dashboard stuff
This commit is contained in:
parent
84662ec948
commit
f5d5923e42
3 changed files with 314 additions and 327 deletions
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@ -312,343 +312,343 @@ if (interactive()){
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options(DT.options = list(scrollX = TRUE))
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#### UI ####
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ui <- dashboardPage(skin="purple",
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dashboardHeader(title = "Drug/Target Explorer"),
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dashboardHeader(title = "Drug/Target Explorer"),
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dashboardSidebar(
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sidebarMenu( id = "sidebar",
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selectInput(
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"switch_target",
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label="Switch to New Target",
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choices = c(
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"alr",
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"embb",
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"gid",
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"katg",
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"pnca",
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"rpob"
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),
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selected="embb"),
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menuItem("LogoP SNP", tabName="LogoP SNP"),
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#menuItem("Lineage Sample Count", tabName="Lineage Sample Count"),
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menuItem("Site SNP count", tabName="Site SNP count"),
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menuItem("Stability SNP by site", tabName="Stability SNP by site"),
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menuItem("DM OM Plots", tabName="DM OM Plots"),
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menuItem("Correlation", tabName="Correlation"),
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#menuItem("Lineage Distribution", tabName="Lineage Distribution"),
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menuItem("Consurf", tabName="Consurf"),
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menuItem("LogoP OR", tabName="LogoP OR"),
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menuItem("Lineage", tabName="Lineage"),
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#menuItem('Stability count', tabName='Stability count'),
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dashboardSidebar(
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sidebarMenu( id = "sidebar",
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selectInput(
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"switch_target",
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label="Switch to New Target",
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choices = c(
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"alr",
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"embb",
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"gid",
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"katg",
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"pnca",
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"rpob"
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),
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selected="embb"),
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menuItem("LogoP SNP", tabName="LogoP SNP"),
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#menuItem("Lineage Sample Count", tabName="Lineage Sample Count"),
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menuItem("Site SNP count", tabName="Site SNP count"),
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menuItem("Stability SNP by site", tabName="Stability SNP by site"),
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menuItem("DM OM Plots", tabName="DM OM Plots"),
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menuItem("Correlation", tabName="Correlation"),
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#menuItem("Lineage Distribution", tabName="Lineage Distribution"),
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menuItem("Consurf", tabName="Consurf"),
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menuItem("LogoP OR", tabName="LogoP OR"),
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menuItem("Lineage", tabName="Lineage"),
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#menuItem('Stability count', tabName='Stability count'),
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# These conditionalPanel()s make extra settings appear in the sidebar when needed
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conditionalPanel(
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condition="input.sidebar == 'LogoP SNP'",
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textInput(
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"omit_snp_count",
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"Omit SNPs",
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value = c(0),
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placeholder = "1,3,6"
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)
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),
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# NOTE:
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# I *think* we can cheat here slightly and use the min/max from
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# merged_df3[['position']] for everything because the various
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# dataframes for a given gene/drug combination have the
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# same range of positions. May need fixing, especially
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# if we get/shrink the imported data files to something
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# more reasonable.
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conditionalPanel(
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condition="
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# These conditionalPanel()s make extra settings appear in the sidebar when needed
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conditionalPanel(
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condition="input.sidebar == 'LogoP SNP'",
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textInput(
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"omit_snp_count",
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"Omit SNPs",
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value = c(0),
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placeholder = "1,3,6"
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)
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),
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# NOTE:
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# I *think* we can cheat here slightly and use the min/max from
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# merged_df3[['position']] for everything because the various
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# dataframes for a given gene/drug combination have the
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# same range of positions. May need fixing, especially
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# if we get/shrink the imported data files to something
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# more reasonable.
