Black",
color = "white"),
paper_bgcolor = "#060606",
plot_bgcolor = "#060606",
margin = list(t = 50, r = 30))
}
} else {
if ((length(row_selection) && any(flower_df$accession_id %in% accessions$name_CW[row_selection]))) {
# Making new column for if it's selected or not
selected_accessions <- accessions$name_CW[row_selection]
flower_df$row_selected <- NA
flower_df$row_selected[flower_df$accession_id %in% selected_accessions] <- "selected"
flower_df$row_selected[is.na(flower_df$row_selected)] <- "not_selected"
# Making the plot
output_plot <- plot_ly(data = flower_df,
x = reorder(flower_df$accession_id, flower_df$pistil_length, median),
y = ~pistil_length,
color = ~row_selected,
colors = c("white", "magenta"),
type = "box",
line = list(width = 1),
marker = list(size = 3))
# Adding aesthetics
output_plot <- output_plot %>% layout(title = list(text = "Pistil lengths by accession",
font = list(size = 22)),
xaxis = list(title = F,
showline = T,
showticklabels = F,
linewidth = 1,
linecolor = "white"),
yaxis = list(title = list(text = "Pistil length (mm)",
font = list(size = 16),
standoff = 0),
range = list(5, 13),
showline = T,
showgrid = F,
linewidth = 1,
linecolor = "white",
tickfont = list(size = 10)),
font = list(family = "Arial Black",
color = "white"),
paper_bgcolor = "#060606",
plot_bgcolor = "#060606",
margin = list(t = 50, r = 30),
showlegend = F)
} else {
# Making the plot
output_plot <- plot_ly(data = flower_df,
x = reorder(flower_df$accession_id, flower_df$pistil_length, median),
y = ~pistil_length,
type = "box",
fillcolor = "#838383",
line = list(width = 1,
color = "#ffffff"),
marker = list(size = 3,
color = "#ffffff"))
# Adding aesthetics
output_plot <- output_plot %>% layout(title = list(text = "Pistil lengths by accession",
font = list(size = 22)),
xaxis = list(title = F,
showline = T,
showticklabels = F,
linewidth = 1,
linecolor = "white"),
yaxis = list(title = list(text = "Pistil length (mm)",
font = list(size = 16),
standoff = 0),
range = list(5, 13),
showline = T,
showgrid = F,
linewidth = 1,
linecolor = "white",
tickfont = list(size = 10)),
font = list(family = "Arial Black",
color = "white"),
paper_bgcolor = "#060606",
plot_bgcolor = "#060606",
margin = list(t = 50, r = 30))
}
}
# Removing toolbar
output_plot <- output_plot %>% config(displayModeBar = F)
return(output_plot)
}
make_burst_plot <- function(plot_type, pollen_df, row_selection) {
pollen_df$accession_id <- as.factor(pollen_df$accession_id)
if (plot_type == "26C") {
pollen_df$accession_id <- reorder(pollen_df$accession_id, pollen_df$burst_2h_26C_adjusted_mean)
if ((length(row_selection) && any(pollen_df$accession_id %in% accessions$name_CW[row_selection]))) {
# Making new column for if it's selected or not
selected_accessions <- accessions$name_CW[row_selection]
pollen_df$row_selected <- NA
pollen_df$row_selected[pollen_df$accession_id %in% selected_accessions] <- "selected"
pollen_df$row_selected[is.na(pollen_df$row_selected)] <- "not_selected"
# Plot for 'not_selected'
output_plot <- plot_ly(data = subset(pollen_df, row_selected == "not_selected"),
x = ~accession_id,
y = ~burst_2h_26C_adjusted_mean,
type = "scatter",
mode = "markers",
marker = list(size = 5, color = "white"),
error_y = list(array = ~burst_2h_26C_adjusted_se, width = 1, color = "white"))
# Add plot for 'selected'
output_plot <- output_plot %>%
