inst/shiny/v1.1/trajectory/server.R
In romanhaa/cerebroApp: Interactive visualization of scRNA-seq data with Cerebro
##----------------------------------------------------------------------------##
## Tab: Trajectory.
##----------------------------------------------------------------------------##
# what needs to be done
# - let user show gene expression as well? probably more complicated
# UI element: display results or alternative text
output[["trajectory_UI"]] <- renderUI({
if ( length(sample_data()$trajectory$monocle2) > 0 ) {
tagList(
fluidRow(
column(width = 3, offset = 0, style = "padding: 0px;",
cerebroBox(
title = "Input parameters",
tagList(
uiOutput("trajectory_input")
)
)
),
column(width = 9, offset = 0, style = "padding: 0px;",
cerebroBox(
title = tagList(
boxTitle("Trajectory"),
actionButton(
inputId = "trajectory_projection_info",
label = "info",
icon = NULL,
class = "btn-xs",
title = "Show additional information for this panel.",
style = "margin-right: 5px"
),
actionButton(
inputId = "trajectory_projection_export",
label = "export to PDF",
icon = NULL,
class = "btn-xs",
title = "Export trajectory to PDF file."
)
),
plotly::plotlyOutput(
"trajectory_projection",
width = "auto",
height = "85vh"
)
)
)
),
fluidRow(
cerebroBox(
title = tagList(
boxTitle("Distribution along pseudotime"),
actionButton(
inputId = "trajectory_density_info",
label = "info",
icon = NULL,
class = "btn-xs",
title = "Show additional information for this panel.",
style = "margin-right: 5px"
)
),
plotly::plotlyOutput("trajectory_density_plot")
)
),
fluidRow(
cerebroBox(
title = tagList(
boxTitle("Number of cells by state"),
actionButton(
inputId = "trajectory_cells_by_state_info",
label = "info",
icon = NULL,
class = "btn-xs",
title = "Show additional information for this panel.",
style = "margin-right: 5px"
)
),
DT::dataTableOutput("trajectory_number_of_cells_by_state_table")
)
),
fluidRow(
cerebroBox(
title = tagList(
boxTitle("States by sample"),
actionButton(
inputId = "states_by_sample_info",
label = "info",
icon = NULL,
class = "btn-xs",
title = "Show additional information for this panel.",
style = "margin-right: 5px"
)
),
plotly::plotlyOutput("states_by_sample_plot")
)
),
fluidRow(
cerebroBox(
title = tagList(
boxTitle("States by cluster"),
actionButton(
inputId = "states_by_cluster_info",
label = "info",
icon = NULL,
class = "btn-xs",
title = "Show additional information for this panel.",
style = "margin-right: 5px"
)
),
plotly::plotlyOutput("states_by_cluster_plot")
)
),
fluidRow(
cerebroBox(
title = tagList(
boxTitle("States by cell cycle (Seurat)"),
actionButton(
inputId = "states_by_cell_cycle_seurat_info",
label = "info",
icon = NULL,
class = "btn-xs",
title = "Show additional information for this panel.",
style = "margin-right: 5px"
)
),
shiny::uiOutput("states_by_cell_cycle_seurat_UI")
)
),
fluidRow(
cerebroBox(
title = tagList(
boxTitle("Number of transcripts by state"),
actionButton(
inputId = "states_nUMI_info",
label = "info",
icon = NULL,
class = "btn-xs",
title = "Show additional information for this panel.",
style = "margin-right: 5px"
)
),
plotly::plotlyOutput("states_nUMI_plot")
)
),
fluidRow(
cerebroBox(
title = tagList(
boxTitle("Number of expressed genes by state"),
actionButton(
inputId = "states_nGene_info",
label = "info",
icon = NULL,
class = "btn-xs",
title = "Show additional information for this panel.",
style = "margin-right: 5px"
)
),
plotly::plotlyOutput("states_nGene_plot")
)
)
)
} else {
cerebroBox(title = "Trajectory", textOutput("trajectory_missing"))
}
})
# alternative text
output[["trajectory_missing"]] <- renderText({
"No trajectories available to display."
})
##----------------------------------------------------------------------------##
## UI elements.
##----------------------------------------------------------------------------##
output[["trajectory_input"]] <- renderUI({
tagList(
selectInput(
"trajectory_to_display",
label = "Trajectory",
choices = names(sample_data()$trajectory$monocle2)
),
shinyWidgets::pickerInput(
"trajectory_samples_to_display",
label = "Samples to display",
choices = sample_data()$sample_names,
selected = sample_data()$sample_names,
options = list("actions-box" = TRUE),
multiple = TRUE
),
shinyWidgets::pickerInput(
"trajectory_clusters_to_display",
label = "Clusters to display",
choices = sample_data()$cluster_names,
selected = sample_data()$cluster_names,
options = list("actions-box" = TRUE),
multiple = TRUE
),
sliderInput(
"trajectory_percentage_cells_to_show",
label = "Show % of cells",
min = scatter_plot_percentage_cells_to_show[["min"]],
max = scatter_plot_percentage_cells_to_show[["max"]],
step = scatter_plot_percentage_cells_to_show[["step"]],
value = scatter_plot_percentage_cells_to_show[["default"]]
),
selectInput(
"trajectory_dot_color",
label = "Color cells by",
choices = c("state","pseudotime",names(sample_data()$cells)[! names(sample_data()$cells) %in% c("cell_barcode")])
),
sliderInput(
"trajectory_dot_size",
label = "Dot size",
min = scatter_plot_dot_size[["min"]],
max = scatter_plot_dot_size[["max"]],
step = scatter_plot_dot_size[["step"]],
value = scatter_plot_dot_size[["default"]]
),
sliderInput(
"trajectory_dot_opacity",
label = "Dot opacity",
min = scatter_plot_dot_opacity[["min"]],
max = scatter_plot_dot_opacity[["max"]],
step = scatter_plot_dot_opacity[["step"]],
value = scatter_plot_dot_opacity[["default"]]
)
)
})
##----------------------------------------------------------------------------##
## Projection.
##----------------------------------------------------------------------------##
output[["trajectory_projection"]] <- plotly::renderPlotly({
# don't do anything before these inputs are selected
req(
input[["trajectory_to_display"]],
input[["trajectory_samples_to_display"]],
input[["trajectory_clusters_to_display"]],
input[["trajectory_percentage_cells_to_show"]],
input[["trajectory_dot_color"]],
input[["trajectory_dot_size"]],
input[["trajectory_dot_opacity"]]
)
trajectory_to_display <- input[["trajectory_to_display"]]
samples_to_display <- input[["trajectory_samples_to_display"]]
clusters_to_display <- input[["trajectory_clusters_to_display"]]
cells_to_display <- which(
(sample_data()$cells$sample %in% samples_to_display) &
(sample_data()$cells$cluster %in% clusters_to_display)
)
# randomly remove cells
if ( input[["trajectory_percentage_cells_to_show"]] < 100 ) {
number_of_cells_to_plot <- ceiling(
input[["trajectory_percentage_cells_to_show"]] / 100 * length(cells_to_display)
)
cells_to_display <- cells_to_display[ sample(1:length(cells_to_display), number_of_cells_to_plot) ]
}
# extract cells to plot
to_plot <- cbind(
sample_data()$trajectory$monocle2[[ trajectory_to_display ]][["meta"]][ cells_to_display , ],
sample_data()$cells[ cells_to_display , ]
) %>%
dplyr::filter(!is.na(pseudotime))
to_plot <- to_plot[ sample(1:nrow(to_plot)) , ]
color_variable <- input[["trajectory_dot_color"]]
# convert edges of trajectory into list format to plot with plotly
trajectory_edges <- sample_data()$trajectory$monocle2[[trajectory_to_display]][["edges"]]
trajectory_lines <- list()
for (i in 1:nrow(trajectory_edges) ) {
line = list(
type = "line",
line = list(color = "black"),
xref = "x",
yref = "y",
x0 = trajectory_edges$source_dim_1[i],
y0 = trajectory_edges$source_dim_2[i],
x1 = trajectory_edges$target_dim_1[i],
y1 = trajectory_edges$target_dim_2[i]
)
trajectory_lines <- c(trajectory_lines, list(line))
