dash
This commit is contained in:
parent
f9db5cbc33
commit
27f70afb2c
2 changed files with 350 additions and 325 deletions
|
|
@ -124,9 +124,18 @@ function(input, output, session) {
|
|||
|
||||
|
||||
# different data ranges required for SNP distances
|
||||
snp_ligand_dist_df3 = merged_df3[merged_df3$ligand_distance<input$snp_ligand_dist,]
|
||||
snp_interface_dist_df3 = merged_df3[merged_df3$interface_dist<input$snp_interface_dist,]
|
||||
snp_nca_dist_df3 = merged_df3[merged_df3$nca_distance<input$snp_nca_dist,]
|
||||
snp_ligand_dist_df3 = merged_df3[merged_df3[['ligand_distance']]<input$snp_ligand_dist,]
|
||||
if ("interface_dist" %in% colnames(merged_df3)){
|
||||
snp_interface_dist_df3 = merged_df3[merged_df3[['interface_dist']]<input$snp_interface_dist,]
|
||||
} else {
|
||||
snp_interface_dist_df3 = NULL
|
||||
}
|
||||
|
||||
if ("nca_distance" %in% colnames(merged_df3)){
|
||||
snp_nca_dist_df3 = merged_df3[merged_df3[['nca_distance']]<input$snp_nca_dist,]
|
||||
} else {
|
||||
snp_nca_dist_df3 = NULL
|
||||
}
|
||||
|
||||
stability_colname = stability_boxes_df[stability_boxes_df$stability_type==input$stability_snp_param,"stability_colname"]
|
||||
outcome_colname = stability_boxes_df[stability_boxes_df$stability_type==input$stability_snp_param,"outcome_colname"]
|
||||
|
|
@ -162,7 +171,8 @@ function(input, output, session) {
|
|||
### NGLViewer ####
|
||||
# Structure Viewer WebGL/NGLViewR window
|
||||
output$structure <- renderNGLVieweR({
|
||||
ngl_gene=isolate(input$switch_target)
|
||||
#ngl_gene=isolate(input$switch_target)
|
||||
ngl_gene=input$switch_target
|
||||
ngl_drug=target_map[[ngl_gene]]
|
||||
ngl_pdb_file=paste0(load_dir, "Data/", ngl_drug, '/output/depth/', ngl_gene, '_complex.pdb')
|
||||
print(ngl_pdb_file)
|
||||
|
|
@ -262,6 +272,8 @@ function(input, output, session) {
|
|||
geom_ls = 4
|
||||
)
|
||||
)
|
||||
|
||||
# if ("interface_dist" %in% colnames(input$switch_target)) {
|
||||
output$site_snp_count_interface = renderPlot(
|
||||
site_snp_count_bp(
|
||||
snp_interface_dist_df3,
|
||||
|
|
@ -272,7 +284,14 @@ function(input, output, session) {
|
|||
geom_ls = 4
|
||||
)
|
||||
)
|
||||
output$site_snp_count_nca = renderPlot(
|
||||
# } #else {
|
||||
# output$site_snp_count_interface = renderPlot(
|
||||
# ggplot() + annotate(x=1,y=1,"text", label="No interface data for this target")+theme_void()
|
||||
# )
|
||||
# }
|
||||
|
||||
output$site_snp_count_nca = renderPlot( #{
|
||||
#if ("nca_distance" %in% colnames(input$switch_target)) {
|
||||
site_snp_count_bp(
|
||||
snp_nca_dist_df3,
|
||||
title_colour = 'black',
|
||||
|
|
@ -281,8 +300,14 @@ function(input, output, session) {
|
|||
axis_label_size = 12,
|
||||
geom_ls = 4
|
||||
)
|
||||
# } else {
|
||||
# ggplot() + annotate(x=1,y=1,"text", label="No RNA data for this target")+theme_void()
|
||||
# }
|
||||
# }
|
||||
)
|
||||
|
||||
|
||||
|
||||
#### DM OM Plots ####
|
||||
#dm_om_param
|
||||
# order needs to be:
|
||||
|
|
|
|||
640
drug-target/ui.R
640
drug-target/ui.R
|
|
@ -8,341 +8,341 @@
|
|||