add_trace(data = subset(pollen_df, row_selected == "selected"),
x = ~accession_id,
y = ~burst_2h_26C_adjusted_mean,
type = "scatter",
mode = "markers",
marker = list(size = 5, color = "magenta"),
error_y = list(array = ~burst_2h_26C_adjusted_se, width = 1, color = "magenta"))
# Adding aesthetics
output_plot <- output_plot %>% layout(title = list(text = "Adjusted burst % at 2 hours, 26 ºC",
font = list(size = 22)),
xaxis = list(title = F,
showline = T,
showticklabels = F,
linewidth = 1,
linecolor = "white"),
yaxis = list(title = list(text = "Percentage",
font = list(size = 16),
standoff = 0),
range = list(-0.1, 1.1),
showline = T,
showgrid = F,
linewidth = 1,
linecolor = "white",
tickfont = list(size = 10)),
font = list(family = "Arial Black",
color = "white"),
paper_bgcolor = "#060606",
plot_bgcolor = "#060606",
margin = list(t = 50, r = 30),
showlegend = F)
} else {
# Making the plot
output_plot <- plot_ly(data = pollen_df,
x = ~accession_id,
y = ~burst_2h_26C_adjusted_mean,
type = "scatter",
mode = "markers",
marker = list(size = 5, color = "#ffffff"),
error_y = list(array = ~burst_2h_26C_adjusted_se,
width = 1,
color = "white"))
# Adding aesthetics
output_plot <- output_plot %>% layout(title = list(text = "Adjusted burst % at 2 hours, 26 ºC",
font = list(size = 22)),
xaxis = list(title = F,
showline = T,
showticklabels = F,
linewidth = 1,
linecolor = "white"),
yaxis = list(title = list(text = "Percentage",
font = list(size = 16),
standoff = 0),
range = list(-0.1, 1.1),
showline = T,
showgrid = F,
linewidth = 1,
linecolor = "white",
tickfont = list(size = 10)),
font = list(family = "Arial Black",
color = "white"),
paper_bgcolor = "#060606",
plot_bgcolor = "#060606",
margin = list(t = 50, r = 30))
}
} else if (plot_type == "34C") {
pollen_df$accession_id <- reorder(pollen_df$accession_id, pollen_df$burst_2h_34C_adjusted_mean)
if ((length(row_selection) && any(pollen_df$accession_id %in% accessions$name_CW[row_selection]))) {
# Making new column for if it's selected or not
selected_accessions <- accessions$name_CW[row_selection]
pollen_df$row_selected <- NA
pollen_df$row_selected[pollen_df$accession_id %in% selected_accessions] <- "selected"
pollen_df$row_selected[is.na(pollen_df$row_selected)] <- "not_selected"
# Plot for 'not_selected'
output_plot <- plot_ly(data = subset(pollen_df, row_selected == "not_selected"),
x = ~accession_id,
y = ~burst_2h_34C_adjusted_mean,
type = "scatter",
mode = "markers",
marker = list(size = 5, color = "white"),
error_y = list(array = ~burst_2h_34C_adjusted_se, width = 1, color = "white"))
# Add plot for 'selected'
output_plot <- output_plot %>%
add_trace(data = subset(pollen_df, row_selected == "selected"),
x = ~accession_id,
y = ~burst_2h_34C_adjusted_mean,
type = "scatter",
mode = "markers",
marker = list(size = 5, color = "magenta"),
error_y = list(array = ~burst_2h_34C_adjusted_se, width = 1, color = "magenta"))
# Adding aesthetics
output_plot <- output_plot %>% layout(title = list(text = "Adjusted burst % at 2 hours, 34 ºC",
font = list(size = 22)),
xaxis = list(title = F,
showline = T,
showticklabels = F,
linewidth = 1,
linecolor = "white"),
yaxis = list(title = list(text = "Percentage",
font = list(size = 16),
standoff = 0),
range = list(-0.1, 1.1),
showline = T,
showgrid = F,
linewidth = 1,
