inst/shiny/shiny_ui/ui_side_templates.R
In matdoering/openPrimeRui: Shiny Application for Multiplex PCR Primer Design and Analysis
###############
# UI panel for inputting templates
##################
tabPanel("Templates",
id = "input_data_tabset",
value = "input_data_panel",
icon = icon("book", lib = "glyphicon"),
br(),
h2(class="inline", "Templates"),
br(),
br(),
# display template introductory text
div(class = "one",
p("Please load a set of template sequences. You can either simply load one of the supplied template data sets or provide your own template data.",
openPrimeRui:::create.help.button("input_templates")
)
),
### template scenario selector (template source)
radioButtons("template_scenario",
tagList(icon("floppy-disk", lib = "glyphicon"),
"Template source"),
choices = c("Available" = "supplied",
"Personal" = "personal"),
selected = "supplied", inline=TRUE
),
shinyBS::bsTooltip("template_scenario",
paste("Load templates provided by openPrimeR or load your own templates?"),
"right", options = list(container = "body")
),
# selection of type of supplied templates
conditionalPanel("input.template_scenario == 'supplied'",
selectizeInput("selected_supplied_templates",
"Template type",
c("Immunology" = "immunological",
"Virology" = "virological"),
selected = "immunological"
)
),
shinyBS::bsTooltip("selected_supplied_templates",
paste("Select one of the available data sets."),
"right", options = list(container = "body"),
trigger = "focus"
),
##############
# COMPARISON TAB
################
conditionalPanel("input.primer_analysis_type == 'compare'",
############
# template selection for primer comparison
###########
conditionalPanel("input.template_scenario == 'personal'",
# personal comparison templates
fileInput("comparison_templates",
tagList(icon("file", lib = "glyphicon"),
"Template CSV"
),
multiple = TRUE, accept = "text/csv"
),
shinyBS::bsTooltip("comparison_templates",
"Upload analyzed, downloaded (raw) template files \\
in csv format corresponding to the \\
input primer sets for comparison.",
"right"
)
),
#######
# SUPPLIED TEMPLATES
#########
conditionalPanel("input.template_scenario == 'supplied'",
# SUPPLIED IMGT TEMPLATES
conditionalPanel("input.selected_supplied_templates == 'immunological'",
div(class = "one",
p("We supply functional template data for IGH,
IGK, and IGL of homo sapiens.")
),
selectizeInput("template_comparison_locus",
tagList(icon("book", lib = "glyphicon"),
"Locus"),
c("IGH", "IGK", "IGL"),
selected = NULL,
options = list(
placeholder = 'Please select one of the available template data sets',
onInitialize = I('function() { this.setValue(""); }')
)
)
),
# SUPPLIED VIRUS TEMPLATES
conditionalPanel("input.selected_supplied_templates == 'virological'",
#div(class = "one",
#p("We supply functional template data for IGH,
#IGK, and IGL of homo sapiens.")
#),
selectInput("virus_type_comparison",
"Virus",
openPrimeRui:::get.available.viruses(),
selected = "HIV-1"),
# locus to retrieve data for
selectizeInput("virus_region_comparison",
"Region",
choices = NULL,
selected = NULL,
options = list(
placeholder = 'Please select one of the available template data sets',
onInitialize = I('function() { this.setValue(""); }')
)
)
),
#######
# RESET BUTTON FOR COMPARISON TEMPLATES
#######
actionButton("reset_rv_comparison.data", "Reset",
icon = icon("refresh", lib = "glyphicon"),
class = "actionStyleSmall"),
shinyBS::bsTooltip("reset_rv_comparison.data",
"Reset uploaded primer and template sets for comparison.",
"right", options = list(container = "body")
)
)),
###########
# Analysis of primers
############
conditionalPanel("input.primer_analysis_type != 'compare'",
shinyBS::bsCollapse(id = "template_collapse_analysis",
open = "template_input_panel",
shinyBS::bsCollapsePanel(tagList(icon("book", lib = "glyphicon"),
"Template input"),
value = "template_input_panel",
style = "primary",
############
# SUPPLIED TEMPLATES: IMMUNOLOGICAL
###############
conditionalPanel("input.template_scenario == 'supplied' && input.selected_supplied_templates == 'immunological'",
# Template upload: other analysis than comparison and IMGT data are used
div(class = "one",
p("Specify the template sequences to be retrieved from ",
HTML("<a href='http://imgt.org/genedb/' target='_blank'>
IMGT Gene-DB</a>"), ".