#### Shiny UI #####
|
||||
|
||||
dashboardPage(skin="purple",
|
||||
dashboardHeader(title = "Drug/Target Explorer"),
|
||||
|
||||
dashboardSidebar(
|
||||
sidebarMenu( id = "sidebar",
|
||||
selectInput(
|
||||
"switch_target",
|
||||
label="Switch to New Target",
|
||||
choices = c(
|
||||
"alr",
|
||||
"embb",
|
||||
"gid",
|
||||
"katg",
|
||||
"pnca",
|
||||
"rpob"
|
||||
),
|
||||
selected="embb"),
|
||||
menuItem("LogoP SNP", tabName="LogoP SNP"),
|
||||
#menuItem("Lineage Sample Count", tabName="Lineage Sample Count"),
|
||||
menuItem("Site SNP count", tabName="Site SNP count"),
|
||||
menuItem("Stability SNP by site", tabName="Stability SNP by site"),
|
||||
menuItem("DM OM Plots", tabName="DM OM Plots"),
|
||||
menuItem("Correlation", tabName="Correlation"),
|
||||
#menuItem("Lineage Distribution", tabName="Lineage Distribution"),
|
||||
menuItem("Consurf", tabName="Consurf"),
|
||||
menuItem("LogoP OR", tabName="LogoP OR"),
|
||||
menuItem("Lineage", tabName="Lineage"),
|
||||
#menuItem('Stability count', tabName='Stability count'),
|
||||
|
||||
# These conditionalPanel()s make extra settings appear in the sidebar when needed
|
||||
conditionalPanel(
|
||||
condition="input.sidebar == 'LogoP SNP'",
|
||||
textInput(
|
||||
"omit_snp_count",
|
||||
"Omit SNPs",
|
||||
value = c(0),
|
||||
placeholder = "1,3,6"
|
||||
)
|
||||
),
|
||||
# NOTE:
|
||||
# I *think* we can cheat here slightly and use the min/max from
|
||||
# merged_df3[['position']] for everything because the various
|
||||
# dataframes for a given gene/drug combination have the
|
||||
# same range of positions. May need fixing, especially
|
||||
# if we get/shrink the imported data files to something
|
||||
# more reasonable.
|
||||
conditionalPanel(
|
||||
condition="
|
||||
dashboardHeader(title = "Drug/Target Explorer"),
|
||||
|
||||
dashboardSidebar(
|
||||
sidebarMenu( id = "sidebar",
|
||||
selectInput(
|
||||
"switch_target",
|
||||
label="Switch to New Target",
|
||||
choices = c(
|
||||
"alr",
|
||||
"embb",
|
||||
"gid",
|
||||
"katg",
|
||||
"pnca",
|
||||
"rpob"
|
||||
),
|
||||
selected="embb"),
|
||||
menuItem("LogoP SNP", tabName="LogoP SNP"),
|
||||
#menuItem("Lineage Sample Count", tabName="Lineage Sample Count"),
|
||||
menuItem("Site SNP count", tabName="Site SNP count"),
|
||||
menuItem("Stability SNP by site", tabName="Stability SNP by site"),
|
||||
menuItem("DM OM Plots", tabName="DM OM Plots"),
|
||||
menuItem("Correlation", tabName="Correlation"),
|
||||
#menuItem("Lineage Distribution", tabName="Lineage Distribution"),
|
||||
menuItem("Consurf", tabName="Consurf"),
|
||||
menuItem("LogoP OR", tabName="LogoP OR"),
|
||||
menuItem("Lineage", tabName="Lineage"),
|
||||
#menuItem('Stability count', tabName='Stability count'),
|
||||
|
||||
# These conditionalPanel()s make extra settings appear in the sidebar when needed
|
||||
conditionalPanel(
|
||||
condition="input.sidebar == 'LogoP SNP'",
|
||||
textInput(
|
||||
"omit_snp_count",
|
||||
"Omit SNPs",
|
||||
value = c(0),
|
||||
placeholder = "1,3,6"
|
||||
)