linecolor = "white",
tickfont = list(size = 10)),
font = list(family = "Arial Black",
color = "white"),
paper_bgcolor = "#060606",
plot_bgcolor = "#060606",
margin = list(t = 50, r = 30),
showlegend = F)
} else {
# Making the plot
output_plot <- plot_ly(data = pollen_df,
x = ~accession_id,
y = ~burst_2h_34C_adjusted_mean,
type = "scatter",
mode = "markers",
marker = list(size = 5, color = "#ffffff"),
error_y = list(array = ~burst_2h_34C_adjusted_se,
width = 1,
color = "white"))
# Adding aesthetics
output_plot <- output_plot %>% layout(title = list(text = "Adjusted burst % at 2 hours, 34 ºC",
font = list(size = 22)),
xaxis = list(title = F,
showline = T,
showticklabels = F,
linewidth = 1,
linecolor = "white"),
yaxis = list(title = list(text = "Percentage",
font = list(size = 16),
standoff = 0),
range = list(-0.1, 1.1),
showline = T,
showgrid = F,
linewidth = 1,
linecolor = "white",
tickfont = list(size = 10)),
font = list(family = "Arial Black",
color = "white"),
paper_bgcolor = "#060606",
plot_bgcolor = "#060606",
margin = list(t = 50, r = 30))
}
} else { # Burst increase plot
pollen_df$accession_id <- reorder(pollen_df$accession_id, pollen_df$adjusted_bursting_increase)
if ((length(row_selection) && any(pollen_df$accession_id %in% accessions$name_CW[row_selection]))) {
# Making new column for if it's selected or not
selected_accessions <- accessions$name_CW[row_selection]
pollen_df$row_selected <- NA
pollen_df$row_selected[pollen_df$accession_id %in% selected_accessions] <- "selected"
pollen_df$row_selected[is.na(pollen_df$row_selected)] <- "not_selected"
# Plot for 'not_selected'
output_plot <- plot_ly(data = subset(pollen_df, row_selected == "not_selected"),
x = ~accession_id,
y = ~adjusted_bursting_increase,
type = "scatter",
mode = "markers",
marker = list(size = 5, color = "white"),
error_y = list(array = ~adjusted_bursting_increase_se, width = 1, color = "white"))
# Add plot for 'selected'
output_plot <- output_plot %>%
add_trace(data = subset(pollen_df, row_selected == "selected"),
x = ~accession_id,
y = ~adjusted_bursting_increase,
type = "scatter",
mode = "markers",
marker = list(size = 5, color = "magenta"),
error_y = list(array = ~adjusted_bursting_increase_se, width = 1, color = "magenta"))
# Adding aesthetics
output_plot <- output_plot %>% layout(title = list(text = "Adjusted burst % increase at 2 hours",
font = list(size = 22)),
xaxis = list(title = F,
showline = T,
showticklabels = F,
linewidth = 1,
linecolor = "white"),
yaxis = list(title = list(text = "Percentage",
font = list(size = 16),
standoff = 0),
range = list(-0.1, 1.1),
showline = T,
showgrid = F,
linewidth = 1,
linecolor = "white",
tickfont = list(size = 10)),
font = list(family = "Arial Black",
color = "white"),
paper_bgcolor = "#060606",
plot_bgcolor = "#060606",
margin = list(t = 50, r = 30),
showlegend = F)
} else {
# Making the plot
output_plot <- plot_ly(data = pollen_df,
x = ~accession_id,
y = ~adjusted_bursting_increase,
type = "scatter",
mode = "markers",
marker = list(size = 5, color = "#ffffff"),
error_y = list(array = ~adjusted_bursting_increase_se,
width = 1,
color = "white"))
# Adding aesthetics
output_plot <- output_plot %>% layout(title = list(text = "Adjusted burst % increase at 2 hours",
font = list(size = 22)),
xaxis = list(title = F,
showline = T,
showticklabels = F,