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conditionalPanel(
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condition="
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input.sidebar == 'LogoP SNP'||
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input.sidebar == 'Stability SNP by site' ||
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input.sidebar == 'Consurf' ||
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input.sidebar == 'LogoP OR'",
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sliderInput(
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"display_position_range"
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, "Display Positions"
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, min=1, max=150, value=c(1,150) # 150 is just a little less than the smallest pos_count
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)
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),
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sliderInput(
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"display_position_range"
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, "Display Positions"
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, min=1, max=150, value=c(1,150) # 150 is just a little less than the smallest pos_count
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)
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),
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conditionalPanel(
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condition="
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conditionalPanel(
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condition="
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input.sidebar == 'LogoP SNP' ||
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input.sidebar == 'LogoP OR' ||
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input.sidebar == 'LogoP ED'",
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selectInput(
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"logoplot_colour_scheme",
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label="Logo Plot Colour Scheme",
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choices = logoPlotSchemes,
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selected="chemistry"
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)
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),
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conditionalPanel(
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condition="input.sidebar == 'Correlation'",
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selectInput(
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"corr_method",
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label="Correlation Method",
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choices = list("spearman",
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"pearson",
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"kendall"),
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selected="spearman"
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)
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),
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conditionalPanel(
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condition="input.sidebar == 'Correlation'",
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numericInput(
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"corr_lig_dist"
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, "Ligand Distance Cutoff (Å)", value=1
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)
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),
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conditionalPanel(
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condition="input.sidebar == 'Site SNP count'",
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numericInput(
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"snp_ligand_dist"
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, "Ligand Distance Cutoff (Å)", value=10
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)
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),
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conditionalPanel(
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condition="input.sidebar == 'Site SNP count'",
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numericInput(
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"snp_interface_dist"
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, "Interface Distance Cutoff (Å)", value=10
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)
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),
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conditionalPanel(
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condition="input.sidebar == 'Site SNP count'",
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numericInput(
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"snp_nca_dist"
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, "NCA Distance Cutoff (Å)", value=10
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)
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),
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selectInput(
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"logoplot_colour_scheme",
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label="Logo Plot Colour Scheme",
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choices = logoPlotSchemes,
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selected="chemistry"
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)
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),
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conditionalPanel(
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condition="input.sidebar == 'Correlation'",
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selectInput(
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"corr_method",
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label="Correlation Method",
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choices = list("spearman",
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"pearson",
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"kendall"),
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selected="spearman"
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)
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),
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conditionalPanel(
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condition="input.sidebar == 'Correlation'",
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numericInput(
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"corr_lig_dist"
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, "Ligand Distance Cutoff (Å)", value=1
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)
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),
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conditionalPanel(
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condition="input.sidebar == 'Site SNP count'",
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numericInput(
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"snp_ligand_dist"
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, "Ligand Distance Cutoff (Å)", value=10
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)
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),
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conditionalPanel(
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condition="input.sidebar == 'Site SNP count'",
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numericInput(
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"snp_interface_dist"
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, "Interface Distance Cutoff (Å)", value=10
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)
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),
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conditionalPanel(
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condition="input.sidebar == 'Site SNP count'",
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numericInput(
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"snp_nca_dist"
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, "NCA Distance Cutoff (Å)", value=10
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)
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),
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conditionalPanel(
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condition="input.sidebar == 'Correlation'",
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checkboxGroupInput(
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"corr_selected",
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"Parameters",
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choiceNames = c(
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"DeepDDG",
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"Dynamut2",
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"FoldX",
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"ConSurf"#,
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),
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choiceValues = c(
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"DeepDDG",
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"Dynamut2",
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"FoldX",
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"ConSurf"#,
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),
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selected = c(
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"DeepDDG",
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"Dynamut2",
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"FoldX",
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"ConSurf"#,
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)
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)
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),
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conditionalPanel(
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condition="input.sidebar == 'Correlation'",
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checkboxGroupInput(
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"corr_selected",
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"Parameters",
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choiceNames = c(
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"DeepDDG",
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"Dynamut2",
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"FoldX",
