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Added fatty acid analysis plots. #159

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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
Package: soda
Title: Simple Omics Data Analysis
Version: 0.8.55
Version: 0.8.55.9000
Authors@R:
c(person(given = "Yassene",
family = "Mohammed",
Expand Down
122 changes: 119 additions & 3 deletions R/class_lips_exp.R
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Original file line number Diff line number Diff line change
Expand Up @@ -272,6 +272,7 @@ Lips_exp = R6::R6Class(
pca_scores_table = NULL,
pca_loadings_table = NULL,
dbplot_table = NULL,
fa_analysis_table = NULL,

# GSEA & over representation
gsea_prot_list = NULL,
Expand All @@ -292,6 +293,7 @@ Lips_exp = R6::R6Class(
heatmap = NULL,
pca_plot = NULL,
double_bond_plot = NULL,
fa_analysis_plot = NULL,

# Functional analysis plots
dotplot = NULL,
Expand Down Expand Up @@ -486,6 +488,14 @@ Lips_exp = R6::R6Class(
self$params$or_emap_plot$enable_physics = enable_physics
},

param_fa_analysis_plot = function(data_table, feature_meta, sample_meta, group_column, pathway, img_format) {
self$params$fa_analysis_plot$data_table = data_table
self$params$fa_analysis_plot$feature_meta = feature_meta
self$params$fa_analysis_plot$sample_meta = sample_meta
self$params$fa_analysis_plot$group_col = group_column
self$params$fa_analysis_plot$pathway = pathway
self$params$fa_analysis_plot$img_format = img_format
},

#-------------------------------------------------------- Table methods ----

Expand Down Expand Up @@ -859,9 +869,12 @@ Lips_exp = R6::R6Class(
self$param_ridge_plot(showCategory = 30,
img_format = "png")




self$param_fa_analysis_plot(data_table = self$tables$raw_data,
feature_meta = self$tables$feature_table,
sample_meta = self$tables$raw_meta,
group_column = self$indices$group_col,
pathway = NULL,
img_format = "png")



Expand Down Expand Up @@ -2246,7 +2259,110 @@ Lips_exp = R6::R6Class(
layout(xaxis = list(title = 'Count')
)
self$plots$or_barplot = fig
},


plot_fa_analysis = function(data_table = self$tables$raw_data,
feature_table = self$tables$feature_table,
sample_meta = self$tables$raw_meta,
group_col = self$indices$group_col,
pathway = self$params$fa_analysis_plot$pathway,
colour_list,
width = NULL,
height = NULL) {

## At the moment this function is using the raw data table
# do the calculations
res <- fa_analysis_calc(data_table = data_table,
feature_table = feature_table,
sample_meta = sample_meta)


# Produce the class x group table
# add ID's, group's and make long
res$ID <- rownames(res)
res$group <- sample_meta[res$ID, group_col]
res_long <- res |>
tidyr::pivot_longer(cols = -c(ID, group),
names_to = "fa_chain",
values_to = "value")

# calculate mean and stdev per group
plot_table <- tapply(as.data.frame(res_long), list(res_long$group, res_long$fa_chain), function(x) {
avg <- mean(x[, "value"], na.rm = TRUE)
stdev <- sd(x[, "value"], na.rm = TRUE)

return(list(avg = avg,
stdev = stdev,
fa_chain = x[1, "fa_chain"],
group = x[1, "group"]))
# print(x)
})

plot_table <- do.call(rbind.data.frame, plot_table)

# filter plot_table based on pathway selection
pathway_fa <- c(
paste(seq(16, 26, 2), 0, sep = ":"),
paste(seq(16, 24, 2), 1, sep = ":"),
c("18:2", "18:3", "20:2", "20:3", "20:4",
"22:4", "22:5","24:4", "24:5"),
c("18:3", "18:4", "20:3", "20:4", "20:5",
"22:5", "22:6", "24:5", "24:6")
)
names(pathway_fa) <- c(rep("SFA", 6),
rep("MUFA", 5),
rep("PUFA6", 9),
rep("PUFA3", 9))

if(!is.null(pathway)) {
selected_pathway_fa <- unique(pathway_fa[names(pathway_fa) %in% pathway])
plot_table <- plot_table[plot_table$fa_chain %in% selected_pathway_fa, ]
}