linewidth = 1,
linecolor = "white"),
yaxis = list(title = list(text = "Percentage",
font = list(size = 16),
standoff = 0),
range = list(-0.1, 1.1),
showline = T,
showgrid = F,
linewidth = 1,
linecolor = "white",
tickfont = list(size = 10)),
font = list(family = "Arial Black",
color = "white"),
paper_bgcolor = "#060606",
plot_bgcolor = "#060606",
margin = list(t = 50, r = 30))
}
}
# Removing toolbar
output_plot <- output_plot %>% config(displayModeBar = F)
return(output_plot)
}
make_germ_plot <- function(plot_type, pollen_df, row_selection) {
pollen_df$accession_id <- as.factor(pollen_df$accession_id)
if (plot_type == "26C") {
pollen_df$accession_id <- reorder(pollen_df$accession_id, pollen_df$germ_2h_26C_adjusted_mean)
if ((length(row_selection) && any(pollen_df$accession_id %in% accessions$name_CW[row_selection]))) {
# Making new column for if it's selected or not
selected_accessions <- accessions$name_CW[row_selection]
pollen_df$row_selected <- NA
pollen_df$row_selected[pollen_df$accession_id %in% selected_accessions] <- "selected"
pollen_df$row_selected[is.na(pollen_df$row_selected)] <- "not_selected"
# Plot for 'not_selected'
output_plot <- plot_ly(data = subset(pollen_df, row_selected == "not_selected"),
x = ~accession_id,
y = ~germ_2h_26C_adjusted_mean,
type = "scatter",
mode = "markers",
marker = list(size = 5, color = "white"),
error_y = list(array = ~germ_2h_26C_adjusted_se, width = 1, color = "white"))
# Add plot for 'selected'
output_plot <- output_plot %>%
add_trace(data = subset(pollen_df, row_selected == "selected"),
x = ~accession_id,
y = ~germ_2h_26C_adjusted_mean,
type = "scatter",
mode = "markers",
marker = list(size = 5, color = "magenta"),
error_y = list(array = ~germ_2h_26C_adjusted_se, width = 1, color = "magenta"))
# Adding aesthetics
output_plot <- output_plot %>% layout(title = list(text = "Adjusted germinated % at 2 hours, 26 ºC",
font = list(size = 22)),
xaxis = list(title = F,
showline = T,
showticklabels = F,
linewidth = 1,
linecolor = "white"),
yaxis = list(title = list(text = "Percentage",
font = list(size = 16),
standoff = 0),
range = list(-0.1, 1.1),
showline = T,
showgrid = F,
linewidth = 1,
linecolor = "white",
tickfont = list(size = 10)),
font = list(family = "Arial Black",
color = "white"),
paper_bgcolor = "#060606",
plot_bgcolor = "#060606",
margin = list(t = 50, r = 30),
showlegend = F)
} else {
# Making the plot
output_plot <- plot_ly(data = pollen_df,
x = ~accession_id,
y = ~germ_2h_26C_adjusted_mean,
type = "scatter",
mode = "markers",
marker = list(size = 5, color = "#ffffff"),
error_y = list(array = ~germ_2h_26C_adjusted_se,
width = 1,
color = "white"))
# Adding aesthetics
output_plot <- output_plot %>% layout(title = list(text = "Adjusted germinated % at 2 hours, 26 ºC",
font = list(size = 22)),
xaxis = list(title = F,
showline = T,
showticklabels = F,
linewidth = 1,
linecolor = "white"),
yaxis = list(title = list(text = "Percentage",
font = list(size = 16),
standoff = 0),
range = list(-0.1, 1.1),
showline = T,
showgrid = F,
linewidth = 1,
linecolor = "white",
tickfont = list(size = 10)),
font = list(family = "Arial Black",
color = "white"),
paper_bgcolor = "#060606",
plot_bgcolor = "#060606",
margin = list(t = 50, r = 30))
}
} else if (plot_type == "34C") {
pollen_df$accession_id <- reorder(pollen_df$accession_id, pollen_df$germ_2h_34C_adjusted_mean)