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"ConSurf"#,
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),
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choiceValues = c(
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"DeepDDG",
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"Dynamut2",
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"FoldX",
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"ConSurf"#,
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),
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selected = c(
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"DeepDDG",
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"Dynamut2",
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"FoldX",
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"ConSurf"#,
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)
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)
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),
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# conditionalPanel(
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# condition="input.sidebar == 'DM OM Plots'",
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# selectInput(
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# "dm_om_param",
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# label="Stability Parameter",
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# choices = keys(dm_om_map),
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# selected="SNAP2")
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# ),
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# colour_categ
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conditionalPanel(
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condition="input.sidebar == 'Stability SNP by site'",
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selectInput(
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"stability_snp_param",
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label="Stability Parameter",
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choices = stability_boxes_df$stability_type,
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selected="Average")
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),
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conditionalPanel(
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condition="input.sidebar == 'Stability SNP by site'",
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checkboxInput("reorder_custom_h",
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label="Reorder by SNP count",
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FALSE)
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),
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conditionalPanel(
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condition="input.sidebar.match(/^Lineage.*/)",
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checkboxInput("all_lineages",
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label="All Lineages",
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FALSE)
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),
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# an example of how you can match multiple things in frontend JS
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conditionalPanel(
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condition="input.sidebar == 'LogoP SNP' ||
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# conditionalPanel(
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# condition="input.sidebar == 'DM OM Plots'",
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# selectInput(
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# "dm_om_param",
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# label="Stability Parameter",
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# choices = keys(dm_om_map),
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# selected="SNAP2")
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# ),
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# colour_categ
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conditionalPanel(
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condition="input.sidebar == 'Stability SNP by site'",
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selectInput(
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"stability_snp_param",
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label="Stability Parameter",
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choices = stability_boxes_df$stability_type,
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selected="Average")
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),
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conditionalPanel(
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condition="input.sidebar == 'Stability SNP by site'",
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checkboxInput("reorder_custom_h",
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label="Reorder by SNP count",
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FALSE)
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),
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conditionalPanel(
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condition="input.sidebar.match(/^Lineage.*/)",
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checkboxInput("all_lineages",
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label="All Lineages",
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FALSE)
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),
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# an example of how you can match multiple things in frontend JS
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conditionalPanel(
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condition="input.sidebar == 'LogoP SNP' ||
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input.sidebar =='Stability SNP by site' ||
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input.sidebar =='Consurf' ||
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input.sidebar =='LogoP OR'",
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actionButton("clear_ngl",
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"Clear Structure")
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),
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conditionalPanel(
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condition="input.sidebar == 'LogoP SNP' ||
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actionButton("clear_ngl",
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"Clear Structure")
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),
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conditionalPanel(
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condition="input.sidebar == 'LogoP SNP' ||
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input.sidebar =='Stability SNP by site' ||
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input.sidebar =='Consurf' ||
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input.sidebar =='LogoP OR'",
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actionButton("test_ngl",
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"Test NGLViewR")
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)#,
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actionButton("test_ngl",
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"Test NGLViewR")
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)#,
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# downloadButton("save",
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# "Download Plot"
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# )
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# actionButton(
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# "reload_target",
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# label="Reload Target\nData (slow!)"
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# )
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# downloadButton("save",
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# "Download Plot"
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# )
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# actionButton(
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# "reload_target",
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# label="Reload Target\nData (slow!)"
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# )
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)
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),
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#### body ####
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body <- dashboardBody(
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)
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),
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#### body ####
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body <- dashboardBody(
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tabItems(
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tabItem(tabName = "dashboard",
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h2("Dashboard tab content")
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),
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tabItems(
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tabItem(tabName = "dashboard",
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h2("Dashboard tab content")
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),
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tabItem(tabName = "widgets",
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h2("Widgets tab content")
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)
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),
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# creates a 'Conditional Panel' containing a plot object from each of our
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# ggplot plot functions (and its associated data frame)
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fluidRow(column(width=12,
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lapply(plot_functions_df$tab_name,
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function(x){
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tabItem(tabName = "widgets",
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h2("Widgets tab content")
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)
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),
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# creates a 'Conditional Panel' containing a plot object from each of our