# Store the plot_table
self$tables$fa_analysis_table <- plot_table

# plotting
i <- 1
fig <- plotly::plot_ly(colors = colour_list, width = width, height = height)
for (grp in unique(plot_table$group)) {
fig <- fig |>
plotly::add_trace(data = plot_table[plot_table$group == grp, ],
x = ~fa_chain,
y = ~avg,
color = colour_list[i],
type = "bar",
name = grp,
error_y = ~ list(array = stdev,
color = "#000000"))
fig <- fig |>
plotly::layout(legend = list(orientation = 'h',
xanchor = "center",
x = 0.5),
xaxis = list(title = "Fatty acid chain"),
yaxis = list(title = "Concentration"))
i <- i + 1
}
fig <- fig |>
plotly::layout(annotations =
list(x = 1,
y = -0.175,
text = "NOTE: error bars are standard deviation",
showarrow = FALSE,
xref = "paper",
yref = "paper",
xanchor = "right",
yanchor = "auto",
xshift = 0,
yshift = 0,
font = list(size = 10))
)
fig

self$plots$fa_analysis_plot <- fig
}

#------------------------------------------------------------------ END ----
)
)
137 changes: 136 additions & 1 deletion R/plotboxes_lipidomics.R
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Original file line number Diff line number Diff line change
Expand Up @@ -1476,4 +1476,139 @@ db_plot_events = function(r6, dimensions_obj, color_palette, input, output, sess
))
}
})
}
}


#-----------------------------------------------------------FA analysis index ----
fa_analysis_generate = function(r6, colour_list, dimensions_obj, input) {
print_tm(r6$name, "Fatty acid analysis index plot: generating plot.")

if (input$fa_analysis_plotbox$maximized){
width = dimensions_obj$xpx_total * dimensions_obj$x_plot_full
height = dimensions_obj$ypx_total * dimensions_obj$y_plot_full
} else {
width = dimensions_obj$xpx * dimensions_obj$x_plot
height = dimensions_obj$ypx * dimensions_obj$y_plot
}

r6$plot_fa_analysis(data_table = r6$tables$raw_data, #table_switch(input$class_comparison_dataset, r6),
group_col = input$fa_analysis_metacol,
colour_list = colour_list,
width = width,
height = height)
}

fa_analysis_spawn = function(r6, format, output) {
print_tm(r6$name, "Fatty acid analysis index: spawning plot.")

output$fa_analysis_plot = plotly::renderPlotly({
r6$plots$fa_analysis_plot
plotly::config(r6$plots$fa_analysis_plot, toImageButtonOptions = list(format = format,
filename = timestamped_name('fa_analysis'),
height = NULL,
width = NULL,
scale = 1))
})
}

fa_analysis_ui = function(dimensions_obj, session) {
# add function to show bs4dash with plotting function
get_plotly_box(id = "fa_analysis",
label = "Fatty acid analysis",
dimensions_obj = dimensions_obj,
session = session)
}

fa_analysis_server = function(r6, output, session) {
ns = session$ns
print_tm(r6$name, "Fatty acid analysis index: START.")