if ((length(row_selection) && any(pollen_df$accession_id %in% accessions$name_CW[row_selection]))) {
# Making new column for if it's selected or not
selected_accessions <- accessions$name_CW[row_selection]
pollen_df$row_selected <- NA
pollen_df$row_selected[pollen_df$accession_id %in% selected_accessions] <- "selected"
pollen_df$row_selected[is.na(pollen_df$row_selected)] <- "not_selected"
# Plot for 'not_selected'
output_plot <- plot_ly(data = subset(pollen_df, row_selected == "not_selected"),
x = ~accession_id,
y = ~germ_2h_34C_adjusted_mean,
type = "scatter",
mode = "markers",
marker = list(size = 5, color = "white"),
error_y = list(array = ~germ_2h_34C_adjusted_se, width = 1, color = "white"))
# Add plot for 'selected'
output_plot <- output_plot %>%
add_trace(data = subset(pollen_df, row_selected == "selected"),
x = ~accession_id,
y = ~germ_2h_34C_adjusted_mean,
type = "scatter",
mode = "markers",
marker = list(size = 5, color = "magenta"),
error_y = list(array = ~germ_2h_34C_adjusted_se, width = 1, color = "magenta"))
# Adding aesthetics
output_plot <- output_plot %>% layout(title = list(text = "Adjusted germinated % at 2 hours, 34 ºC",
font = list(size = 22)),
xaxis = list(title = F,
showline = T,
showticklabels = F,
linewidth = 1,
linecolor = "white"),
yaxis = list(title = list(text = "Percentage",
font = list(size = 16),
standoff = 0),
range = list(-0.1, 1.1),
showline = T,
showgrid = F,
linewidth = 1,
linecolor = "white",
tickfont = list(size = 10)),
font = list(family = "Arial Black",
color = "white"),
paper_bgcolor = "#060606",
plot_bgcolor = "#060606",
margin = list(t = 50, r = 30),
showlegend = F)
} else {
# Making the plot
output_plot <- plot_ly(data = pollen_df,
x = ~accession_id,
y = ~germ_2h_34C_adjusted_mean,
type = "scatter",
mode = "markers",
marker = list(size = 5, color = "#ffffff"),
error_y = list(array = ~germ_2h_34C_adjusted_se,
width = 1,
color = "white"))
# Adding aesthetics
output_plot <- output_plot %>% layout(title = list(text = "Adjusted germinated % at 2 hours, 34 ºC",
font = list(size = 22)),
xaxis = list(title = F,
showline = T,
showticklabels = F,
linewidth = 1,
linecolor = "white"),
yaxis = list(title = list(text = "Percentage",
font = list(size = 16),
standoff = 0),
range = list(-0.1, 1.1),
showline = T,
showgrid = F,
linewidth = 1,
linecolor = "white",
tickfont = list(size = 10)),
font = list(family = "Arial Black",
color = "white"),
paper_bgcolor = "#060606",
plot_bgcolor = "#060606",
margin = list(t = 50, r = 30))
}
} else { # Germinated decrease plot
pollen_df$accession_id <- reorder(pollen_df$accession_id, pollen_df$adjusted_germ_decrease)
if ((length(row_selection) && any(pollen_df$accession_id %in% accessions$name_CW[row_selection]))) {
# Making new column for if it's selected or not
selected_accessions <- accessions$name_CW[row_selection]
pollen_df$row_selected <- NA
pollen_df$row_selected[pollen_df$accession_id %in% selected_accessions] <- "selected"
pollen_df$row_selected[is.na(pollen_df$row_selected)] <- "not_selected"
# Plot for 'not_selected'
output_plot <- plot_ly(data = subset(pollen_df, row_selected == "not_selected"),
x = ~accession_id,
y = ~adjusted_germ_decrease,
type = "scatter",
mode = "markers",
marker = list(size = 5, color = "white"),