|
||||
),
|
||||
# NOTE:
|
||||
# I *think* we can cheat here slightly and use the min/max from
|
||||
# merged_df3[['position']] for everything because the various
|
||||
# dataframes for a given gene/drug combination have the
|
||||
# same range of positions. May need fixing, especially
|
||||
# if we get/shrink the imported data files to something
|
||||
# more reasonable.
|
||||
conditionalPanel(
|
||||
condition="
|
||||
input.sidebar == 'LogoP SNP'||
|
||||
input.sidebar == 'Stability SNP by site' ||
|
||||
input.sidebar == 'Consurf' ||
|
||||
input.sidebar == 'LogoP OR'",
|
||||
sliderInput(
|
||||
"display_position_range"
|
||||
, "Display Positions"
|
||||
, min=1, max=150, value=c(1,150) # 150 is just a little less than the smallest pos_count
|
||||
)
|
||||
),
|
||||
|
||||
conditionalPanel(
|
||||
condition="
|
||||
sliderInput(
|
||||
"display_position_range"
|
||||
, "Display Positions"
|
||||
, min=1, max=150, value=c(1,150) # 150 is just a little less than the smallest pos_count
|
||||
)
|
||||
),
|
||||
|
||||
conditionalPanel(
|
||||
condition="
|
||||
input.sidebar == 'LogoP SNP' ||
|
||||
input.sidebar == 'LogoP OR' ||
|
||||
input.sidebar == 'LogoP ED'",
|
||||
selectInput(
|
||||
"logoplot_colour_scheme",
|
||||
label="Logo Plot Colour Scheme",
|
||||
choices = logoPlotSchemes,
|
||||
selected="chemistry"
|
||||
)
|
||||
),
|
||||
conditionalPanel(
|
||||
condition="input.sidebar == 'Correlation'",
|
||||
selectInput(
|
||||
"corr_method",
|
||||
label="Correlation Method",
|
||||
choices = list("spearman",
|
||||
"pearson",
|
||||
"kendall"),
|
||||
selected="spearman"
|
||||
)
|
||||
),
|
||||
conditionalPanel(
|
||||
condition="input.sidebar == 'Correlation'",
|
||||
numericInput(
|
||||
"corr_lig_dist"
|
||||
, "Ligand Distance Cutoff (Å)", value=1
|
||||
)
|
||||
),
|
||||
conditionalPanel(
|
||||
condition="input.sidebar == 'Site SNP count'",
|
||||
numericInput(
|
||||
"snp_ligand_dist"
|
||||
, "Ligand Distance Cutoff (Å)", value=10
|
||||
)
|
||||
),
|
||||
conditionalPanel(
|
||||
condition="input.sidebar == 'Site SNP count'",
|
||||
numericInput(
|
||||
"snp_interface_dist"
|
||||
, "Interface Distance Cutoff (Å)", value=10
|
||||
)
|
||||
),
|
||||
conditionalPanel(
|
||||
condition="input.sidebar == 'Site SNP count'",
|
||||
numericInput(
|
||||
"snp_nca_dist"
|
||||
, "NCA Distance Cutoff (Å)", value=10
|
||||
)
|
||||
),
|
||||
|
||||
conditionalPanel(
|
||||
condition="input.sidebar == 'Correlation'",
|
||||
checkboxGroupInput(
|
||||
"corr_selected",
|
||||
"Parameters",
|
||||
choiceNames = c(
|
||||
"DeepDDG",
|
||||
"Dynamut2",
|
||||
"FoldX",
|
||||
"ConSurf"#,
|
||||
),
|
||||
choiceValues = c(
|
||||
"DeepDDG",
|
||||
"Dynamut2",
|
||||
"FoldX",
|
||||
"ConSurf"#,
|
||||
),
|
||||
selected = c(
|
||||
"DeepDDG",
|
||||
"Dynamut2",
|
||||
"FoldX",
|
||||
"ConSurf"#,
|
||||
)
|
||||
)
|
||||
),
|
||||
|
||||
# conditionalPanel(
|
||||
# condition="input.sidebar == 'DM OM Plots'",
|
||||
# selectInput(
|
||||
# "dm_om_param",
|
||||
# label="Stability Parameter",
|
||||
# choices = keys(dm_om_map),
|
||||
# selected="SNAP2")
|
||||
# ),
|
||||
# colour_categ
|
||||