The allowed primer binding region is automatically set
to the leader region."
)
),
# species to retrieve data for
selectInput("IMGT_DB_species",
"Species",
openPrimeRui:::get.IMGT.settings()[["model.gene.id.species.txt"]],
selected = "Homo sapiens"),
# locus to retrieve data for
selectInput("IMGT_DB_locus",
"Locus",
openPrimeRui:::get.IMGT.settings()[["model.locusLike.txt"]],
selected = "IGH"
),
# IMGT function to retrieve data for
selectInput("IMGT_DB_function",
"Function",
openPrimeRui:::get.IMGT.settings()[["model.allele.fcode.txt"]],
selected = "functional"
),
# remove partial seqs?
checkboxInput("remove_partial_seqs",
"Remove partial sequences",
TRUE
),
shinyBS::bsTooltip("remove_partial_seqs",
"Exclude sequences that are incomplete and augment IMGT data with new sequencing results (if available).",
"right", options = list(container = "body")
),
# re-load IMGT data stored on disk?
checkboxInput("update_IMGT_DB_data",
"Update existing data",
FALSE
),
shinyBS::bsTooltip("update_IMGT_DB_data",
"Reload data from IMGT?",
"right", options = list(container = "body")
),
# template retrieve button
actionButton("IMGT_template_button",
"Retrieve templates",
icon = icon("database"),
class="actionStyle btn-primary"
),
shinyBS::bsTooltip("IMGT_template_button",
"Retrieve selected templates from IMGT.",
"right", options = list(container = "body")
),
# confirm templates button
div(class="rightAligned",
shinyBS::bsButton("IMGT_template_confirm_button",
"Confirm templates",
icon = icon("check"),
class="actionStyleSmall",
disabled = TRUE)
)
), # conditional panel for IMGT template ends
########## CONDITIONAL PANEL FOR VIROLOGICAL TEMPLATES
conditionalPanel("input.template_scenario == 'supplied' && input.selected_supplied_templates == 'virological'",
# Template upload: other analysis than comparison and IMGT data are used
div(class = "one",
p("Specify the virological template sequences to be analyzed.")
),
# species to retrieve data for
selectInput("virus_type",
"Virus",
openPrimeRui:::get.available.viruses(),
selected = "HIV-1"),
# locus to retrieve data for
selectInput("virus_region",
"Region",
NULL,
),
# template retrieve button for virusees
actionButton("Virus_template_button",
"Retrieve templates",
icon = icon("database"),
class="actionStyle btn-primary"
),
shinyBS::bsTooltip("Virus_template_button",
"Retrieve selected viral templates.",
"right", options = list(container = "body")
)
),
################
###############
# PERSONAL TEMPLATES
#############
conditionalPanel("input.template_scenario == 'personal'",
########
# TEMPLATE INPUT OPTIONS
#########
#value = "config_template_header_structure",
#style = "primary",
div(p("Please customize the following settings according to the data contained in your FASTA file headers and then upload the FASTA file you want to analyze."),
class = "two"
),
shinyBS::bsCollapse(id = "personal_template_options",
open = NULL,
#####
# start of basic template options
######
shinyBS::bsCollapsePanel(
tagList(
icon("menu-hamburger", lib = "glyphicon"),
"Basic options"),
value = "basic_personal_template_options",
# header structure choice
uiOutput("header_structure", width = "50%"),
# header delimiter symbol
textInput(inputId = "template_header_delim",
label = tagList(icon("list-alt", lib = "glyphicon"),
"Header field delimiter"),
value = "|"
),
shinyBS::bsTooltip("header_structure",
"The metadata fields appearing in the headers of the template FASTA file.",
"right",
options = list(container = "body"),
trigger = "focus"
),
shinyBS::bsTooltip("template_header_delim",
"The character separating individual fields in the template headers.",
"right", options = list(container = "body")
)
),
######
# END OF basic options
###########
shinyBS::bsCollapsePanel(
tagList(
icon("menu-hamburger", lib = "glyphicon"),
"Expert options"),
value = "template_expert_panel",
# column to be used as template identifier
selectInput("template_header_ID_column",
tagList(icon("key"), "Header ID field"),
choices = c("ACCESSION", "GROUP", "SPECIES", "FUNCTION"),
selected = "ACCESSION"
),
shinyBS::bsTooltip("template_header_ID_column", "The field in the template header to be used as the identifier of the templates.",
"right", options = list(container = "body",
trigger = "focus")
),
# the character indicating gaps in the templates
textInput("gap_char",
tagList(icon("scissors"), "Alignment gap character"),
value = "-"
),
shinyBS::bsTooltip("gap_char", "The character used to indicate gaps in case of aligned input.",
"right", options = list(container = "body")