error_y = list(array = ~adjusted_germ_decrease_se, width = 1, color = "white"))
# Add plot for 'selected'
output_plot <- output_plot %>%
add_trace(data = subset(pollen_df, row_selected == "selected"),
x = ~accession_id,
y = ~adjusted_germ_decrease,
type = "scatter",
mode = "markers",
marker = list(size = 5, color = "magenta"),
error_y = list(array = ~adjusted_germ_decrease_se, width = 1, color = "magenta"))
# Adding aesthetics
output_plot <- output_plot %>% layout(title = list(text = "Adjusted germinated % decrease at 2 hours",
font = list(size = 22)),
xaxis = list(title = F,
showline = T,
showticklabels = F,
linewidth = 1,
linecolor = "white"),
yaxis = list(title = list(text = "Percentage",
font = list(size = 16),
standoff = 0),
range = list(-0.5, 0.5),
showline = T,
showgrid = F,
linewidth = 1,
linecolor = "white",
tickfont = list(size = 10)),
font = list(family = "Arial Black",
color = "white"),
paper_bgcolor = "#060606",
plot_bgcolor = "#060606",
margin = list(t = 50, r = 30),
showlegend = F)
} else {
# Making the plot
output_plot <- plot_ly(data = pollen_df,
x = ~accession_id,
y = ~adjusted_germ_decrease,
type = "scatter",
mode = "markers",
marker = list(size = 5, color = "#ffffff"),
error_y = list(array = ~adjusted_germ_decrease_se,
width = 1,
color = "white"))
# Adding aesthetics
output_plot <- output_plot %>% layout(title = list(text = "Adjusted germinated % decrease at 2 hours",
font = list(size = 22)),
xaxis = list(title = F,
showline = T,
showticklabels = F,
linewidth = 1,
linecolor = "white"),
yaxis = list(title = list(text = "Percentage",
font = list(size = 16),
standoff = 0),
range = list(-0.5, 0.5),
showline = T,
showgrid = F,
linewidth = 1,
linecolor = "white",
tickfont = list(size = 10)),
font = list(family = "Arial Black",
color = "white"),
paper_bgcolor = "#060606",
plot_bgcolor = "#060606",
margin = list(t = 50, r = 30))
}
}
# Removing toolbar
output_plot <- output_plot %>% config(displayModeBar = F)
return(output_plot)
}
make_integral_plot <- function(plot_type, pollen_df, row_selection) {
pollen_df$accession_id <- as.factor(pollen_df$accession_id)
# Getting rid of the NAs which are breaking the error bars
pollen_df <- pollen_df[!is.na(pollen_df$burst_integral_26C_adjusted_mean), ]
if (plot_type == "26C") {
pollen_df$accession_id <- reorder(pollen_df$accession_id, pollen_df$burst_integral_26C_adjusted_mean)
if ((length(row_selection) && any(pollen_df$accession_id %in% accessions$name_CW[row_selection]))) {
# Making new column for if it's selected or not
selected_accessions <- accessions$name_CW[row_selection]
pollen_df$row_selected <- NA
pollen_df$row_selected[pollen_df$accession_id %in% selected_accessions] <- "selected"
pollen_df$row_selected[is.na(pollen_df$row_selected)] <- "not_selected"
# Plot for 'not_selected'
output_plot <- plot_ly(data = subset(pollen_df, row_selected == "not_selected"),
x = ~accession_id,
y = ~burst_integral_26C_adjusted_mean,
type = "scatter",
mode = "markers",
marker = list(size = 5, color = "white"),
error_y = list(array = ~burst_integral_26C_adjusted_se, width = 1, color = "white"))
# Add plot for 'selected'
output_plot <- output_plot %>%
add_trace(data = subset(pollen_df, row_selected == "selected"),
x = ~accession_id,
y = ~burst_integral_26C_adjusted_mean,
type = "scatter",
mode = "markers",
marker = list(size = 5, color = "magenta"),