}
if ( is.factor(to_plot[[ color_variable ]]) || is.character(to_plot[[ color_variable ]]) ) {
cols <- if ( color_variable == "sample" ) {
if ( !is.null(sample_data()$samples$colors) ) {
sample_data()$samples$colors
} else {
colors
}
} else if ( color_variable == "cluster" ) {
if ( !is.null(sample_data()$clusters$colors) ) {
sample_data()$clusters$colors
} else {
colors
}
} else if ( color_variable %in% c("cell_cycle_seurat","cell_cycle_cyclone") ) {
cell_cycle_colorset
} else if ( is.factor(to_plot[[ color_variable ]]) ) {
setNames(colors[1:length(levels(to_plot[[ color_variable ]]))], levels(to_plot[[ color_variable ]]))
} else {
colors
}
plot <- plotly::plot_ly(
to_plot,
x = ~DR_1,
y = ~DR_2,
color = ~to_plot[[ color_variable ]],
colors = cols,
type = "scatter",
mode = "markers",
marker = list(
opacity = input[["trajectory_dot_opacity"]],
line = list(
color = "rgb(196,196,196)",
width = 1
),
size = input[["trajectory_dot_size"]]
),
hoverinfo = "text",
text = ~paste(
"<b>Cell</b>: ", to_plot[ , "cell_barcode" ], "<br>",
"<b>Sample</b>: ", to_plot[ , "sample" ], "<br>",
"<b>Cluster</b>: ", to_plot[ , "cluster" ], "<br>",
"<b>Transcripts</b>: ", formatC(to_plot[ , "nUMI" ], format = "f", big.mark = ",", digits = 0), "<br>",
"<b>Expressed genes</b>: ", formatC(to_plot[ , "nGene" ], format = "f", big.mark = ",", digits = 0), "<br>",
"<b>State</b>: ", to_plot[ , "state" ], "<br>",
"<b>Pseudotime</b>: ", round(to_plot[ , "pseudotime" ], 3)
)
) %>%
plotly::layout(
shapes = trajectory_lines,
xaxis = list(
mirror = TRUE,
showline = TRUE,
zeroline = FALSE,
range = range(to_plot$DR_1) * 1.1
),
yaxis = list(
mirror = TRUE,
showline = TRUE,
zeroline = FALSE,
range = range(to_plot$DR_2) * 1.1
),
hoverlabel = list(font = list(size = 11))
)
if ( preferences[["use_webgl"]] == TRUE ) {
plot %>% plotly::toWebGL()
} else {
plot
}
} else {
plot <- plotly::plot_ly(
data = to_plot,
x = ~DR_1,
y = ~DR_2,
type = "scatter",
mode = "markers",
marker = list(
colorbar = list(
title = colnames(to_plot)[which(colnames(to_plot) == color_variable)]
),
color = ~to_plot[[ color_variable ]],
opacity = input[["trajectory_dot_opacity"]],
colorscale = "YlGnBu",
reversescale = TRUE,
line = list(
color = "rgb(196,196,196)",
width = 1
),
size = input[["trajectory_dot_size"]]
),
hoverinfo = "text",
text = ~paste(
"<b>Cell</b>: ", to_plot[ , "cell_barcode" ], "<br>",
"<b>Sample</b>: ", to_plot[ , "sample" ], "<br>",
"<b>Cluster</b>: ", to_plot[ , "cluster" ], "<br>",
"<b>Transcripts</b>: ", formatC(to_plot[ , "nUMI" ], format = "f", big.mark = ",", digits = 0), "<br>",
"<b>Expressed genes</b>: ", formatC(to_plot[ , "nGene" ], format = "f", big.mark = ",", digits = 0), "<br>",
"<b>State</b>: ", to_plot[ , "state" ], "<br>",
"<b>Pseudotime</b>: ", round(to_plot[ , "pseudotime" ], 3)
)
) %>%
plotly::layout(
shapes = trajectory_lines,
xaxis = list(
title = colnames(to_plot)[1],
mirror = TRUE,
showline = TRUE,
zeroline = FALSE,
range = range(to_plot$DR_1) * 1.1
),
yaxis = list(
title = colnames(to_plot)[2],
mirror = TRUE,
showline = TRUE,
zeroline = FALSE,
range = range(to_plot$DR_2) * 1.1
),
hoverlabel = list(font = list(size = 11))
)
if ( preferences$use_webgl == TRUE ) {
plotly::toWebGL(plot)
} else {
plot
}
}
})
##----------------------------------------------------------------------------##
## Info button.
##----------------------------------------------------------------------------##
observeEvent(input[["trajectory_projection_info"]], {
showModal(
modalDialog(
trajectory_projection_info[["text"]],
title = trajectory_projection_info[["title"]],
easyClose = TRUE,
footer = NULL
)
)
})
##----------------------------------------------------------------------------##
## Export projection.
##----------------------------------------------------------------------------##
observeEvent(input[["trajectory_projection_export"]], {
req(
input[["trajectory_to_display"]],
input[["trajectory_samples_to_display"]],
input[["trajectory_clusters_to_display"]],
input[["trajectory_percentage_cells_to_show"]],
input[["trajectory_dot_color"]],
input[["trajectory_dot_size"]],
input[["trajectory_dot_opacity"]]
)
library("ggplot2")
if ( exists("plot_export_path") ) {
trajectory_to_display <- input[["trajectory_to_display"]]
samples_to_display <- input[["trajectory_samples_to_display"]]
clusters_to_display <- input[["trajectory_clusters_to_display"]]
cells_to_display <- which(
(sample_data()$cells$sample %in% samples_to_display) &
(sample_data()$cells$cluster %in% clusters_to_display)
)
to_plot <- cbind(
sample_data()$trajectory$monocle2[[ trajectory_to_display ]][[ "meta" ]][ cells_to_display , ],
sample_data()$cells[ cells_to_display , ]
) %>%
dplyr::filter(!is.na(pseudotime))
to_plot <- to_plot[ sample(1:nrow(to_plot)) , ]
color_variable <- input[["trajectory_dot_color"]]
if ( is.factor(to_plot[[ color_variable ]]) || is.character(to_plot[[ color_variable ]]) ) {
if ( color_variable == "sample" ) {
cols <- sample_data()$samples$colors
} else if ( color_variable == "cluster" ) {
cols <- sample_data()$clusters$colors
} else if ( color_variable %in% c("cell_cycle_seurat","cell_cycle_cyclone") ) {
cols <- cell_cycle_colorset
} else if ( is.factor(to_plot[ , color_variable ]) ) {
cols <- setNames(colors[1:length(levels(to_plot[ , color_variable ]))], levels(to_plot[ , color_variable ]))
} else {
cols <- colors
}
p <- ggplot() +
geom_point(
data = to_plot,
aes_string(x = colnames(to_plot)[1], y = colnames(to_plot)[2], fill = color_variable),
shape = 21,
size = input[["trajectory_dot_size"]]/3,
stroke = 0.2,
color = "#c4c4c4",
alpha = input[["trajectory_dot_opacity"]]
) +
geom_segment(
data = sample_data()$trajectory$monocle2[[ trajectory_to_display ]]$edges,
aes(source_dim_1, source_dim_2, xend = target_dim_1, yend = target_dim_2),
size = 0.75, linetype = "solid", na.rm = TRUE
) +
scale_fill_manual(values = cols) +
theme_bw()
} else {
p <- ggplot() +
geom_point(
data = to_plot,
aes_string(x = colnames(to_plot)[1], y = colnames(to_plot)[2], fill = color_variable),
shape = 21,
size = input[["trajectory_dot_size"]]/3,
stroke = 0.2,
color = "#c4c4c4",
alpha = input[["trajectory_dot_opacity"]]
) +
geom_segment(
data = sample_data()$trajectory$monocle2[[ trajectory_to_display ]]$edges,
aes(source_dim_1, source_dim_2, xend = target_dim_1, yend = target_dim_2),
size = 0.75, linetype = "solid", na.rm = TRUE
) +
scale_fill_distiller(
palette = "YlGnBu",
direction = 1,
guide = guide_colorbar(frame.colour = "black", ticks.colour = "black")
) +
theme_bw()
}
out_filename <- paste0(
plot_export_path, "Cerebro_",
gsub(
sample_data()$experiment$experiment_name,
pattern = " ", replacement = "_"
),
"_trajectory_", trajectory_to_display, "_by_",
gsub(
color_variable,
pattern = "\\.", replacement = "_"
),
".pdf"
)
pdf(NULL)
ggsave(out_filename, p, height = 8, width = 11)
if ( file.exists(out_filename) ) {
shinyWidgets::sendSweetAlert(
session = session,
title = "Success!",
text = paste0("Plot saved successfully as: ", out_filename),
type = "success"
)
} else {
shinyWidgets::sendSweetAlert(
session = session,
title = "Error!",
text = "Sorry, it seems something went wrong...",
type = "error"
)
}
} else {
shinyWidgets::sendSweetAlert(
session = session,
title = "Error!",
text = "Sorry, we couldn't find a place to store the figure. Please submit an issue on GitHub @ https://github.com/romanhaa/cerebroApp",
type = "error"
)
}
})