conditionalPanel(
|
||||
condition="input.sidebar == 'Stability SNP by site'",
|
||||
selectInput(
|
||||
"stability_snp_param",
|
||||
label="Stability Parameter",
|
||||
choices = stability_boxes_df$stability_type,
|
||||
selected="Average")
|
||||
),
|
||||
conditionalPanel(
|
||||
condition="input.sidebar == 'Stability SNP by site'",
|
||||
checkboxInput("reorder_custom_h",
|
||||
label="Reorder by SNP count",
|
||||
FALSE)
|
||||
),
|
||||
conditionalPanel(
|
||||
condition="input.sidebar.match(/^Lineage.*/)",
|
||||
checkboxInput("all_lineages",
|
||||
label="All Lineages",
|
||||
FALSE)
|
||||
),
|
||||
# an example of how you can match multiple things in frontend JS
|
||||
conditionalPanel(
|
||||
condition="input.sidebar == 'LogoP SNP' ||
|
||||
input.sidebar =='Stability SNP by site' ||
|
||||
input.sidebar =='Consurf' ||
|
||||
input.sidebar =='LogoP OR'",
|
||||
actionButton("clear_ngl",
|
||||
"Clear Structure")
|
||||
),
|
||||
conditionalPanel(
|
||||
condition="input.sidebar == 'LogoP SNP' ||
|
||||
input.sidebar =='Stability SNP by site' ||
|
||||
input.sidebar =='Consurf' ||
|
||||
input.sidebar =='LogoP OR'",
|
||||
actionButton("test_ngl",
|
||||
"Test NGLViewR")
|
||||
)#,
|
||||
|
||||
# downloadButton("save",
|
||||
# "Download Plot"
|
||||
# )
|
||||
# actionButton(
|
||||
# "reload_target",
|
||||
# label="Reload Target\nData (slow!)"
|
||||
# )
|
||||
|
||||
)
|
||||
),
|
||||
#### body ####
|
||||
body <- dashboardBody(
|
||||
|
||||
tabItems(
|
||||
tabItem(tabName = "dashboard",
|
||||
h2("Dashboard tab content")
|
||||
),
|
||||
|
||||
tabItem(tabName = "widgets",
|
||||
h2("Widgets tab content")
|
||||
)
|
||||
),
|
||||
# creates a 'Conditional Panel' containing a plot object from each of our
|
||||
# ggplot plot functions (and its associated data frame)
|
||||
fluidRow(column(width=12,
|
||||
lapply(plot_functions_df$tab_name,
|
||||
function(x){
|
||||
|
||||
plot_function=plot_functions_df[
|
||||
plot_functions_df$tab_name==x,
|
||||
"plot_function"]
|
||||
|
||||
plot_df=plot_functions_df[
|
||||
plot_functions_df$tab_name==x,
|
||||
"plot_df"]
|
||||
cat(paste0('\nCreating output: ', x))
|
||||
generate_conditionalPanel(x, plot_function, plot_df)
|
||||
|
||||
}
|
||||
selectInput(
|
||||
"logoplot_colour_scheme",
|
||||
label="Logo Plot Colour Scheme",
|
||||
choices = logoPlotSchemes,
|
||||
selected="chemistry"
|
||||
)
|
||||
)
|
||||
),
|
||||
# Explicit fluidRow() for Lineage plots together
|
||||
fluidRow(
|
||||
column(conditionalPanel(
|
||||
condition="input.sidebar.match(/^Lineage.*/)", box(
|
||||
title="Lineage Distribution"
|
||||
, status = "info"
|
||||
, width=NULL
|
||||
, plotOutput("lineage_distP", height="700px") %>% withSpinner(color="#0dc5c1"),
|
||||
height=800
|
||||
)
|
||||
), width=6
|
||||
),
|
||||
column(conditionalPanel(
|
||||
condition="input.sidebar.match(/^Lineage.*/)", box(
|
||||
title="Lineage SNP Diversity"
|
||||
, status = "info"
|
||||
, width=NULL
|
||||
, plotOutput("lin_sc", height="700px") %>% withSpinner(color="#0dc5c1"),
|
||||
height=800
|
||||
)
|
||||
), width=6
|
||||
)
|
||||
|
||||
),
|
||||
# Explicit fluidRow() for Site SNP Count
|
