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Changes also for deseq2
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@PaulJonasJost
PaulJonasJost committed Jan 30, 2025
1 parent bd008f5 commit 76bd6ee
Showing 1 changed file with 70 additions and 37 deletions.
107 changes: 70 additions & 37 deletions program/shinyApp/R/significance_analysis/util.R
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Original file line number Diff line number Diff line change
Expand Up @@ -374,13 +374,15 @@ create_new_tab_manual <- function(title, targetPanel, result, contrast, alpha, n

output[[ns(paste(contrast[1], contrast[2], "Volcano", sep = "_"))]] <- renderPlotly({ggplotly(
sig_ana_reactive$VolcanoPlot,
legendgroup="color"
tooltip = ifelse(is.null(sig_ana_reactive$Volcano_anno_tooltip),"all","chosenAnno"),
legendgroup = "color"
) %>% layout(
showlegend = TRUE
)})
output[[ns(paste(contrast[1], contrast[2], "Volcano_praw", sep = "_"))]] <- renderPlotly({ggplotly(
sig_ana_reactive$VolcanoPlot_raw,
legendgroup="color"
tooltip = ifelse(is.null(sig_ana_reactive$Volcano_anno_tooltip),"all","chosenAnno"),
legendgroup = "color"
) %>% layout(
showlegend = TRUE
)})
Expand Down Expand Up @@ -675,20 +677,32 @@ create_new_tab_DESeq <- function(title, targetPanel, result, contrast, alpha, ns
),
tabPanel(
title = "Volcano",
splitLayout(
style = "border: 1px solid silver:",
cellWidths = c("40%", "60%"),
plotlyOutput(
outputId = ns(paste(contrast[1], contrast[2], "Volcano", sep = "_"))
),
plotlyOutput(
outputId = ns(paste(contrast[1], contrast[2], "Volcano_praw", sep = "_"))
)
plotlyOutput(
outputId = ns(paste(contrast[1], contrast[2], "Volcano", sep = "_"))
),
plotlyOutput(
outputId = ns(paste(contrast[1], contrast[2], "Volcano_praw", sep = "_"))
),
hr(style = "border-top: 1px solid #000000;"),
uiOutput(outputId = ns(paste(contrast[1], contrast[2], "psig_th_ui", sep = "_"))),
uiOutput(outputId = ns(paste(contrast[1], contrast[2], "lfc_th_ui", sep = "_"))),
uiOutput(outputId = ns(paste(contrast[1], contrast[2], "Volcano_anno_tooltip_ui", sep = "_"))),
fluidRow(
id = ns("aligned_row"), # Assign an ID to apply CSS
class = "align-bottom",
column(3, uiOutput(outputId = ns(paste(contrast[1], contrast[2], "psig_th_ui", sep = "_")))),
column(3, uiOutput(outputId = ns(paste(contrast[1], contrast[2], "lfc_th_ui", sep = "_")))),
column(3, uiOutput(outputId = ns(paste(contrast[1], contrast[2], "Volcano_anno_tooltip_ui", sep = "_")))),
column(3,
checkboxInput(
ns(paste(contrast[1], contrast[2], "show_legend_adj", sep = "_")),
"Show Legend Corrected",
value = TRUE
),
checkboxInput(
ns(paste(contrast[1], contrast[2], "show_legend_raw", sep = "_")),
"Show Legend Uncorrected",
value = TRUE
),
)
),
splitLayout(
style = "border: 1px solid silver:",
cellWidths = c("35%","35%", "30%"),
Expand Down Expand Up @@ -813,6 +827,9 @@ create_new_tab_DESeq <- function(title, targetPanel, result, contrast, alpha, ns
psig_th <- ns(paste(contrast[1], contrast[2], "psig_th", sep = "_"))
lfc_th <- ns(paste(contrast[1], contrast[2], "lfc_th", sep = "_"))
Volcano_anno_tooltip <- ns(paste(contrast[1], contrast[2], "Volcano_anno_tooltip", sep = "_"))
show_legend_adj <- ns(paste(contrast[1], contrast[2], "show_legend_adj", sep = "_"))
show_legend_raw <- ns(paste(contrast[1], contrast[2], "show_legend_raw", sep = "_"))