),
# remove duplicate seqs?
checkboxInput("remove_duplicated_seqs",
"Remove duplicate sequences",
FALSE
),
shinyBS::bsTooltip("remove_duplicated_seqs",
"Exclude sequences that are duplicated.",
"right", options = list(container = "body")
)
) # end of expert options
), # close options bscollapse/panel
br(),
shinyBS::bsTooltip("help_input_templates_header",
"View help on defining the template input settings.",
"right", options = list(container = "body")
),
# PESRSONAL OPTIONS END
##########
# START PERSONAL TEMPLATE INPUT
##########
# template input panel
fileInput(inputId = "sequence_file",
label = tagList(icon("file"),
"Template FASTA/CSV file"
)
),
shinyBS::bsTooltip("sequence_file", "The PCR template sequences in FASTA or CSV format.",
"right", options = list(container = "body")
),
# confirm templates button
div(class = "rightAligned",
shinyBS::bsButton("confirm_uploaded_templates",
"Confirm templates", icon = icon("check"),
class = "actionStyleSmall", disabled = TRUE,
style = "primary"
)
)
) # close conditional panel for personal input
), # close panel for template input
############ INSERT START
shinyBS::bsCollapsePanel(tagList(icon("bookmark"), "Allowed regions"),
########
# allowed regions panel
#######
value = "allowed_template_panel",
radioButtons("selected_allowed_region_definition",
label = tagList("Definition of allowed binding region"),
choices = c("Template-specific" = "Template-specific" ,
"Uniform" = "Uniform"
),
inline = TRUE
),
shinyBS::bsTooltip("selected_allowed_region_definition",
paste("Define the binding region either individually",
"for each template or provide uniform binding intervals"),
"right", options = list(container = "body")
),
conditionalPanel("input.selected_allowed_region_definition == 'Template-specific'",
# Template-specific binding regions
div(p("To restrict the allowed sites for primer binding for each template individually,
please input a FASTA file specifying the allowed binding regions for each template.",
openPrimeRui:::create.help.button("input_templates_allowed")),
class = "two"
),
fileInput(inputId = "leader_file", # input of fw allowed regions file
label = tagList(icon("arrow-right", lib = "glyphicon"),
"Allowed regions for forward primers (FASTA)")
),
# tooltips for fileinputs don't seem to work
shinyBS::bsTooltip("leader_file",
paste("A FASTA file with the template binding regions",
"(5\\' to 3\\' for forward primers."),
"right", options = list(container = "body")
),
fileInput(inputId = "leader_file_rev", # input of rev allowed regions file
label = tagList(icon("arrow-left", lib = "glyphicon"),
"Allowed regions for reverse primers (FASTA)")
),
shinyBS::bsTooltip("leader_file_rev",
paste("A FASTA file with the template binding regions",
"(5\\' to 3\\' for reverse primers."),
"right", options = list(container = "body")
),
##########
### CONFIRM REGIONS BUTTON:
###########
shinyBS::bsTooltip("help_input_templates_allowed",
"Help on setting the allowed regions for primer binding.",
"right", options = list(container = "body")
)
########
),
conditionalPanel("input.selected_allowed_region_definition == 'Uniform'",
# Uniform binding regions
div(p("To restrict the allowed sites for primer binding, please enter the positional range in the templates where the primers should bind. ",
openPrimeRui:::create.help.button("input_templates_uniform")),
class = "two"
),
# allowed regions fw
sliderInput("uniform_allowed_regions_fw",
label = tagList(icon("arrow-right", lib = "glyphicon"),
"5' Binding region: forward primers"),
min = 0,
max = 1000,
value = c(1,30)
),
shinyBS::bsTooltip("uniform_allowed_regions_fw",