# set some UI
output$fa_analysis_sidebar_ui = shiny::renderUI({
shiny::tagList(
shiny::selectInput(
inputId = ns("fa_analysis_metacol"),
label = "Select group column",
choices = colnames(r6$tables$raw_meta),
selected = r6$params$fa_analysis_plot$group_col
),
shiny::selectInput(
inputId = ns("fa_analysis_pathway"),
label = "Select pathway",
choices = c("SFA" = "SFA",
"MUFA" = "MUFA",
"PUFA(n-6)" = "PUFA6",
"PUFA(n-3)" = "PUFA3"),
selected = "",
multiple = TRUE,
width = "100%"),
shiny::hr(style = "border-top: 1px solid #7d7d7d;"),
shiny::selectInput(
inputId = ns("fa_analysis_img_format"),
label = "Image format",
choices = c("png", "svg", "jpeg", "webp"),
selected = r6$params$fa_analysis_plot$img_format,
width = "100%"),
shiny::downloadButton(
outputId = ns("download_fa_analysis_table"),
label = "Download associated table",
style = "width:100%;"
)
)
})
}

fa_analysis_events = function(r6, dimensions_obj, color_palette, input, output, session) {
# Generate the plot
shiny::observeEvent(c(input$fa_analysis_metacol,
input$fa_analysis_pathway,
input$fa_analysis_img_format), {
print_tm(r6$name, "Fatty acid analysis: Updating params...")

r6$param_fa_analysis_plot(data_table = r6$tables$raw_data,
feature_meta = r6$tables$feature_table,
sample_meta = r6$tables$raw_meta,
group_col = input$fa_analysis_metacol,
pathway = input$fa_analysis_pathway,
img_format = input$fa_analysis_img_format)

base::tryCatch({
fa_analysis_generate(r6, color_palette, dimensions_obj, input)
fa_analysis_spawn(r6, input$fa_analysis_img_format, output)
},
error = function(e) {
print_tm(r6$name, 'Fatty acid analysis error, missing data.')
print(e)
},
finally = {}
)
})

# Download associated table
output$download_fa_analysis_table = shiny::downloadHandler(
filename = function(){timestamped_name("fa_analysis_table.csv")},
content = function(file_name){
write.csv(r6$tables$fa_analysis_table, file_name)
}
)

# Expanded boxes
fa_analysis_proxy = plotly::plotlyProxy(outputId = "fa_analysis_plot",
session = session)

shiny::observeEvent(input$fa_analysis_plotbox,{
if (input$fa_analysis_plotbox$maximized) {
plotly::plotlyProxyInvoke(p = fa_analysis_proxy,
method = "relayout",
list(width = dimensions_obj$xpx_total * dimensions_obj$x_plot_full,
height = dimensions_obj$ypx_total * dimensions_obj$y_plot_full
))
} else {
plotly::plotlyProxyInvoke(p = fa_analysis_proxy,
method = "relayout",
list(width = dimensions_obj$xpx * dimensions_obj$x_plot,
height = dimensions_obj$ypx * dimensions_obj$y_plot
))
}
})
}
8 changes: 6 additions & 2 deletions R/serv_lipidomics.R
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,8 @@ plotbox_switch_ui_lips = function(selection_list){
"select_volcano_plot" = volcano_plot_ui,
"select_heatmap" = heatmap_ui,
"select_pca" = pca_ui,
"select_double_bond_plot" = double_bonds_ui
"select_double_bond_plot" = double_bonds_ui,
"select_fa_analysis_plot" = fa_analysis_ui
)
)
}
Expand All @@ -25,7 +26,8 @@ plotbox_switch_server_lips = function(selection_list){
"select_volcano_plot" = volcano_plot_server,
"select_heatmap" = heatmap_server,
"select_pca" = pca_server,
"select_double_bond_plot" = double_bonds_server
"select_double_bond_plot" = double_bonds_server,
"select_fa_analysis_plot" = fa_analysis_server
)
)
}
Expand Down Expand Up @@ -2124,6 +2126,8 @@ lipidomics_server = function(id, ns, input, output, session, module_controler) {
heatmap_events(r6, dimensions_obj, color_palette, input, output, session)
pca_events(r6, dimensions_obj, color_palette, input, output, session)
db_plot_events(r6, dimensions_obj, color_palette, input, output, session)
fa_analysis_events(r6, dimensions_obj, color_palette, input, output, session)

session$userData[[id]]$showPlots = shiny::observeEvent(input$showPlots,{

# Update x dimensions in px and bs, and y in px
Expand Down
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