output[[ns(paste(contrast[1], contrast[2], "Volcano_anno_tooltip_ui", sep = "_"))]] <- renderUI({
selectInput(
inputId = Volcano_anno_tooltip,
Expand Down Expand Up @@ -848,6 +865,16 @@ create_new_tab_DESeq <- function(title, targetPanel, result, contrast, alpha, ns
input[[lfc_th]]
)
})
observeEvent(input[[show_legend_adj]], {
print("Show legend adjusted")
plotlyProxy(paste(contrast[1], contrast[2], "Volcano", sep = "_")) %>%
plotlyProxyInvoke(method = "relayout", list(showlegend = input[[show_legend_adj]]))
})
observeEvent(input[[show_legend_raw]], {
print("Show legend raw")
plotlyProxy(paste(contrast[1], contrast[2], "Volcano_praw", sep = "_")) %>%
plotlyProxyInvoke(method = "relayout", list(showlegend = input[[show_legend_raw]]))
})
observeEvent(toPlotVolcano(), {
req(input[[psig_th]], input[[lfc_th]])
waiter <- Waiter$new(
Expand Down Expand Up @@ -894,55 +921,61 @@ create_new_tab_DESeq <- function(title, targetPanel, result, contrast, alpha, ns
aes(label=chosenAnno)
) +
geom_point(aes(
x = log2FoldChange,
y = -log10(padj),
x = -log10(padj),
y = log2FoldChange,
colour = combined
)) +
geom_hline(
yintercept = -log10(sig_ana_reactive$th_psig),
geom_vline(
xintercept = -log10(sig_ana_reactive$th_psig),
color="lightgrey"
) +
geom_vline(
xintercept = c(-sig_ana_reactive$th_lfc,sig_ana_reactive$th_lfc),
geom_hline(
yintercept = c(-sig_ana_reactive$th_lfc,sig_ana_reactive$th_lfc),
color="lightgrey"
) +
scale_color_manual(values=colorScheme2, name="") +
xlab("Log FoldChange") +
ylab("-log10(p_adj-value)") +
ylab("Log FoldChange") +
xlab("-log10(p_adj-value)") +
ggtitle(label="Corrected p-Values") +
CUSTOM_THEME

output[[ns(paste(contrast[1], contrast[2], "Volcano", sep = "_"))]] <- renderPlotly({ggplotly(
sig_ana_reactive$VolcanoPlot + theme(legend.position = "none"),
tooltip = ifelse(is.null(sig_ana_reactive$Volcano_anno_tooltip),"all","chosenAnno"),
legendgroup="color"
)})


sig_ana_reactive$VolcanoPlot_raw <- ggplot(
sig_ana_reactive$data4Volcano,
aes(label=chosenAnno)
) +
geom_point(aes(
x = log2FoldChange,
y = -log10(pvalue),
x = -log10(pvalue),
y = log2FoldChange,
colour = combined_raw)) +
geom_hline(
yintercept = -log10(sig_ana_reactive$th_psig),
geom_vline(
xintercept = -log10(sig_ana_reactive$th_psig),
color="lightgrey"
) +
geom_vline(
xintercept = c(-sig_ana_reactive$th_lfc,sig_ana_reactive$th_lfc),
geom_hline(
yintercept = c(-sig_ana_reactive$th_lfc,sig_ana_reactive$th_lfc),
color="lightgrey"
) +
scale_color_manual(values=colorScheme2, name="") +
xlab("Log FoldChange") +
ylab("-log10(p-value)") +
ggtitle(label="Uncorrected p-Values")+
ylab("Log FoldChange") +
xlab("-log10(p-value)") +
ggtitle(label="Uncorrected p-Values") +
CUSTOM_THEME

output[[ns(paste(contrast[1], contrast[2], "Volcano_praw", sep = "_"))]] <- renderPlotly({ggplotly(
sig_ana_reactive$VolcanoPlot_raw,
tooltip = ifelse(is.null(sig_ana_reactive$Volcano_anno_tooltip),"all","chosenAnno"),
legendgroup = "color"
) %>% layout(
showlegend = TRUE
)})

output[[ns(paste(contrast[1], contrast[2], "Volcano", sep = "_"))]] <- renderPlotly({ggplotly(
sig_ana_reactive$VolcanoPlot + theme(legend.position = "none"),
tooltip = ifelse(is.null(sig_ana_reactive$Volcano_anno_tooltip),"all","chosenAnno"),
legendgroup="color"
) %>% layout(
showlegend = TRUE
)})
})

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