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# ggplot plot functions (and its associated data frame)
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fluidRow(column(width=12,
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lapply(plot_functions_df$tab_name,
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function(x){
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plot_function=plot_functions_df[
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plot_functions_df$tab_name==x,
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"plot_function"]
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plot_function=plot_functions_df[
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plot_functions_df$tab_name==x,
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"plot_function"]
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plot_df=plot_functions_df[
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plot_functions_df$tab_name==x,
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"plot_df"]
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cat(paste0('\nCreating output: ', x))
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generate_conditionalPanel(x, plot_function, plot_df)
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plot_df=plot_functions_df[
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plot_functions_df$tab_name==x,
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"plot_df"]
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cat(paste0('\nCreating output: ', x))
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generate_conditionalPanel(x, plot_function, plot_df)
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}
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)
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)
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),
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# Explicit fluidRow() for Lineage plots together
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fluidRow(
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column(conditionalPanel(
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condition="input.sidebar.match(/^Lineage.*/)", box(
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title="Lineage Distribution"
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, status = "info"
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, width=NULL
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, plotOutput("lineage_distP", height="700px") %>% withSpinner(color="#0dc5c1"),
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height=800
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)
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), width=6
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),
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column(conditionalPanel(
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condition="input.sidebar.match(/^Lineage.*/)", box(
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title="Lineage SNP Diversity"
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, status = "info"
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, width=NULL
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, plotOutput("lin_sc", height="700px") %>% withSpinner(color="#0dc5c1"),
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height=800
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)
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), width=6
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)
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}
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)
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)
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),
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# Explicit fluidRow() for Lineage plots together
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fluidRow(
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column(conditionalPanel(
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condition="input.sidebar.match(/^Lineage.*/)", box(
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title="Lineage Distribution"
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, status = "info"
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, width=NULL
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, plotOutput("lineage_distP", height="700px") %>% withSpinner(color="#0dc5c1"),
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height=800
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)
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), width=6
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),
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column(conditionalPanel(
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condition="input.sidebar.match(/^Lineage.*/)", box(
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title="Lineage SNP Diversity"
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, status = "info"
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, width=NULL
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, plotOutput("lin_sc", height="700px") %>% withSpinner(color="#0dc5c1"),
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height=800
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)
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), width=6
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)
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),
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# Explicit fluidRow() for Site SNP Count
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fluidRow(
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column(conditionalPanel(
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condition="input.sidebar == 'Site SNP count'",
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box(
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title="Site SNP count"
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, status = "info"
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, width=NULL
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, plotOutput("site_snp_count_bp") %>% withSpinner(color="#0dc5c1")
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)
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), width=6
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),
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column(conditionalPanel(
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condition="input.sidebar == 'Site SNP count'",
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box(
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title="Ligand Distance"
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, status = "info"
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, width=NULL
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, plotOutput("site_snp_count_bp_ligand") %>% withSpinner(color="#0dc5c1")
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)
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), width=6
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),
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column(conditionalPanel(
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condition="input.sidebar == 'Site SNP count'",
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box(
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title="Interface Distance"
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, status = "info"
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, width=NULL
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, plotOutput("site_snp_count_interface") %>% withSpinner(color="#0dc5c1")
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)
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), width=6
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),
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column(conditionalPanel(
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condition="input.sidebar == 'Site SNP count'",
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box(
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title="RNA Distance"
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, status = "info"
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, width=NULL
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, plotOutput("site_snp_count_nca") %>% withSpinner(color="#0dc5c1")
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)
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), width=6
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)
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),
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),
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# Explicit fluidRow() for Site SNP Count
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fluidRow(
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column(conditionalPanel(
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condition="input.sidebar == 'Site SNP count'",
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box(
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title="Site SNP count"
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||||
, 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$outcome_colname %in% colnames(embb_merged_df3),"outcome_colname"],
|
||||
# function(x){
|
||||
# print(paste0("outcome_colname: ",x))
|
||||
# box(plotOutput(x), width=4)
|
||||
# }
|
||||
# ),
|
||||
# width=12
|
||||
# )
|
||||
# )
|
||||
# ),
|
||||
# # Explicit fluidRow() for Stability Count
|
||||
# fluidRow(
|
||||
# column(
|
||||
# conditionalPanel(
|
||||
# condition="input.sidebar.match(/^Lineage.*/)",
|
||||
# lapply(
|
||||
# # FIXME: using a hardcoded target DF for this IS WRONG AND WILL BREAK
|
||||
# stability_boxes_df[stability_boxes_df$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="
|
||||
#### 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
|
||||
)
|
||||
)
|
||||
),
|
||||
)
|
||||
)
|
||||
),
|
||||
)
|
||||
)
|
||||
server <- function(input, output, session) {
|
||||
|
||||
|
|
|
|||
|
|
@ -1,9 +1,3 @@
|
|||
# library(shiny)
|
||||
# library(shinycssloaders)
|
||||
# library(DT)
|
||||
# library(NGLVieweR)
|
||||
# library(hash)
|
||||
|
||||
function(input, output, session) {
|
||||
|
||||
#output$LogoPlotSnps = renderPlot(LogoPlotSnps(mutable_df3))
|
||||
|
|
|
|||
|
|
@ -1,10 +1,3 @@
|
|||
# library(shiny)
|
||||
# library(shinydashboard)
|
||||
# library(shinycssloaders)
|
||||
# library(DT)
|
||||
# library(NGLVieweR)
|
||||
# library(hash)
|
||||
|
||||
#### Shiny UI #####
|
||||
|
||||
dashboardPage(skin="purple",
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue