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This commit is contained in:
Tanushree Tunstall 2022-09-04 18:45:35 +01:00
parent 74df62bb85
commit d627e88aeb
3 changed files with 99 additions and 77 deletions
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30
ml/global.R
View file

@ -56,6 +56,8 @@ split_map = data.frame(
)
)
colour_range=c("#605ca8", "#bebddb", "#221e70")
metadata_cols = c("n_training_size", "n_test_size", "n_trainingY_ratio", "n_testY_ratio", "resampling", "n_features")
# hardcoded list of drugs
@ -159,9 +161,6 @@ makeplot = function(x, # the DataFrame to plot
, position=position_dodge2(padding=0.1, preserve='total', reverse=TRUE)
) +
coord_cartesian(ylim = c(y_coord_min, 1)) +
#scale_fill_manual(values = c("BT" = "#605ca8",
# "CV" = "#bebddb") ) +
#guides=guide_legend(reverse=TRUE) +
annotation_custom(grob) +
# doesn't work with plotly but looks nice :-(
geom_label(aes_string(label=selection),
@ -172,14 +171,9 @@ makeplot = function(x, # the DataFrame to plot
fill="white"
) +
scale_color_manual(values = colour_range) +
scale_fill_manual(values = colour_range) +
# works with plotly but i can't figure out the background yet
# geom_text(aes_string(label=selection, group=selection),
# position=position_dodge(width = -0.75),
# vjust = 1.5,
# alpha=0.75,
#
# ) +
# add little numbers for the BT bars only
labs(x="",y=paste(selection,"Score")) +
@ -210,7 +204,21 @@ if (interactive()){
combined_training_genes = input$combined_training_genes
selected_gene = combo[combo$drug == selected_drug,'gene']
if (combined_data == "FS"){
updateRadioButtons(
inputId="combined_training_genes",
choiceNames = c("One", "Two"),
choiceValues = c("1", "2"),
selected = "2"
)
} else{
updateRadioButtons(
inputId="combined_training_genes",
choiceNames = c("Five", "Six"),
choiceValues = c("5","6"),
selected = "5"
)
}
# hide stuff if selected
if(combined_model == "combined") {
#if(combined_model == TRUE) {

20
ml/server.R
View file

@ -20,10 +20,24 @@ shinyServer(function(input, output) {
combined_training_genes = input$combined_training_genes
selected_gene = combo[combo$drug == selected_drug,'gene']
if (combined_data == "FS"){
updateRadioButtons(
inputId="combined_training_genes",
choiceNames = c("One", "Two"),
choiceValues = c("1", "2"),
selected = "2"
)
} else{
updateRadioButtons(
inputId="combined_training_genes",
choiceNames = c("Five", "Six"),
choiceValues = c("5","6"),
selected = "5"
)
}
# hide stuff if selected
if(combined_model == "combined") {
#if(combined_model == TRUE) {
#if(combined_model == TRUE) {
hide("split_dropdown")
#show("resample_dropdown")
@ -73,6 +87,6 @@ shinyServer(function(input, output) {
# filedata example for combined: 6genes_logo_skf_BT_embb_actual
# 6genes_logo_skf_BT_embb_combined
})
})
}
)

110
ml/ui.R
View file

@ -9,61 +9,61 @@ library(plotly)
library(shinycssloaders)
dashboardPage(skin="purple",
dashboardHeader(title="Score Selector"),
dashboardSidebar(
radioButtons("combined_model",
label="Graph Model",
choiceNames = c("Combined", "Gene"),
choiceValues = c("combined", "gene"),
selected="gene"
),
dashboardHeader(title="Score Selector"),
dashboardSidebar(
radioButtons("combined_model",
label="Graph Model",
choiceNames = c("Combined", "Gene"),
choiceValues = c("combined", "gene"),
selected="gene"
),
# checkboxInput("combined_model",
# "Combined Model",
# value=FALSE
# ),
#),
# checkboxInput("combined_model",
# "Combined Model",
# value=FALSE
# ),
#),
radioButtons("combined_data",
label="Data Type",
choiceNames = c("Complete", "Actual", "Feature Selection"),
choiceValues = c("complete", "actual", "FS"),
selected="complete"
),
radioButtons("combined_training_genes",
label="Training Genes",
choiceNames = c("One", "Two", "Five", "Six"),
choiceValues = c("1", "2", "5","6"),
selected = "5"
),
radioButtons("drug_dropdown",
label="Drug",
choices = drug,
selected="pyrazinamide"
),
radioButtons("split_dropdown",
label="Split",
choices = split_type,
selected="cd_7030"
),
radioButtons("score_dropdown",
label="Score",
choices = scores,
selected="MCC"
),
radioButtons("resample_dropdown",
label="Resampling",
choices = resample_types,
selected="none" # "none" is a value
)
),
dashboardBody(
useShinyjs(),
#plotlyOutput("plot", height = 800),
plotOutput("plot", height = 800),
# %>% withSpinner(color="#0dc5c1"), # uncomment if you want the spinner
#downloadButton("save", "Download Plot"),
#DT::dataTableOut("plotdata"),
verbatimTextOutput("debug")
)
radioButtons("combined_data",
label="Data Type",
choiceNames = c("Complete", "Actual", "Feature Selection"),
choiceValues = c("complete", "actual", "FS"),
selected="complete"
),
radioButtons("combined_training_genes",
label="Training Genes",
choiceNames = c("One", "Two", "Five", "Six"),
choiceValues = c("1", "2", "5","6"),
selected = "5"
),
radioButtons("drug_dropdown",
label="Drug",
choices = drug,
selected="pyrazinamide"
),
radioButtons("split_dropdown",
label="Split",
choices = split_type,
selected="cd_7030"
),
radioButtons("score_dropdown",
label="Score",
choices = scores,
selected="MCC"
),
radioButtons("resample_dropdown",
label="Resampling",
choices = resample_types,
selected="none" # "none" is a value
)
),
dashboardBody(
useShinyjs(),
#plotlyOutput("plot", height = 800),
plotOutput("plot", height = 800),
# %>% withSpinner(color="#0dc5c1"), # uncomment if you want the spinner
#downloadButton("save", "Download Plot"),
#DT::dataTableOut("plotdata"),
verbatimTextOutput("debug")
)
)