##----------------------------------------------------------------------------##
## Distribution along pseudotime.
##----------------------------------------------------------------------------##
output[["trajectory_density_plot"]] <- plotly::renderPlotly({
# don't do anything before these inputs are selected
req(
input[["trajectory_to_display"]],
input[["trajectory_samples_to_display"]],
input[["trajectory_clusters_to_display"]],
input[["trajectory_dot_color"]]
)
trajectory_to_display <- input[["trajectory_to_display"]]
samples_to_display <- input[["trajectory_samples_to_display"]]
clusters_to_display <- input[["trajectory_clusters_to_display"]]
cells_to_display <- which(
(sample_data()$cells$sample %in% samples_to_display) &
(sample_data()$cells$cluster %in% clusters_to_display)
)
# extract cells to plot
to_plot <- cbind(
sample_data()$trajectory$monocle2[[ trajectory_to_display ]][["meta"]][ cells_to_display , ],
sample_data()$cells[ cells_to_display , ]
) %>%
dplyr::filter(!is.na(pseudotime))
to_plot <- to_plot[ sample(1:nrow(to_plot)) , ]
color_variable <- input[["trajectory_dot_color"]]
if ( is.factor(to_plot[[ color_variable ]]) || is.character(to_plot[[ color_variable ]]) ) {
cols <- if ( color_variable == "sample" ) {
sample_data()$samples$colors
} else if ( color_variable == "cluster" ) {
sample_data()$clusters$colors
} else if ( color_variable %in% c("cell_cycle_seurat","cell_cycle_cyclone") ) {
cell_cycle_colorset
} else if ( is.factor(to_plot[[ color_variable ]]) ) {
setNames(colors[1:length(levels(to_plot[[ color_variable ]]))], levels(to_plot[[ color_variable ]]))
} else {
colors
}
p <- ggplot(to_plot, aes_string(x = "pseudotime", fill = color_variable)) +
geom_density(alpha = 0.4, color = "black") +
theme_bw() +
labs(x = "Pseudotime", y = "Density") +
scale_fill_manual(values = cols) +
guides(fill = guide_legend(override.aes = list(alpha = 1)))
plotly::ggplotly(p, tooltip = "text") %>%
plotly::style(
hoveron = "fill"
)
} else {
colorset <- setNames(
colors[1:length(levels(sample_data()$trajectory$monocle2[[ input[["trajectory_to_display"]] ]][["meta"]]$state))],
levels(sample_data()$trajectory$monocle2[[ input[["trajectory_to_display"]] ]][["meta"]]$state)
)
plot <- plotly::plot_ly(
data = to_plot,
x = ~pseudotime,
y = ~to_plot[[ color_variable ]],
type = "scatter",
mode = "markers",
color = ~state,
colors = colorset,
marker = list(
opacity = input[["trajectory_dot_opacity"]],
line = list(
color = "rgb(196,196,196)",
width = 1
),
size = input[["trajectory_dot_size"]]
),
hoverinfo = "text",
text = ~paste(
"<b>Cell</b>: ", to_plot[ , "cell_barcode" ], "<br>",
"<b>Sample</b>: ", to_plot[ , "sample" ], "<br>",
"<b>Cluster</b>: ", to_plot[ , "cluster" ], "<br>",
"<b>Transcripts</b>: ", formatC(to_plot[ , "nUMI" ], format = "f", big.mark = ",", digits = 0), "<br>",
"<b>Expressed genes</b>: ", formatC(to_plot[ , "nGene" ], format = "f", big.mark = ",", digits = 0), "<br>",
"<b>State</b>: ", to_plot[ , "state" ], "<br>",
"<b>Pseudotime</b>: ", round(to_plot[ , "pseudotime" ], 3)
)
) %>%
plotly::layout(
xaxis = list(
title = "Pseudotime",
mirror = TRUE,
showline = TRUE,
zeroline = FALSE
),
yaxis = list(
title = color_variable,
mirror = TRUE,
showline = TRUE,
zeroline = FALSE
),
hoverlabel = list(font = list(size = 11))
)
if ( preferences$use_webgl == TRUE ) {
plotly::toWebGL(plot)
} else {
plot
}
}
})
# info button
observeEvent(input[["trajectory_density_info"]], {
showModal(
modalDialog(
trajectory_density_info[["text"]],
title = trajectory_density_info[["title"]],
easyClose = TRUE,
footer = NULL
)
)
})
##----------------------------------------------------------------------------##
## Table of cells by state.
##----------------------------------------------------------------------------##
# table
output[["trajectory_number_of_cells_by_state_table"]] <- DT::renderDataTable(server = FALSE, {
req(,
input[["trajectory_to_display"]],
input[["trajectory_dot_color"]]
)
if ( is.numeric(sample_data()$cells[[ input[["trajectory_dot_color"]] ]]) || input[["trajectory_dot_color"]] == "state" || input[["trajectory_dot_color"]] == "pseudotime" ) {
table <- sample_data()$trajectory$monocle2[[ input[["trajectory_to_display"]] ]][["meta"]] %>%
dplyr::filter(!is.na(pseudotime)) %>%
dplyr::group_by(state) %>%
dplyr::summarize(total_cell_count = n())
} else {
table <- cbind(
sample_data()$trajectory$monocle2[[ input[["trajectory_to_display"]] ]][["meta"]],
sample_data()$cells[[ input[["trajectory_dot_color"]] ]]
) %>%
dplyr::filter(!is.na(pseudotime)) %>%
dplyr::rename(selected_group = 5) %>%
dplyr::group_by(state, selected_group) %>%
dplyr::summarize(count = n()) %>%
tidyr::spread(selected_group, count, fill = 0) %>%
dplyr::ungroup() %>%
dplyr::mutate(total_cell_count = rowSums(.[,2:ncol(.)])) %>%
dplyr::select(state,total_cell_count,everything())
}
DT::datatable(
table,
filter = "none",
selection = "none",
escape = FALSE,
autoHideNavigation = TRUE,
rownames = FALSE,
extensions = c("Buttons"),
class = "cell-border stripe",
options = list(
dom = "Brti",
pageLength = 100,
buttons = list(
"colvis",
list(
extend = "collection",
text = "Download",
buttons = list(
list(
extend = "csv",
filename = "cells_by_state",
title = "Cells by state"
),
list(
extend = "excel",
filename = "cells_by_state",
title = "Cells by state"
)
)
)
)
)
)
})
# info button
observeEvent(input[["trajectory_number_of_cells_by_state_info"]], {
showModal(
modalDialog(
trajectory_number_of_cells_by_state_info[["text"]],
title = trajectory_number_of_cells_by_state_info[["title"]],
easyClose = TRUE,
footer = NULL
)
)
})
##----------------------------------------------------------------------------##
## States by sample.
##----------------------------------------------------------------------------##
# bar plot
output[["states_by_sample_plot"]] <- plotly::renderPlotly({
req(input[["trajectory_to_display"]])
# merge meta data with trajectory info
cell_count_by_state_total <- cbind(
sample_data()$trajectory$monocle2[[ input[["trajectory_to_display"]] ]][["meta"]],
sample_data()$cells
) %>%
dplyr::filter(!is.na(pseudotime)) %>%
dplyr::group_by(state) %>%
dplyr::summarize(total = n()) %>%
dplyr::ungroup()
# make plot
cbind(
sample_data()$trajectory$monocle2[[ input[["trajectory_to_display"]] ]][["meta"]],
sample_data()$cells
) %>%
dplyr::filter(!is.na(pseudotime)) %>%
dplyr::group_by(state, sample) %>%
dplyr::summarize(count = n()) %>%
tidyr::spread(sample, count, fill = 0) %>%
dplyr::ungroup() %>%
reshape2::melt(id.vars = "state") %>%
dplyr::left_join(., cell_count_by_state_total, by = "state") %>%
dplyr::rename(sample = variable, cells = value) %>%
dplyr::mutate(pct = cells / total * 100) %>%
plotly::plot_ly(
x = ~state,
y = ~pct,
type = "bar",
color = ~sample,
colors = sample_data()$samples$colors,
hoverinfo = "text",
text = ~paste0("<b>Sample ", .$sample, ": </b>", format(round(.$pct, 1), nsmall = 1), "%")
) %>%
plotly::layout(
xaxis = list(
title = "",
mirror = TRUE,
showline = TRUE
),
yaxis = list(
title = "Percentage (%)",
range = c(0,100),
hoverformat = ".2f",
mirror = TRUE,
zeroline = FALSE,
showline = TRUE
),
barmode = "stack",
hovermode = "closest"
)
})
# info button
observeEvent(input[["states_by_sample_info"]], {
showModal(
modalDialog(
states_by_sample_info[["text"]],
title = states_by_sample_info[["title"]],
easyClose = TRUE,
footer = NULL
)
)
})