||||
fluidRow(
|
||||
column(conditionalPanel(
|
||||
condition="input.sidebar == 'Site SNP count'",
|
||||
box(
|
||||
title="Site SNP count"
|
||||
, status = "info"
|
||||
, width=NULL
|
||||
, plotOutput("site_snp_count_bp") %>% withSpinner(color="#0dc5c1")
|
||||
)
|
||||
), width=6
|
||||
),
|
||||
column(conditionalPanel(
|
||||
condition="input.sidebar == 'Site SNP count'",
|
||||
box(
|
||||
title="Ligand Distance"
|
||||
, status = "info"
|
||||
, width=NULL
|
||||
, plotOutput("site_snp_count_bp_ligand") %>% withSpinner(color="#0dc5c1")
|
||||
)
|
||||
), width=6
|
||||
),
|
||||
column(conditionalPanel(
|
||||
condition="input.sidebar == 'Site SNP count'",
|
||||
box(
|
||||
title="Interface Distance"
|
||||
, status = "info"
|
||||
, width=NULL
|
||||
, plotOutput("site_snp_count_interface") %>% withSpinner(color="#0dc5c1")
|
||||
)
|
||||
), width=6
|
||||
),
|
||||
column(conditionalPanel(
|
||||
condition="input.sidebar == 'Site SNP count'",
|
||||
box(
|
||||
title="NCA Distance"
|
||||
, status = "info"
|
||||
, width=NULL
|
||||
, plotOutput("site_snp_count_nca") %>% withSpinner(color="#0dc5c1")
|
||||
)
|
||||
), width=6
|
||||
)
|
||||
),
|
||||
|
||||
# # Explicit fluidRow() for Stability Count
|
||||
# fluidRow(
|
||||
# column(
|
||||
# conditionalPanel(
|
||||
# condition="input.sidebar.match(/^Lineage.*/)",
|
||||
# lapply(
|
||||
# # FIXME: using a hardcoded target DF for this IS WRONG AND WILL BREAK
|
||||
# stability_boxes_df[stability_boxes_df$outcome_colname %in% colnames(embb_merged_df3),"outcome_colname"],
|
||||
# function(x){
|
||||
# print(paste0("outcome_colname: ",x))
|
||||
# box(plotOutput(x), width=4)
|
||||
# }
|
||||
# ),
|
||||
# width=12
|
||||
# )
|
||||
# )
|
||||
# ),
|
||||
|
||||
#### fluidRow()s for "Stability Count" in the sidebar ####
|
||||
fluidRow(
|
||||
conditionalPanel(
|
||||
condition="
|
||||
),
|
||||
conditionalPanel(
|
||||
condition="input.sidebar == 'Correlation'",
|
||||
selectInput(
|
||||
"corr_method",
|
||||
label="Correlation Method",
|
||||
choices = list("spearman",
|
||||
"pearson",
|
||||
"kendall"),
|
||||
selected="spearman"
|
||||
)
|
||||
),
|
||||
conditionalPanel(
|
||||
condition="input.sidebar == 'Correlation'",
|
||||
numericInput(
|
||||
"corr_lig_dist"
|
||||
, "Ligand Distance Cutoff (Å)", value=1
|
||||
)
|
||||
),
|
||||
conditionalPanel(
|
||||
condition="input.sidebar == 'Site SNP count'",
|
||||
numericInput(
|
||||
"snp_ligand_dist"
|
||||
, "Ligand Distance Cutoff (Å)", value=10
|
||||
)
|
||||
),
|
||||
conditionalPanel(
|
||||
condition="input.sidebar == 'Site SNP count'",
|
||||
numericInput(
|
||||
"snp_interface_dist"
|
||||
, "Interface Distance Cutoff (Å)", value=10
|
||||
)
|
||||
),
|
||||
conditionalPanel(
|
||||
condition="input.sidebar == 'Site SNP count'",
|
||||
numericInput(
|
||||
"snp_nca_dist"
|
||||
, "NCA Distance Cutoff (Å)", value=10
|
||||
)
|
||||
),
|
||||
|
||||
conditionalPanel(
|
||||
condition="input.sidebar == 'Correlation'",
|
||||
checkboxGroupInput(
|
||||
"corr_selected",
|
||||
"Parameters",
|
||||
choiceNames = c(
|
||||
"DeepDDG",
|
||||
"Dynamut2",
|
||||
"FoldX",
