ml dash
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3 changed files with 99 additions and 77 deletions
32
ml/global.R
32
ml/global.R
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@ -56,6 +56,8 @@ split_map = data.frame(
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)
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)
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)
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)
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colour_range=c("#605ca8", "#bebddb", "#221e70")
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metadata_cols = c("n_training_size", "n_test_size", "n_trainingY_ratio", "n_testY_ratio", "resampling", "n_features")
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metadata_cols = c("n_training_size", "n_test_size", "n_trainingY_ratio", "n_testY_ratio", "resampling", "n_features")
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# hardcoded list of drugs
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# hardcoded list of drugs
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@ -159,9 +161,6 @@ makeplot = function(x, # the DataFrame to plot
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, position=position_dodge2(padding=0.1, preserve='total', reverse=TRUE)
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, position=position_dodge2(padding=0.1, preserve='total', reverse=TRUE)
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) +
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) +
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coord_cartesian(ylim = c(y_coord_min, 1)) +
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coord_cartesian(ylim = c(y_coord_min, 1)) +
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#scale_fill_manual(values = c("BT" = "#605ca8",
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# "CV" = "#bebddb") ) +
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#guides=guide_legend(reverse=TRUE) +
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annotation_custom(grob) +
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annotation_custom(grob) +
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# doesn't work with plotly but looks nice :-(
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# doesn't work with plotly but looks nice :-(
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geom_label(aes_string(label=selection),
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geom_label(aes_string(label=selection),
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@ -172,15 +171,10 @@ makeplot = function(x, # the DataFrame to plot
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fill="white"
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fill="white"
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) +
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) +
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scale_color_manual(values = colour_range) +
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scale_fill_manual(values = colour_range) +
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# works with plotly but i can't figure out the background yet
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# geom_text(aes_string(label=selection, group=selection),
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# position=position_dodge(width = -0.75),
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# vjust = 1.5,
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# alpha=0.75,
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#
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# ) +
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# add little numbers for the BT bars only
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# add little numbers for the BT bars only
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labs(x="",y=paste(selection,"Score")) +
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labs(x="",y=paste(selection,"Score")) +
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theme(
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theme(
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@ -210,7 +204,21 @@ if (interactive()){
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combined_training_genes = input$combined_training_genes
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combined_training_genes = input$combined_training_genes
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selected_gene = combo[combo$drug == selected_drug,'gene']
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selected_gene = combo[combo$drug == selected_drug,'gene']
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if (combined_data == "FS"){
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updateRadioButtons(
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inputId="combined_training_genes",
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choiceNames = c("One", "Two"),
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choiceValues = c("1", "2"),
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selected = "2"
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)
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} else{
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updateRadioButtons(
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inputId="combined_training_genes",
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choiceNames = c("Five", "Six"),
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choiceValues = c("5","6"),
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selected = "5"
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)
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}
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# hide stuff if selected
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# hide stuff if selected
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if(combined_model == "combined") {
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if(combined_model == "combined") {
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#if(combined_model == TRUE) {
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#if(combined_model == TRUE) {
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28
ml/server.R
28
ml/server.R
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@ -18,12 +18,26 @@ shinyServer(function(input, output) {
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selected_split = input$split_dropdown
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selected_split = input$split_dropdown
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combined_data = input$combined_data
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combined_data = input$combined_data
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combined_training_genes = input$combined_training_genes
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combined_training_genes = input$combined_training_genes
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selected_gene = combo[combo$drug == selected_drug,'gene']
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selected_gene = combo[combo$drug == selected_drug,'gene']
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if (combined_data == "FS"){
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updateRadioButtons(
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inputId="combined_training_genes",
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choiceNames = c("One", "Two"),
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choiceValues = c("1", "2"),
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selected = "2"
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)
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} else{
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updateRadioButtons(
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inputId="combined_training_genes",
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choiceNames = c("Five", "Six"),
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choiceValues = c("5","6"),
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selected = "5"
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)
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}
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# hide stuff if selected
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# hide stuff if selected
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if(combined_model == "combined") {
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if(combined_model == "combined") {
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#if(combined_model == TRUE) {
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#if(combined_model == TRUE) {
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hide("split_dropdown")
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hide("split_dropdown")
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#show("resample_dropdown")
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#show("resample_dropdown")
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@ -66,13 +80,13 @@ shinyServer(function(input, output) {
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display_combined = FALSE,
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display_combined = FALSE,
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)
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)
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)
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)
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}
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}
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# 6genes_logo_skf_BT_gid_complete