# ##----------------------------------------------------------------------------##
# ## States by cluster.
# ##----------------------------------------------------------------------------##
# bar plot
output[["states_by_cluster_plot"]] <- plotly::renderPlotly({
req(input[["trajectory_to_display"]])
# merge meta data with trajectory info
cell_count_by_state_total <- cbind(
sample_data()$trajectory$monocle2[[ input[["trajectory_to_display"]] ]][["meta"]],
sample_data()$cells
) %>%
dplyr::filter(!is.na(pseudotime)) %>%
dplyr::group_by(state) %>%
dplyr::summarize(total = n()) %>%
dplyr::ungroup()
# make plot
cbind(
sample_data()$trajectory$monocle2[[ input[["trajectory_to_display"]] ]][["meta"]],
sample_data()$cells
) %>%
dplyr::filter(!is.na(pseudotime)) %>%
dplyr::group_by(state, cluster) %>%
dplyr::summarize(count = n()) %>%
tidyr::spread(cluster, count, fill = 0) %>%
dplyr::ungroup() %>%
reshape2::melt(id.vars = "state") %>%
dplyr::left_join(., cell_count_by_state_total, by = "state") %>%
dplyr::rename(cluster = variable, cells = value) %>%
dplyr::mutate(pct = cells / total * 100) %>%
plotly::plot_ly(
x = ~state,
y = ~pct,
type = "bar",
color = ~cluster,
colors = sample_data()$clusters$colors,
hoverinfo = "text",
text = ~paste0("<b>Cluster ", .$cluster, ": </b>", format(round(.$pct, 1), nsmall = 1), "%")
) %>%
plotly::layout(
xaxis = list(
title = "",
mirror = TRUE,
showline = TRUE
),
yaxis = list(
title = "Percentage (%)",
range = c(0,100),
hoverformat = ".2f",
mirror = TRUE,
zeroline = FALSE,
showline = TRUE
),
barmode = "stack",
hovermode = "closest"
)
})
# info button
observeEvent(input[["states_by_cluster_info"]], {
showModal(
modalDialog(
states_by_cluster_info[["text"]],
title = states_by_cluster_info[["title"]],
easyClose = TRUE,
footer = NULL
)
)
})
# ##----------------------------------------------------------------------------##
# ## States by cell cycle status (Seurat).
# ##----------------------------------------------------------------------------##
# UI element
output[["states_by_cell_cycle_seurat_UI"]] <- renderUI({
if ( !is.null(sample_data()$cells$cell_cycle_seurat) ) {
plotly::plotlyOutput("states_by_cell_cycle_seurat_plot")
} else {
textOutput("states_by_cell_cycle_seurat_text")
}
})
output[["states_by_cell_cycle_seurat_plot"]] <- plotly::renderPlotly({
req(input[["trajectory_to_display"]])
# merge meta data with trajectory info
cell_count_by_state_total <- cbind(
sample_data()$trajectory$monocle2[[ input[["trajectory_to_display"]] ]][["meta"]],
sample_data()$cells
) %>%
dplyr::filter(!is.na(pseudotime)) %>%
dplyr::group_by(state) %>%
dplyr::summarize(total = n()) %>%
dplyr::ungroup()
# make plot
cbind(
sample_data()$trajectory$monocle2[[ input[["trajectory_to_display"]] ]][["meta"]],
sample_data()$cells
) %>%
dplyr::filter(!is.na(pseudotime)) %>%
dplyr::group_by(state, cell_cycle_seurat) %>%
dplyr::summarize(count = n()) %>%
tidyr::spread(cell_cycle_seurat, count, fill = 0) %>%
dplyr::ungroup() %>%
reshape2::melt(id.vars = "state") %>%
dplyr::mutate(
variable = factor(variable, levels = c("G1", "S", "G2M")),
) %>%
dplyr::left_join(., cell_count_by_state_total, by = "state") %>%
dplyr::rename(cell_cycle_seurat = variable, cells = value) %>%
dplyr::mutate(pct = cells / total * 100) %>%
plotly::plot_ly(
x = ~state,
y = ~pct,
type = "bar",
color = ~cell_cycle_seurat,
colors = cell_cycle_colorset,
hoverinfo = "text",
text = ~paste0("<b>", .$cell_cycle_seurat, ": </b>", format(round(.$pct, 1), nsmall = 1), "%")
) %>%
plotly::layout(
xaxis = list(
title = "",
mirror = TRUE,
showline = TRUE
),
yaxis = list(
title = "Percentage (%)",
range = c(0,100),
hoverformat = ".2f",
mirror = TRUE,
zeroline = FALSE,
showline = TRUE
),
barmode = "stack",
hovermode = "closest"
)
})
# alternative text
output[["states_by_cell_cycle_seurat_text"]] <- renderText({
"Data not available."
})
# info button
observeEvent(input[["states_by_cell_cycle_seurat_info"]], {
showModal(
modalDialog(
states_by_cell_cycle_seurat_info[["text"]],
title = states_by_cell_cycle_seurat_info[["title"]],
easyClose = TRUE,
footer = NULL
)
)
})
##----------------------------------------------------------------------------##
## nUMI by state.
##----------------------------------------------------------------------------##
# violin plot
output[["states_nUMI_plot"]] <- plotly::renderPlotly({
req(input[["trajectory_to_display"]])
colorset <- setNames(
colors[1:length(levels(sample_data()$trajectory$monocle2[[ input[["trajectory_to_display"]] ]][["meta"]]$state))],
levels(sample_data()$trajectory$monocle2[[ input[["trajectory_to_display"]] ]][["meta"]]$state)
)
cbind(
sample_data()$trajectory$monocle2[[ input[["trajectory_to_display"]] ]][["meta"]],
sample_data()$cells
) %>%
dplyr::filter(!is.na(pseudotime)) %>%
plotly::plot_ly(
x = ~state,
y = ~nUMI,
type = "violin",
box = list(
visible = TRUE
),
meanline = list(
visible = TRUE
),
color = ~state,
colors = colorset,
source = "subset",
showlegend = FALSE,
hoverinfo = "y",
marker = list(
size = 5
)
) %>%
plotly::layout(
title = "",
xaxis = list(
title = "",
mirror = TRUE,
showline = TRUE
),
yaxis = list(
title = "Number of transcripts",
hoverformat = ".0f",
mirror = TRUE,
showline = TRUE
),
dragmode = "select",
hovermode = "compare"
)
})
# info button
observeEvent(input[["states_nUMI_info"]], {
showModal(
modalDialog(
states_nUMI_info[["text"]],
title = states_nUMI_info[["title"]],
easyClose = TRUE,
footer = NULL
)
)
})
##----------------------------------------------------------------------------##
## nGene by state.
##----------------------------------------------------------------------------##
# violin plot
output[["states_nGene_plot"]] <- plotly::renderPlotly({
req(input[["trajectory_to_display"]])
colorset <- setNames(
colors[1:length(levels(sample_data()$trajectory$monocle2[[ input[["trajectory_to_display"]] ]][["meta"]]$state))],
levels(sample_data()$trajectory$monocle2[[ input[["trajectory_to_display"]] ]][["meta"]]$state)
)
cbind(
sample_data()$trajectory$monocle2[[ input[["trajectory_to_display"]] ]][["meta"]],
sample_data()$cells
) %>%
dplyr::filter(!is.na(pseudotime)) %>%
plotly::plot_ly(
x = ~state,
y = ~nGene,
type = "violin",
box = list(
visible = TRUE
),
meanline = list(
visible = TRUE
),
color = ~state,
colors = colorset,
source = "subset",
showlegend = FALSE,
hoverinfo = "y",
marker = list(
size = 5
)
) %>%
plotly::layout(
title = "",
xaxis = list(
title = "",
mirror = TRUE,
showline = TRUE
),
yaxis = list(
title = "Number of expressed genes",
hoverformat = ".0f",
mirror = TRUE,
showline = TRUE
),
dragmode = "select",
hovermode = "compare"
)
})
# info button
observeEvent(input[["states_nGene_info"]], {
showModal(
modalDialog(
states_nGene_info[["text"]],
title = states_nGene_info[["title"]],
easyClose = TRUE,
footer = NULL
)
)
})
romanhaa/cerebroApp documentation built on Nov. 25, 2021, 5:29 p.m.