|
||||
"ConSurf"#,
|
||||
),
|
||||
choiceValues = c(
|
||||
"DeepDDG",
|
||||
"Dynamut2",
|
||||
"FoldX",
|
||||
"ConSurf"#,
|
||||
),
|
||||
selected = c(
|
||||
"DeepDDG",
|
||||
"Dynamut2",
|
||||
"FoldX",
|
||||
"ConSurf"#,
|
||||
)
|
||||
)
|
||||
),
|
||||
|
||||
# conditionalPanel(
|
||||
# condition="input.sidebar == 'DM OM Plots'",
|
||||
# selectInput(
|
||||
# "dm_om_param",
|
||||
# label="Stability Parameter",
|
||||
# choices = keys(dm_om_map),
|
||||
# selected="SNAP2")
|
||||
# ),
|
||||
# colour_categ
|
||||
conditionalPanel(
|
||||
condition="input.sidebar == 'Stability SNP by site'",
|
||||
selectInput(
|
||||
"stability_snp_param",
|
||||
label="Stability Parameter",
|
||||
choices = stability_boxes_df$stability_type,
|
||||
selected="Average")
|
||||
),
|
||||
conditionalPanel(
|
||||
condition="input.sidebar == 'Stability SNP by site'",
|
||||
checkboxInput("reorder_custom_h",
|
||||
label="Reorder by SNP count",
|
||||
FALSE)
|
||||
),
|
||||
conditionalPanel(
|
||||
condition="input.sidebar.match(/^Lineage.*/)",
|
||||
checkboxInput("all_lineages",
|
||||
label="All Lineages",
|
||||
FALSE)
|
||||
),
|
||||
# an example of how you can match multiple things in frontend JS
|
||||
conditionalPanel(
|
||||
condition="input.sidebar == 'LogoP SNP' ||
|
||||
input.sidebar =='Stability SNP by site' ||
|
||||
input.sidebar =='Consurf' ||
|
||||
input.sidebar =='LogoP OR'",
|
||||
actionButton("clear_ngl",
|
||||
"Clear Structure")
|
||||
),
|
||||
conditionalPanel(
|
||||
condition="input.sidebar == 'LogoP SNP' ||
|
||||
input.sidebar =='Stability SNP by site' ||
|
||||
input.sidebar =='Consurf' ||
|
||||
input.sidebar =='LogoP OR'",
|
||||
actionButton("test_ngl",
|
||||
"Test NGLViewR")
|
||||
)#,
|
||||
|
||||
# downloadButton("save",
|
||||
# "Download Plot"
|
||||
# )
|
||||
# actionButton(
|
||||
# "reload_target",
|
||||
# label="Reload Target\nData (slow!)"
|
||||
# )
|
||||
|
||||
)
|
||||
),
|
||||
#### body ####
|
||||
body <- dashboardBody(
|
||||
|
||||
tabItems(
|
||||
tabItem(tabName = "dashboard",
|
||||
h2("Dashboard tab content")
|
||||
),
|
||||
|
||||
tabItem(tabName = "widgets",
|
||||
h2("Widgets tab content")
|
||||
)
|
||||
),
|
||||
# creates a 'Conditional Panel' containing a plot object from each of our
|
||||
# ggplot plot functions (and its associated data frame)
|
||||
fluidRow(column(width=12,
|
||||
lapply(plot_functions_df$tab_name,
|
||||
function(x){
|
||||
|
||||
plot_function=plot_functions_df[
|
||||
plot_functions_df$tab_name==x,
|
||||
"plot_function"]
|
||||
|
||||
plot_df=plot_functions_df[
|
||||
plot_functions_df$tab_name==x,
|
||||
"plot_df"]
|
||||
cat(paste0('\nCreating output: ', x))
|
||||
generate_conditionalPanel(x, plot_function, plot_df)
|
||||
|
||||
}
|
||||
)
|
||||
)
|
||||
),
|
||||
# Explicit fluidRow() for Lineage plots together
|
||||
fluidRow(
|
||||
column(conditionalPanel(
|
||||
condition="input.sidebar.match(/^Lineage.*/)", box(
|
||||
title="Lineage Distribution"
|
||||
, status = "info"
|
||||
, width=NULL
|
||||
, plotOutput("lineage_distP", height="700px") %>% withSpinner(color="#0dc5c1"),
|
||||
height=800
|
||||
)
|
||||
