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Allow for selecting negative slider values #18

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Allow for selecting negative slider values #18

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47 changes: 24 additions & 23 deletions R/get_customize_landmark.R
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Original file line number Diff line number Diff line change
Expand Up @@ -9,24 +9,25 @@
#' @examples
#' \dontrun{
#' get_customize_landmark(
#' cell_x_adt_sample,
#' landmark_pos,
#' bw,
#' adt_marker_select_name,
#' cell_x_adt_sample,
#' landmark_pos,
#' bw,
#' adt_marker_select_name,
#' brewer_palettes = "Set1"
#' )}
#' @export
#' @import ggplot2 ggridges shiny
get_customize_landmark = function(cell_x_adt_sample, landmark_pos, bw, adt_marker_select_name, brewer_palettes = "Set1"){

min_value = floor(min(cell_x_adt_sample[, 1], na.rm = TRUE))
max_value = ceiling(max(cell_x_adt_sample[, 1], na.rm = TRUE)) + 2
# cell_x_adt_sample_filter = cell_x_adt_sample %>% dplyr::filter(!is.na(adt))
sample_num = levels(cell_x_adt_sample$sample) %>% length
plot_height = paste0(sample_num * 50, "px")
cell_x_adt_sample$sample_ordered = factor(cell_x_adt_sample$sample, levels = levels(cell_x_adt_sample$sample))
## Create an example UI
ui <- create_ui(landmark_pos, max_value, bw, plot_height)
server <- create_server(landmark_pos, cell_x_adt_sample, bw, adt_marker_select_name, brewer_palettes, max_value)
server <- create_server(landmark_pos, cell_x_adt_sample, bw, adt_marker_select_name, brewer_palettes, min_value, max_value)

## Return user input, vals can change
res <- shiny::runApp(shinyApp(ui, server))
Expand Down Expand Up @@ -74,33 +75,33 @@ create_ui <- function(landmark_pos, max_value, bw, plot_height) {
}


create_server <- function(landmark_pos, cell_x_adt_sample, bw = 0.1, adt_marker_select_name, brewer_palettes = "Set1", max_value) {
create_server <- function(landmark_pos, cell_x_adt_sample, bw = 0.1, adt_marker_select_name, brewer_palettes = "Set1", min_value, max_value) {

fillColor <- grDevices::colorRampPalette(RColorBrewer::brewer.pal(8, brewer_palettes))(length(unique(cell_x_adt_sample$batch)))


server <- function(input, output, session) {
vals <- shiny::reactiveValues(
landmark_pos = landmark_pos,
slider_values = flat_table(landmark_pos),
fig = NULL
)

output$table <- DT::renderDataTable(vals$landmark_pos %>% DT::datatable() %>% DT::formatRound(columns = colnames(landmark_pos), digits = 3))

output$plot <- renderPlot({
bw_value <- input$bandwidth_slider
# no_mis_idx = !is.na(cell_x_adt_sample$adt)
vals$fig <- ggplot(cell_x_adt_sample, aes_string(x = "adt", y = "sample_ordered")) +

vals$fig <- ggplot(cell_x_adt_sample, aes_string(x = "adt", y = "sample_ordered")) +
ggridges::geom_density_ridges2(aes(fill = factor(batch)), bandwidth = bw_value) +
theme_bw(base_size = 20) +
ggpubr::rotate_x_text(angle = 90) +
ggpubr::rremove("legend") +
xlab(paste0(adt_marker_select_name, " ADT Counts")) +
ylab("Sample") +
scale_fill_manual(values = fillColor) +
scale_x_continuous(breaks = seq(0, max_value, 0.5)) +
scale_x_continuous(breaks = seq(min_value, max_value, 0.5)) +
# geom_point(data = vals$slider_values, aes_string(x = "x", y = "y", shape = "type"), size = 5)
geom_segment(
data = vals$slider_values,
Expand All @@ -112,7 +113,7 @@ create_server <- function(landmark_pos, cell_x_adt_sample, bw = 0.1, adt_marker_
vals$fig
})


output$landmark_slider_ui <- renderUI({
if (!is.null(input$landmark_select)) {
fluidRow(
Expand All @@ -132,7 +133,7 @@ create_server <- function(landmark_pos, cell_x_adt_sample, bw = 0.1, adt_marker_
sliderInput(
inputId = paste0(colnames(landmark_pos)[j]),
label = colnames(landmark_pos)[j],
min = 0,
min = min_value,
max = max_value,
value = val,
step = 0.0001
Expand All @@ -143,7 +144,7 @@ create_server <- function(landmark_pos, cell_x_adt_sample, bw = 0.1, adt_marker_
)
}
})

observeEvent(input$applied, {
i <- which(rownames(landmark_pos) == input$landmark_select)
for (j in 1:ncol(landmark_pos)) {
Expand All @@ -154,22 +155,22 @@ create_server <- function(landmark_pos, cell_x_adt_sample, bw = 0.1, adt_marker_
}
}
output$table <- DT::renderDataTable(vals$landmark_pos %>% DT::datatable() %>% DT::formatRound(columns = colnames(landmark_pos), digits = 3))

slider_values <- flat_table(vals$landmark_pos)

output$plot <- renderPlot({
bw_value <- input$bandwidth_slider
vals$fig <- ggplot(cell_x_adt_sample, aes_string(x = "adt", y = "sample_ordered")) +

vals$fig <- ggplot(cell_x_adt_sample, aes_string(x = "adt", y = "sample_ordered")) +
ggridges::geom_density_ridges2(aes(fill = factor(batch)), bandwidth = bw_value) +
theme_bw(base_size = 20) +
ggpubr::rotate_x_text(angle = 90) +
ggpubr::rremove("legend") +
xlab(paste0(adt_marker_select_name, " ADT Counts")) +
ylab("Sample") +
scale_fill_manual(values = fillColor) +
scale_x_continuous(breaks = seq(0, max_value, 0.5)) +
# geom_point(data = slider_values, aes_string(x = "x", y = "y", shape = "type"), size = 5)
scale_x_continuous(breaks = seq(min_value, max_value, 0.5)) +
# geom_point(data = slider_values, aes_string(x = "x", y = "y", shape = "type"), size = 5)
geom_segment(
data = slider_values,
aes(x = x, xend = x, y = peaky, yend = peaky+0.5, color = type),
Expand All @@ -179,12 +180,12 @@ create_server <- function(landmark_pos, cell_x_adt_sample, bw = 0.1, adt_marker_
vals$fig
})
})

shiny::observeEvent(input$done, {
shiny::stopApp(vals$landmark_pos)
})
}

return(server)

}
Expand Down