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##----------------------------------------------------------------------------##
## Tab: Trajectory.
##----------------------------------------------------------------------------##
# what needs to be done
# - let user show gene expression as well? probably more complicated
# UI element: display results or alternative text
output[["trajectory_UI"]] <- renderUI({
if ( length(sample_data()$trajectory$monocle2) > 0 ) {
tagList(
fluidRow(
column(width = 3, offset = 0, style = "padding: 0px;",
cerebroBox(
title = "Input parameters",
tagList(
uiOutput("trajectory_input")
)
)
),
column(width = 9, offset = 0, style = "padding: 0px;",
cerebroBox(
title = tagList(
boxTitle("Trajectory"),
actionButton(
inputId = "trajectory_projection_info",
label = "info",
icon = NULL,
class = "btn-xs",
title = "Show additional information for this panel.",
style = "margin-right: 5px"
),
actionButton(
inputId = "trajectory_projection_export",
label = "export to PDF",
icon = NULL,
class = "btn-xs",
title = "Export trajectory to PDF file."
)
),
plotly::plotlyOutput(
"trajectory_projection",
width = "auto",
height = "85vh"
)
)
)
),
fluidRow(
cerebroBox(
title = tagList(
boxTitle("Distribution along pseudotime"),
actionButton(
inputId = "trajectory_density_info",
label = "info",
icon = NULL,
class = "btn-xs",
title = "Show additional information for this panel.",
style = "margin-right: 5px"
)
),
plotly::plotlyOutput("trajectory_density_plot")
)
),
fluidRow(
cerebroBox(
title = tagList(
boxTitle("Number of cells by state"),
actionButton(
inputId = "trajectory_cells_by_state_info",
label = "info",
icon = NULL,
class = "btn-xs",
title = "Show additional information for this panel.",
style = "margin-right: 5px"
)
),
DT::dataTableOutput("trajectory_number_of_cells_by_state_table")
)
),
fluidRow(
cerebroBox(
title = tagList(
boxTitle("States by sample"),
actionButton(
inputId = "states_by_sample_info",
label = "info",
icon = NULL,
class = "btn-xs",
title = "Show additional information for this panel.",
style = "margin-right: 5px"
)
),
plotly::plotlyOutput("states_by_sample_plot")
)
),
fluidRow(
cerebroBox(
title = tagList(
boxTitle("States by cluster"),
actionButton(
inputId = "states_by_cluster_info",
label = "info",
icon = NULL,
class = "btn-xs",
title = "Show additional information for this panel.",
style = "margin-right: 5px"
)
),
plotly::plotlyOutput("states_by_cluster_plot")
)
),
fluidRow(
cerebroBox(
title = tagList(
boxTitle("States by cell cycle (Seurat)"),
actionButton(
inputId = "states_by_cell_cycle_seurat_info",
label = "info",
icon = NULL,
class = "btn-xs",
title = "Show additional information for this panel.",
style = "margin-right: 5px"
)
),
shiny::uiOutput("states_by_cell_cycle_seurat_UI")
)
),
fluidRow(
cerebroBox(
title = tagList(
boxTitle("Number of transcripts by state"),
actionButton(
inputId = "states_nUMI_info",
label = "info",
icon = NULL,
class = "btn-xs",
title = "Show additional information for this panel.",
style = "margin-right: 5px"
)
),
plotly::plotlyOutput("states_nUMI_plot")
)
),
fluidRow(
cerebroBox(
title = tagList(
boxTitle("Number of expressed genes by state"),
actionButton(
inputId = "states_nGene_info",
label = "info",
icon = NULL,
class = "btn-xs",
title = "Show additional information for this panel.",
style = "margin-right: 5px"
)
),
plotly::plotlyOutput("states_nGene_plot")
)
)
)
} else {
cerebroBox(title = "Trajectory", textOutput("trajectory_missing"))
}
})
# alternative text
output[["trajectory_missing"]] <- renderText({
"No trajectories available to display."
})
##----------------------------------------------------------------------------##
## UI elements.
##----------------------------------------------------------------------------##
output[["trajectory_input"]] <- renderUI({
tagList(
selectInput(
"trajectory_to_display",
label = "Trajectory",
choices = names(sample_data()$trajectory$monocle2)
),
shinyWidgets::pickerInput(
"trajectory_samples_to_display",
label = "Samples to display",
choices = sample_data()$sample_names,
selected = sample_data()$sample_names,
options = list("actions-box" = TRUE),
multiple = TRUE
),
shinyWidgets::pickerInput(
"trajectory_clusters_to_display",
label = "Clusters to display",
choices = sample_data()$cluster_names,
selected = sample_data()$cluster_names,
options = list("actions-box" = TRUE),
multiple = TRUE
),
sliderInput(
"trajectory_percentage_cells_to_show",
label = "Show % of cells",
min = scatter_plot_percentage_cells_to_show[["min"]],
max = scatter_plot_percentage_cells_to_show[["max"]],
step = scatter_plot_percentage_cells_to_show[["step"]],
value = scatter_plot_percentage_cells_to_show[["default"]]
),
selectInput(
"trajectory_dot_color",
label = "Color cells by",
choices = c("state","pseudotime",names(sample_data()$cells)[! names(sample_data()$cells) %in% c("cell_barcode")])
),
sliderInput(
"trajectory_dot_size",
label = "Dot size",
min = scatter_plot_dot_size[["min"]],
max = scatter_plot_dot_size[["max"]],
step = scatter_plot_dot_size[["step"]],
value = scatter_plot_dot_size[["default"]]
),
sliderInput(
"trajectory_dot_opacity",
label = "Dot opacity",
min = scatter_plot_dot_opacity[["min"]],
max = scatter_plot_dot_opacity[["max"]],
step = scatter_plot_dot_opacity[["step"]],
value = scatter_plot_dot_opacity[["default"]]
)
)
})
##----------------------------------------------------------------------------##
## Projection.
##----------------------------------------------------------------------------##
output[["trajectory_projection"]] <- plotly::renderPlotly({
# don't do anything before these inputs are selected
req(
input[["trajectory_to_display"]],
input[["trajectory_samples_to_display"]],
input[["trajectory_clusters_to_display"]],
input[["trajectory_percentage_cells_to_show"]],
input[["trajectory_dot_color"]],
input[["trajectory_dot_size"]],
input[["trajectory_dot_opacity"]]
)
trajectory_to_display <- input[["trajectory_to_display"]]
samples_to_display <- input[["trajectory_samples_to_display"]]
clusters_to_display <- input[["trajectory_clusters_to_display"]]
cells_to_display <- which(
(sample_data()$cells$sample %in% samples_to_display) &
(sample_data()$cells$cluster %in% clusters_to_display)
)
# randomly remove cells
if ( input[["trajectory_percentage_cells_to_show"]] < 100 ) {
number_of_cells_to_plot <- ceiling(
input[["trajectory_percentage_cells_to_show"]] / 100 * length(cells_to_display)
)
cells_to_display <- cells_to_display[ sample(1:length(cells_to_display), number_of_cells_to_plot) ]
}
# extract cells to plot
to_plot <- cbind(
sample_data()$trajectory$monocle2[[ trajectory_to_display ]][["meta"]][ cells_to_display , ],
sample_data()$cells[ cells_to_display , ]
) %>%
dplyr::filter(!is.na(pseudotime))
to_plot <- to_plot[ sample(1:nrow(to_plot)) , ]
color_variable <- input[["trajectory_dot_color"]]
# convert edges of trajectory into list format to plot with plotly
trajectory_edges <- sample_data()$trajectory$monocle2[[trajectory_to_display]][["edges"]]
trajectory_lines <- list()
for (i in 1:nrow(trajectory_edges) ) {
line = list(
type = "line",
line = list(color = "black"),
xref = "x",
yref = "y",
x0 = trajectory_edges$source_dim_1[i],
y0 = trajectory_edges$source_dim_2[i],
x1 = trajectory_edges$target_dim_1[i],
y1 = trajectory_edges$target_dim_2[i]
)
trajectory_lines <- c(trajectory_lines, list(line))
}