), width=6
|
||||
),
|
||||
column(conditionalPanel(
|
||||
condition="input.sidebar.match(/^Lineage.*/)", box(
|
||||
title="Lineage SNP Diversity"
|
||||
, status = "info"
|
||||
, width=NULL
|
||||
, plotOutput("lin_sc", height="700px") %>% withSpinner(color="#0dc5c1"),
|
||||
height=800
|
||||
)
|
||||
), width=6
|
||||
)
|
||||
|
||||
),
|
||||
# Explicit fluidRow() for Site SNP Count
|
||||
fluidRow(
|
||||
column(conditionalPanel(
|
||||
condition="input.sidebar == 'Site SNP count'",
|
||||
box(
|
||||
title="Site SNP count"
|
||||
, status = "info"
|
||||
, width=NULL
|
||||
, plotOutput("site_snp_count_bp") %>% withSpinner(color="#0dc5c1")
|
||||
)
|
||||
), width=6
|
||||
),
|
||||
column(conditionalPanel(
|
||||
condition="input.sidebar == 'Site SNP count'",
|
||||
box(
|
||||
title="Ligand Distance"
|
||||
, status = "info"
|
||||
, width=NULL
|
||||
, plotOutput("site_snp_count_bp_ligand") %>% withSpinner(color="#0dc5c1")
|
||||
)
|
||||
), width=6
|
||||
),
|
||||
column(conditionalPanel(
|
||||
condition="input.sidebar == 'Site SNP count'",
|
||||
box(
|
||||
title="Interface Distance"
|
||||
, status = "info"
|
||||
, width=NULL
|
||||
, plotOutput("site_snp_count_interface") %>% withSpinner(color="#0dc5c1")
|
||||
)
|
||||
), width=6
|
||||
),
|
||||
column(conditionalPanel(
|
||||
condition="input.sidebar == 'Site SNP count'",
|
||||
box(
|
||||
title="RNA Distance"
|
||||
, status = "info"
|
||||
, width=NULL
|
||||
, plotOutput("site_snp_count_nca") %>% withSpinner(color="#0dc5c1")
|
||||
)
|
||||
), width=6
|
||||
)
|
||||
),
|
||||
|
||||
# # Explicit fluidRow() for Stability Count
|
||||
# fluidRow(
|
||||
# column(
|
||||
# conditionalPanel(
|
||||
# condition="input.sidebar.match(/^Lineage.*/)",
|
||||
# lapply(
|
||||
# # FIXME: using a hardcoded target DF for this IS WRONG AND WILL BREAK
|
||||
# stability_boxes_df[stability_boxes_df$outcome_colname %in% colnames(embb_merged_df3),"outcome_colname"],
|
||||
# function(x){
|
||||
# print(paste0("outcome_colname: ",x))
|
||||
# box(plotOutput(x), width=4)
|
||||
# }
|
||||
# ),
|
||||
# width=12
|
||||
# )
|
||||
# )
|
||||
# ),
|
||||
|
||||
#### fluidRow()s for "Stability Count" in the sidebar ####
|
||||
fluidRow(
|
||||
conditionalPanel(
|
||||
condition="
|
||||
input.sidebar == 'LogoP SNP' ||
|
||||
input.sidebar =='Stability SNP by site' ||
|
||||
input.sidebar =='Consurf' ||
|
||||
input.sidebar =='LogoP OR'",
|
||||
column(NGLVieweROutput("structure"),
|
||||
width=3
|
||||
)
|
||||
),
|
||||
conditionalPanel(
|
||||
condition="
|
||||
column(NGLVieweROutput("structure"),
|
||||
width=3
|
||||
)
|
||||
),
|
||||
conditionalPanel(
|
||||
condition="
|
||||
input.sidebar == 'LogoP SNP' ||
|
||||
input.sidebar == 'Stability SNP by site' ||
|
||||
input.sidebar == 'Site SNP count' ||
|
||||
input.sidebar == 'Consurf' ||
|
||||
input.sidebar == 'LogoP OR'",
|
||||
column(
|
||||
DT::dataTableOutput('table'),
|
||||
width=9
|
||||
)
|
||||
)
|
||||
),
|
||||
)
|
||||
column(
|
||||
DT::dataTableOutput('table'),
|
||||
width=9
|
||||
)
|
||||
)
|
||||
),
|
||||
)
|
||||
)
|
||||
Loading…
Add table
Add a link
Reference in a new issue