error_y = list(array = ~burst_integral_26C_adjusted_se, width = 1, color = "magenta"))
# Adding aesthetics
output_plot <- output_plot %>% layout(title = list(text = "Adjusted burst integral, 26 ºC",
font = list(size = 22)),
xaxis = list(title = F,
showline = T,
showticklabels = F,
linewidth = 1,
linecolor = "white"),
yaxis = list(title = list(text = "Integral",
font = list(size = 16),
standoff = 0),
range = list(-3.5, 60),
showline = T,
showgrid = F,
linewidth = 1,
linecolor = "white",
tickfont = list(size = 10)),
font = list(family = "Arial Black",
color = "white"),
paper_bgcolor = "#060606",
plot_bgcolor = "#060606",
margin = list(t = 50, r = 30),
showlegend = F)
} else {
# Making the plot
output_plot <- plot_ly(data = pollen_df,
x = ~accession_id,
y = ~burst_integral_26C_adjusted_mean,
type = "scatter",
mode = "markers",
marker = list(size = 5, color = "#ffffff"),
error_y = list(array = ~burst_integral_26C_adjusted_se,
width = 1,
color = "white"))
# Adding aesthetics
output_plot <- output_plot %>% layout(title = list(text = "Adjusted burst integral, 26 ºC",
font = list(size = 22)),
xaxis = list(title = F,
showline = T,
showticklabels = F,
linewidth = 1,
linecolor = "white"),
yaxis = list(title = list(text = "Integral",
font = list(size = 16),
standoff = 0),
range = list(-3.5, 60),
showline = T,
showgrid = F,
linewidth = 1,
linecolor = "white",
tickfont = list(size = 10)),
font = list(family = "Arial Black",
color = "white"),
paper_bgcolor = "#060606",
plot_bgcolor = "#060606",
margin = list(t = 50, r = 30))
}
} else if (plot_type == "34C") {
pollen_df$accession_id <- reorder(pollen_df$accession_id, pollen_df$burst_integral_34C_adjusted_mean)
if ((length(row_selection) && any(pollen_df$accession_id %in% accessions$name_CW[row_selection]))) {
# Making new column for if it's selected or not
selected_accessions <- accessions$name_CW[row_selection]
pollen_df$row_selected <- NA
pollen_df$row_selected[pollen_df$accession_id %in% selected_accessions] <- "selected"
pollen_df$row_selected[is.na(pollen_df$row_selected)] <- "not_selected"
# Plot for 'not_selected'
output_plot <- plot_ly(data = subset(pollen_df, row_selected == "not_selected"),
x = ~accession_id,
y = ~burst_integral_34C_adjusted_mean,
type = "scatter",
mode = "markers",
marker = list(size = 5, color = "white"),
error_y = list(array = ~burst_integral_34C_adjusted_se, width = 1, color = "white"))
# Add plot for 'selected'
output_plot <- output_plot %>%
add_trace(data = subset(pollen_df, row_selected == "selected"),
x = ~accession_id,
y = ~burst_integral_34C_adjusted_mean,
type = "scatter",
mode = "markers",
marker = list(size = 5, color = "magenta"),
error_y = list(array = ~burst_integral_34C_adjusted_se, width = 1, color = "magenta"))
# Adding aesthetics
output_plot <- output_plot %>% layout(title = list(text = "Adjusted burst integral, 34 ºC",
font = list(size = 22)),
xaxis = list(title = F,
showline = T,
showticklabels = F,
linewidth = 1,
linecolor = "white"),
yaxis = list(title = list(text = "Integral",
font = list(size = 16),
standoff = 0),
range = list(-3.5, 60),
showline = T,
showgrid = F,
linewidth = 1,
linecolor = "white",
tickfont = list(size = 10)),
font = list(family = "Arial Black",
color = "white"),
paper_bgcolor = "#060606",
plot_bgcolor = "#060606",
margin = list(t = 50, r = 30),
showlegend = F)