if ( is.factor(to_plot[[ color_variable ]]) || is.character(to_plot[[ color_variable ]]) ) {
cols <- if ( color_variable == "sample" ) {
if ( !is.null(sample_data()$samples$colors) ) {
sample_data()$samples$colors
} else {
colors
}
} else if ( color_variable == "cluster" ) {
if ( !is.null(sample_data()$clusters$colors) ) {
sample_data()$clusters$colors
} else {
colors
}
} else if ( color_variable %in% c("cell_cycle_seurat","cell_cycle_cyclone") ) {
cell_cycle_colorset
} else if ( is.factor(to_plot[[ color_variable ]]) ) {
setNames(colors[1:length(levels(to_plot[[ color_variable ]]))], levels(to_plot[[ color_variable ]]))
} else {
colors
}
plot <- plotly::plot_ly(
to_plot,
x = ~DR_1,
y = ~DR_2,
color = ~to_plot[[ color_variable ]],
colors = cols,
type = "scatter",
mode = "markers",
marker = list(
opacity = input[["trajectory_dot_opacity"]],
line = list(
color = "rgb(196,196,196)",
width = 1
),
size = input[["trajectory_dot_size"]]
),
hoverinfo = "text",
text = ~paste(
"<b>Cell</b>: ", to_plot[ , "cell_barcode" ], "<br>",
"<b>Sample</b>: ", to_plot[ , "sample" ], "<br>",
"<b>Cluster</b>: ", to_plot[ , "cluster" ], "<br>",
"<b>Transcripts</b>: ", formatC(to_plot[ , "nUMI" ], format = "f", big.mark = ",", digits = 0), "<br>",
"<b>Expressed genes</b>: ", formatC(to_plot[ , "nGene" ], format = "f", big.mark = ",", digits = 0), "<br>",
"<b>State</b>: ", to_plot[ , "state" ], "<br>",
"<b>Pseudotime</b>: ", round(to_plot[ , "pseudotime" ], 3)
)
) %>%
plotly::layout(
shapes = trajectory_lines,
xaxis = list(
mirror = TRUE,
showline = TRUE,
zeroline = FALSE,
range = range(to_plot$DR_1) * 1.1
),
yaxis = list(
mirror = TRUE,
showline = TRUE,
zeroline = FALSE,
range = range(to_plot$DR_2) * 1.1
),
hoverlabel = list(font = list(size = 11))
)
if ( preferences[["use_webgl"]] == TRUE ) {
plot %>% plotly::toWebGL()
} else {
plot
}
} else {
plot <- plotly::plot_ly(
data = to_plot,
x = ~DR_1,
y = ~DR_2,
type = "scatter",
mode = "markers",
marker = list(
colorbar = list(
title = colnames(to_plot)[which(colnames(to_plot) == color_variable)]
),
color = ~to_plot[[ color_variable ]],
opacity = input[["trajectory_dot_opacity"]],
colorscale = "YlGnBu",
reversescale = TRUE,
line = list(
color = "rgb(196,196,196)",
width = 1
),
size = input[["trajectory_dot_size"]]
),
hoverinfo = "text",
text = ~paste(
"<b>Cell</b>: ", to_plot[ , "cell_barcode" ], "<br>",
"<b>Sample</b>: ", to_plot[ , "sample" ], "<br>",
"<b>Cluster</b>: ", to_plot[ , "cluster" ], "<br>",
"<b>Transcripts</b>: ", formatC(to_plot[ , "nUMI" ], format = "f", big.mark = ",", digits = 0), "<br>",
"<b>Expressed genes</b>: ", formatC(to_plot[ , "nGene" ], format = "f", big.mark = ",", digits = 0), "<br>",
"<b>State</b>: ", to_plot[ , "state" ], "<br>",
"<b>Pseudotime</b>: ", round(to_plot[ , "pseudotime" ], 3)
)
) %>%
plotly::layout(
shapes = trajectory_lines,
xaxis = list(
title = colnames(to_plot)[1],
mirror = TRUE,
showline = TRUE,
zeroline = FALSE,
range = range(to_plot$DR_1) * 1.1
),
yaxis = list(
title = colnames(to_plot)[2],
mirror = TRUE,
showline = TRUE,
zeroline = FALSE,
range = range(to_plot$DR_2) * 1.1
),
hoverlabel = list(font = list(size = 11))
)
if ( preferences$use_webgl == TRUE ) {
plotly::toWebGL(plot)
} else {
plot
}
}
})
##----------------------------------------------------------------------------##
## Info button.
##----------------------------------------------------------------------------##
observeEvent(input[["trajectory_projection_info"]], {
showModal(
modalDialog(
trajectory_projection_info[["text"]],
title = trajectory_projection_info[["title"]],
easyClose = TRUE,
footer = NULL
)
)
})
##----------------------------------------------------------------------------##
## Export projection.
##----------------------------------------------------------------------------##
observeEvent(input[["trajectory_projection_export"]], {
req(
input[["trajectory_to_display"]],
input[["trajectory_samples_to_display"]],
input[["trajectory_clusters_to_display"]],
input[["trajectory_percentage_cells_to_show"]],
input[["trajectory_dot_color"]],
input[["trajectory_dot_size"]],
input[["trajectory_dot_opacity"]]
)
library("ggplot2")
if ( exists("plot_export_path") ) {
trajectory_to_display <- input[["trajectory_to_display"]]
samples_to_display <- input[["trajectory_samples_to_display"]]
clusters_to_display <- input[["trajectory_clusters_to_display"]]
cells_to_display <- which(
(sample_data()$cells$sample %in% samples_to_display) &
(sample_data()$cells$cluster %in% clusters_to_display)
)
to_plot <- cbind(
sample_data()$trajectory$monocle2[[ trajectory_to_display ]][[ "meta" ]][ cells_to_display , ],
sample_data()$cells[ cells_to_display , ]
) %>%
dplyr::filter(!is.na(pseudotime))
to_plot <- to_plot[ sample(1:nrow(to_plot)) , ]
color_variable <- input[["trajectory_dot_color"]]
if ( is.factor(to_plot[[ color_variable ]]) || is.character(to_plot[[ color_variable ]]) ) {
if ( color_variable == "sample" ) {
cols <- sample_data()$samples$colors
} else if ( color_variable == "cluster" ) {
cols <- sample_data()$clusters$colors
} else if ( color_variable %in% c("cell_cycle_seurat","cell_cycle_cyclone") ) {
cols <- cell_cycle_colorset
} else if ( is.factor(to_plot[ , color_variable ]) ) {
cols <- setNames(colors[1:length(levels(to_plot[ , color_variable ]))], levels(to_plot[ , color_variable ]))
} else {
cols <- colors
}
p <- ggplot() +
geom_point(
data = to_plot,
aes_string(x = colnames(to_plot)[1], y = colnames(to_plot)[2], fill = color_variable),
shape = 21,
size = input[["trajectory_dot_size"]]/3,
stroke = 0.2,
color = "#c4c4c4",
alpha = input[["trajectory_dot_opacity"]]
) +
geom_segment(
data = sample_data()$trajectory$monocle2[[ trajectory_to_display ]]$edges,
aes(source_dim_1, source_dim_2, xend = target_dim_1, yend = target_dim_2),
size = 0.75, linetype = "solid", na.rm = TRUE
) +
scale_fill_manual(values = cols) +
theme_bw()
} else {
p <- ggplot() +
geom_point(
data = to_plot,
aes_string(x = colnames(to_plot)[1], y = colnames(to_plot)[2], fill = color_variable),
shape = 21,
size = input[["trajectory_dot_size"]]/3,
stroke = 0.2,
color = "#c4c4c4",
alpha = input[["trajectory_dot_opacity"]]
) +
geom_segment(
data = sample_data()$trajectory$monocle2[[ trajectory_to_display ]]$edges,
aes(source_dim_1, source_dim_2, xend = target_dim_1, yend = target_dim_2),
size = 0.75, linetype = "solid", na.rm = TRUE
) +
scale_fill_distiller(
palette = "YlGnBu",
direction = 1,
guide = guide_colorbar(frame.colour = "black", ticks.colour = "black")
) +
theme_bw()
}
out_filename <- paste0(
plot_export_path, "Cerebro_",
gsub(
sample_data()$experiment$experiment_name,
pattern = " ", replacement = "_"
),
"_trajectory_", trajectory_to_display, "_by_",
gsub(
color_variable,
pattern = "\\.", replacement = "_"
),
".pdf"
)
pdf(NULL)
ggsave(out_filename, p, height = 8, width = 11)
if ( file.exists(out_filename) ) {
shinyWidgets::sendSweetAlert(
session = session,
title = "Success!",
text = paste0("Plot saved successfully as: ", out_filename),
type = "success"
)
} else {
shinyWidgets::sendSweetAlert(
session = session,
title = "Error!",
text = "Sorry, it seems something went wrong...",
type = "error"
)
}
} else {
shinyWidgets::sendSweetAlert(
session = session,
title = "Error!",
text = "Sorry, we couldn't find a place to store the figure. Please submit an issue on GitHub @ https://github.com/romanhaa/cerebroApp",
type = "error"
)
}
})