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# 6genes_logo_skf_BT_gid_complete
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# filedata example for combined: 6genes_logo_skf_BT_embb_actual
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# filedata example for combined: 6genes_logo_skf_BT_embb_actual
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# 6genes_logo_skf_BT_embb_combined
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# 6genes_logo_skf_BT_embb_combined
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})
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})
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}
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}
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)
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)
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116
ml/ui.R
116
ml/ui.R
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@ -9,61 +9,61 @@ library(plotly)
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library(shinycssloaders)
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library(shinycssloaders)
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dashboardPage(skin="purple",
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dashboardPage(skin="purple",
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dashboardHeader(title="Score Selector"),
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dashboardHeader(title="Score Selector"),
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dashboardSidebar(
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dashboardSidebar(
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radioButtons("combined_model",
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radioButtons("combined_model",
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label="Graph Model",
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label="Graph Model",
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choiceNames = c("Combined", "Gene"),
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choiceNames = c("Combined", "Gene"),
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choiceValues = c("combined", "gene"),
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choiceValues = c("combined", "gene"),
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selected="gene"
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selected="gene"
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),
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),
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# checkboxInput("combined_model",
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# checkboxInput("combined_model",
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# "Combined Model",
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# "Combined Model",
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# value=FALSE
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# value=FALSE
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# ),
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# ),
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#),
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#),
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radioButtons("combined_data",
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radioButtons("combined_data",
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label="Data Type",
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label="Data Type",
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choiceNames = c("Complete", "Actual", "Feature Selection"),
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choiceNames = c("Complete", "Actual", "Feature Selection"),
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choiceValues = c("complete", "actual", "FS"),
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choiceValues = c("complete", "actual", "FS"),
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selected="complete"
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selected="complete"
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),
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),
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radioButtons("combined_training_genes",
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radioButtons("combined_training_genes",
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label="Training Genes",
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label="Training Genes",
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choiceNames = c("One", "Two", "Five", "Six"),
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choiceNames = c("One", "Two", "Five", "Six"),
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choiceValues = c("1", "2", "5","6"),
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choiceValues = c("1", "2", "5","6"),
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selected = "5"
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selected = "5"
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),
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),
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radioButtons("drug_dropdown",
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radioButtons("drug_dropdown",
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label="Drug",
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label="Drug",
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choices = drug,
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choices = drug,
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selected="pyrazinamide"
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selected="pyrazinamide"
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),
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),
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radioButtons("split_dropdown",
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radioButtons("split_dropdown",
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label="Split",
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label="Split",
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choices = split_type,
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choices = split_type,
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selected="cd_7030"
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selected="cd_7030"
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),
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),
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radioButtons("score_dropdown",
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radioButtons("score_dropdown",
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label="Score",
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label="Score",
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choices = scores,
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choices = scores,
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selected="MCC"
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selected="MCC"
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),
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),
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radioButtons("resample_dropdown",
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radioButtons("resample_dropdown",
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label="Resampling",
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label="Resampling",
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choices = resample_types,
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choices = resample_types,
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selected="none" # "none" is a value
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selected="none" # "none" is a value
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)
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)
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),
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),
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dashboardBody(
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dashboardBody(
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useShinyjs(),
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useShinyjs(),
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#plotlyOutput("plot", height = 800),
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#plotlyOutput("plot", height = 800),
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plotOutput("plot", height = 800),
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plotOutput("plot", height = 800),
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# %>% withSpinner(color="#0dc5c1"), # uncomment if you want the spinner
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# %>% withSpinner(color="#0dc5c1"), # uncomment if you want the spinner
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#downloadButton("save", "Download Plot"),
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#downloadButton("save", "Download Plot"),
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#DT::dataTableOut("plotdata"),
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#DT::dataTableOut("plotdata"),
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verbatimTextOutput("debug")
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verbatimTextOutput("debug")
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)
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)
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)
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)
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