##----------------------------------------------------------------------------##
## Distribution along pseudotime.
##----------------------------------------------------------------------------##
output[["trajectory_density_plot"]] <- plotly::renderPlotly({
# don't do anything before these inputs are selected
req(
input[["trajectory_to_display"]],
input[["trajectory_samples_to_display"]],
input[["trajectory_clusters_to_display"]],
input[["trajectory_dot_color"]]
)
trajectory_to_display <- input[["trajectory_to_display"]]
samples_to_display <- input[["trajectory_samples_to_display"]]
clusters_to_display <- input[["trajectory_clusters_to_display"]]
cells_to_display <- which(
(sample_data()$cells$sample %in% samples_to_display) &
(sample_data()$cells$cluster %in% clusters_to_display)
)
# extract cells to plot
to_plot <- cbind(
sample_data()$trajectory$monocle2[[ trajectory_to_display ]][["meta"]][ cells_to_display , ],
sample_data()$cells[ cells_to_display , ]
) %>%
dplyr::filter(!is.na(pseudotime))
to_plot <- to_plot[ sample(1:nrow(to_plot)) , ]
color_variable <- input[["trajectory_dot_color"]]
if ( is.factor(to_plot[[ color_variable ]]) || is.character(to_plot[[ color_variable ]]) ) {
cols <- if ( color_variable == "sample" ) {
sample_data()$samples$colors
} else if ( color_variable == "cluster" ) {
sample_data()$clusters$colors
} else if ( color_variable %in% c("cell_cycle_seurat","cell_cycle_cyclone") ) {
cell_cycle_colorset
} else if ( is.factor(to_plot[[ color_variable ]]) ) {
setNames(colors[1:length(levels(to_plot[[ color_variable ]]))], levels(to_plot[[ color_variable ]]))
} else {
colors
}
p <- ggplot(to_plot, aes_string(x = "pseudotime", fill = color_variable)) +
geom_density(alpha = 0.4, color = "black") +
theme_bw() +
labs(x = "Pseudotime", y = "Density") +
scale_fill_manual(values = cols) +
guides(fill = guide_legend(override.aes = list(alpha = 1)))
plotly::ggplotly(p, tooltip = "text") %>%
plotly::style(
hoveron = "fill"
)
} else {
colorset <- setNames(
colors[1:length(levels(sample_data()$trajectory$monocle2[[ input[["trajectory_to_display"]] ]][["meta"]]$state))],
levels(sample_data()$trajectory$monocle2[[ input[["trajectory_to_display"]] ]][["meta"]]$state)
)
plot <- plotly::plot_ly(
data = to_plot,
x = ~pseudotime,
y = ~to_plot[[ color_variable ]],
type = "scatter",
mode = "markers",
color = ~state,
colors = colorset,
marker = list(
opacity = input[["trajectory_dot_opacity"]],
line = list(
color = "rgb(196,196,196)",
width = 1
),
size = input[["trajectory_dot_size"]]
),
hoverinfo = "text",
text = ~paste(
"<b>Cell</b>: ", to_plot[ , "cell_barcode" ], "<br>",
"<b>Sample</b>: ", to_plot[ , "sample" ], "<br>",
"<b>Cluster</b>: ", to_plot[ , "cluster" ], "<br>",
"<b>Transcripts</b>: ", formatC(to_plot[ , "nUMI" ], format = "f", big.mark = ",", digits = 0), "<br>",
"<b>Expressed genes</b>: ", formatC(to_plot[ , "nGene" ], format = "f", big.mark = ",", digits = 0), "<br>",
"<b>State</b>: ", to_plot[ , "state" ], "<br>",
"<b>Pseudotime</b>: ", round(to_plot[ , "pseudotime" ], 3)
)
) %>%
plotly::layout(
xaxis = list(
title = "Pseudotime",
mirror = TRUE,
showline = TRUE,
zeroline = FALSE
),
yaxis = list(
title = color_variable,
mirror = TRUE,
showline = TRUE,
zeroline = FALSE
),
hoverlabel = list(font = list(size = 11))
)
if ( preferences$use_webgl == TRUE ) {
plotly::toWebGL(plot)
} else {
plot
}
}
})
# info button
observeEvent(input[["trajectory_density_info"]], {
showModal(
modalDialog(
trajectory_density_info[["text"]],
title = trajectory_density_info[["title"]],
easyClose = TRUE,
footer = NULL
)
)
})
##----------------------------------------------------------------------------##
## Table of cells by state.
##----------------------------------------------------------------------------##
# table
output[["trajectory_number_of_cells_by_state_table"]] <- DT::renderDataTable(server = FALSE, {
req(,
input[["trajectory_to_display"]],
input[["trajectory_dot_color"]]
)
if ( is.numeric(sample_data()$cells[[ input[["trajectory_dot_color"]] ]]) || input[["trajectory_dot_color"]] == "state" || input[["trajectory_dot_color"]] == "pseudotime" ) {
table <- sample_data()$trajectory$monocle2[[ input[["trajectory_to_display"]] ]][["meta"]] %>%
dplyr::filter(!is.na(pseudotime)) %>%
dplyr::group_by(state) %>%
dplyr::summarize(total_cell_count = n())
} else {
table <- cbind(
sample_data()$trajectory$monocle2[[ input[["trajectory_to_display"]] ]][["meta"]],
sample_data()$cells[[ input[["trajectory_dot_color"]] ]]
) %>%
dplyr::filter(!is.na(pseudotime)) %>%
dplyr::rename(selected_group = 5) %>%
dplyr::group_by(state, selected_group) %>%
dplyr::summarize(count = n()) %>%
tidyr::spread(selected_group, count, fill = 0) %>%
dplyr::ungroup() %>%
dplyr::mutate(total_cell_count = rowSums(.[,2:ncol(.)])) %>%
dplyr::select(state,total_cell_count,everything())
}
DT::datatable(
table,
filter = "none",
selection = "none",
escape = FALSE,
autoHideNavigation = TRUE,
rownames = FALSE,
extensions = c("Buttons"),
class = "cell-border stripe",
options = list(
dom = "Brti",
pageLength = 100,
buttons = list(
"colvis",
list(
extend = "collection",
text = "Download",
buttons = list(
list(
extend = "csv",
filename = "cells_by_state",
title = "Cells by state"
),
list(
extend = "excel",
filename = "cells_by_state",
title = "Cells by state"
)
)
)
)
)
)
})
# info button
observeEvent(input[["trajectory_number_of_cells_by_state_info"]], {
showModal(
modalDialog(
trajectory_number_of_cells_by_state_info[["text"]],
title = trajectory_number_of_cells_by_state_info[["title"]],
easyClose = TRUE,
footer = NULL
)
)
})
##----------------------------------------------------------------------------##
## States by sample.
##----------------------------------------------------------------------------##
# bar plot
output[["states_by_sample_plot"]] <- plotly::renderPlotly({
req(input[["trajectory_to_display"]])
# merge meta data with trajectory info
cell_count_by_state_total <- cbind(
sample_data()$trajectory$monocle2[[ input[["trajectory_to_display"]] ]][["meta"]],
sample_data()$cells
) %>%
dplyr::filter(!is.na(pseudotime)) %>%
dplyr::group_by(state) %>%
dplyr::summarize(total = n()) %>%
dplyr::ungroup()
# make plot
cbind(
sample_data()$trajectory$monocle2[[ input[["trajectory_to_display"]] ]][["meta"]],
sample_data()$cells
) %>%
dplyr::filter(!is.na(pseudotime)) %>%
dplyr::group_by(state, sample) %>%
dplyr::summarize(count = n()) %>%
tidyr::spread(sample, count, fill = 0) %>%
dplyr::ungroup() %>%
reshape2::melt(id.vars = "state") %>%
dplyr::left_join(., cell_count_by_state_total, by = "state") %>%
dplyr::rename(sample = variable, cells = value) %>%
dplyr::mutate(pct = cells / total * 100) %>%
plotly::plot_ly(
x = ~state,
y = ~pct,
type = "bar",
color = ~sample,
colors = sample_data()$samples$colors,
hoverinfo = "text",
text = ~paste0("<b>Sample ", .$sample, ": </b>", format(round(.$pct, 1), nsmall = 1), "%")
) %>%
plotly::layout(
xaxis = list(
title = "",
mirror = TRUE,
showline = TRUE
),
yaxis = list(
title = "Percentage (%)",
range = c(0,100),
hoverformat = ".2f",
mirror = TRUE,
zeroline = FALSE,
showline = TRUE
),
barmode = "stack",
hovermode = "closest"
)
})
# info button
observeEvent(input[["states_by_sample_info"]], {
showModal(
modalDialog(
states_by_sample_info[["text"]],
title = states_by_sample_info[["title"]],
easyClose = TRUE,
footer = NULL
)
)
})
# ##----------------------------------------------------------------------------##
# ## States by cluster.
# ##----------------------------------------------------------------------------##
# bar plot
output[["states_by_cluster_plot"]] <- plotly::renderPlotly({
req(input[["trajectory_to_display"]])
# merge meta data with trajectory info
cell_count_by_state_total <- cbind(
sample_data()$trajectory$monocle2[[ input[["trajectory_to_display"]] ]][["meta"]],
sample_data()$cells
) %>%
dplyr::filter(!is.na(pseudotime)) %>%
dplyr::group_by(state) %>%
dplyr::summarize(total = n()) %>%
dplyr::ungroup()
# make plot
cbind(
sample_data()$trajectory$monocle2[[ input[["trajectory_to_display"]] ]][["meta"]],
sample_data()$cells
) %>%
dplyr::filter(!is.na(pseudotime)) %>%
dplyr::group_by(state, cluster) %>%
dplyr::summarize(count = n()) %>%
tidyr::spread(cluster, count, fill = 0) %>%
dplyr::ungroup() %>%
reshape2::melt(id.vars = "state") %>%
dplyr::left_join(., cell_count_by_state_total, by = "state") %>%
dplyr::rename(cluster = variable, cells = value) %>%
dplyr::mutate(pct = cells / total * 100) %>%
plotly::plot_ly(
x = ~state,
y = ~pct,
type = "bar",
color = ~cluster,
colors = sample_data()$clusters$colors,
hoverinfo = "text",
text = ~paste0("<b>Cluster ", .$cluster, ": </b>", format(round(.$pct, 1), nsmall = 1), "%")
) %>%
plotly::layout(
xaxis = list(
title = "",
mirror = TRUE,
showline = TRUE
),
yaxis = list(
title = "Percentage (%)",
range = c(0,100),
hoverformat = ".2f",
mirror = TRUE,
zeroline = FALSE,
showline = TRUE
),
barmode = "stack",
hovermode = "closest"
)
})
# info button
observeEvent(input[["states_by_cluster_info"]], {
showModal(
modalDialog(
states_by_cluster_info[["text"]],
title = states_by_cluster_info[["title"]],
easyClose = TRUE,
footer = NULL
)
)
})
# ##----------------------------------------------------------------------------##
# ## States by cell cycle status (Seurat).
# ##----------------------------------------------------------------------------##
# UI element
output[["states_by_cell_cycle_seurat_UI"]] <- renderUI({
if ( !is.null(sample_data()$cells$cell_cycle_seurat) ) {
plotly::plotlyOutput("states_by_cell_cycle_seurat_plot")
} else {
textOutput("states_by_cell_cycle_seurat_text")
}
})
output[["states_by_cell_cycle_seurat_plot"]] <- plotly::renderPlotly({
req(input[["trajectory_to_display"]])
# merge meta data with trajectory info
cell_count_by_state_total <- cbind(
sample_data()$trajectory$monocle2[[ input[["trajectory_to_display"]] ]][["meta"]],
sample_data()$cells
) %>%
dplyr::filter(!is.na(pseudotime)) %>%
dplyr::group_by(state) %>%
dplyr::summarize(total = n()) %>%
dplyr::ungroup()
# make plot
cbind(
sample_data()$trajectory$monocle2[[ input[["trajectory_to_display"]] ]][["meta"]],
sample_data()$cells
) %>%
dplyr::filter(!is.na(pseudotime)) %>%
dplyr::group_by(state, cell_cycle_seurat) %>%
dplyr::summarize(count = n()) %>%
tidyr::spread(cell_cycle_seurat, count, fill = 0) %>%
dplyr::ungroup() %>%
reshape2::melt(id.vars = "state") %>%
dplyr::mutate(
variable = factor(variable, levels = c("G1", "S", "G2M")),
) %>%
dplyr::left_join(., cell_count_by_state_total, by = "state") %>%
dplyr::rename(cell_cycle_seurat = variable, cells = value) %>%
dplyr::mutate(pct = cells / total * 100) %>%
plotly::plot_ly(
x = ~state,
y = ~pct,
type = "bar",
color = ~cell_cycle_seurat,
colors = cell_cycle_colorset,
hoverinfo = "text",
text = ~paste0("<b>", .$cell_cycle_seurat, ": </b>", format(round(.$pct, 1), nsmall = 1), "%")
) %>%
plotly::layout(
xaxis = list(
title = "",
mirror = TRUE,
showline = TRUE
),
yaxis = list(
title = "Percentage (%)",
range = c(0,100),
hoverformat = ".2f",
mirror = TRUE,
zeroline = FALSE,
showline = TRUE
),
barmode = "stack",
hovermode = "closest"
)
})
# alternative text
output[["states_by_cell_cycle_seurat_text"]] <- renderText({
"Data not available."
})
# info button
observeEvent(input[["states_by_cell_cycle_seurat_info"]], {
showModal(
modalDialog(
states_by_cell_cycle_seurat_info[["text"]],
title = states_by_cell_cycle_seurat_info[["title"]],
easyClose = TRUE,
footer = NULL
)
)
})
##----------------------------------------------------------------------------##
## nUMI by state.
##----------------------------------------------------------------------------##
# violin plot
output[["states_nUMI_plot"]] <- plotly::renderPlotly({
req(input[["trajectory_to_display"]])
colorset <- setNames(
colors[1:length(levels(sample_data()$trajectory$monocle2[[ input[["trajectory_to_display"]] ]][["meta"]]$state))],
levels(sample_data()$trajectory$monocle2[[ input[["trajectory_to_display"]] ]][["meta"]]$state)
)
cbind(
sample_data()$trajectory$monocle2[[ input[["trajectory_to_display"]] ]][["meta"]],
sample_data()$cells
) %>%
dplyr::filter(!is.na(pseudotime)) %>%
plotly::plot_ly(
x = ~state,
y = ~nUMI,
type = "violin",
box = list(
visible = TRUE
),
meanline = list(
visible = TRUE
),
color = ~state,
colors = colorset,
source = "subset",
showlegend = FALSE,
hoverinfo = "y",
marker = list(
size = 5
)
) %>%
plotly::layout(
title = "",
xaxis = list(
title = "",
mirror = TRUE,
showline = TRUE
),
yaxis = list(
title = "Number of transcripts",
hoverformat = ".0f",
mirror = TRUE,
showline = TRUE
),
dragmode = "select",
hovermode = "compare"
)
})
# info button
observeEvent(input[["states_nUMI_info"]], {
showModal(
modalDialog(
states_nUMI_info[["text"]],
title = states_nUMI_info[["title"]],
easyClose = TRUE,
footer = NULL
)
)
})
##----------------------------------------------------------------------------##
## nGene by state.
##----------------------------------------------------------------------------##
# violin plot
output[["states_nGene_plot"]] <- plotly::renderPlotly({
req(input[["trajectory_to_display"]])
colorset <- setNames(
colors[1:length(levels(sample_data()$trajectory$monocle2[[ input[["trajectory_to_display"]] ]][["meta"]]$state))],
levels(sample_data()$trajectory$monocle2[[ input[["trajectory_to_display"]] ]][["meta"]]$state)
)
cbind(
sample_data()$trajectory$monocle2[[ input[["trajectory_to_display"]] ]][["meta"]],
sample_data()$cells
) %>%
dplyr::filter(!is.na(pseudotime)) %>%
plotly::plot_ly(
x = ~state,
y = ~nGene,
type = "violin",
box = list(
visible = TRUE
),
meanline = list(
visible = TRUE
),
color = ~state,
colors = colorset,
source = "subset",
showlegend = FALSE,
hoverinfo = "y",
marker = list(
size = 5
)
) %>%
plotly::layout(
title = "",
xaxis = list(
title = "",
mirror = TRUE,
showline = TRUE
),
yaxis = list(
title = "Number of expressed genes",
hoverformat = ".0f",
mirror = TRUE,
showline = TRUE
),
dragmode = "select",
hovermode = "compare"
)
})
# info button
observeEvent(input[["states_nGene_info"]], {
showModal(
modalDialog(
states_nGene_info[["text"]],
title = states_nGene_info[["title"]],
easyClose = TRUE,
footer = NULL
)
)
})
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