paste("The positional range from the 5\\'",
"end of the templates where the forward",
"primers should bind."),
"right", options = list(container = "body")
),
sliderInput("uniform_allowed_regions_rev",
label = tagList(icon("arrow-left", lib = "glyphicon"),
"3' Binding region: reverse primers"),
min = 0, # if set to 0 -> primer starts with 1
max = 1000,
value = c(1,30)
),
shinyBS::bsTooltip("uniform_allowed_regions_rev",
paste("The positional range from the 5\\'",
"end of the templates where the reverse",
"primers should bind."),
"right", options = list(container = "body")
),
div(class="leftAligned",
actionButton("uniform_region_confirm_button",
"Update binding regions", icon = icon("check"),
class="actionStyle btn-primary",
)
)
), # uniform panel ends
############
# CUSTOMIZATION OF REGIONS
# -> only for template-specific / supplied templates
########
conditionalPanel("input.selected_allowed_region_definition == 'Template-specific'",
# individualization of regions
div(p("Define the binding range of forward/reverse
primers in relation to the target region."),
class = "two"
),
conditionalPanel("input.individual_allowed_regions_fw[0] != -0.99", # if leaders were loaded correctly
# modify fw binding region relative to defined binding region
sliderInput("individual_allowed_regions_fw",
label = tagList(icon("arrow-right", lib = "glyphicon"),
"Modify the allowed region for forward primers"),
min = -1,
max = 40,
value = c(-0.99, -0.99), step = 1
)
),
shinyBS::bsTooltip("individual_allowed_regions_fw",
paste("The upstream (5\\') binding region for forward primers.",
"<br>Negative positions correspond to positions",
"upstream of the target amplification site."),
"right", options = list(container = "body")
),
conditionalPanel("input.individual_allowed_regions_rev[0] != -0.99",
# modify rev binding region relative to defined binding region
sliderInput("individual_allowed_regions_rev",
label = tagList(icon("arrow-left", lib = "glyphicon"), "Modify the allowed region for reverse primers"),
min = -1, # if set to 0 -> primer starts with 1
max = 40, value = c(-0.99,-0.99),
step = 1
)
),
shinyBS::bsTooltip("individual_allowed_regions_rev",
paste("The downstream (3\\') binding region for reverse primers.",
"<br>Negative positions correspond to positions",
"downstream of the target amplification site."),
"right", options = list(container = "body")
),
# confirm button to delay updates from slides until button is pressed
div(class="leftAligned",
actionButton("individual_region_confirm_button",
"Update binding regions", icon = icon("check"),
class="actionStyle btn-primary"
)
)
) # customize conditional ends
) # allowed regions panel ends
) # template collapse ends
) # analysis conditional ends
) # template tab ends
matdoering/openPrimeRui documentation built on Aug. 15, 2020, 2:37 p.m.
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###############
# UI panel for inputting templates
##################
tabPanel("Templates",
id = "input_data_tabset",
value = "input_data_panel",
icon = icon("book", lib = "glyphicon"),
br(),
h2(class="inline", "Templates"),
br(),
br(),
# display template introductory text
div(class = "one",
p("Please load a set of template sequences. You can either simply load one of the supplied template data sets or provide your own template data.",
openPrimeRui:::create.help.button("input_templates")
)
),
### template scenario selector (template source)
radioButtons("template_scenario",
tagList(icon("floppy-disk", lib = "glyphicon"),
"Template source"),
choices = c("Available" = "supplied",
"Personal" = "personal"),
selected = "supplied", inline=TRUE
),
shinyBS::bsTooltip("template_scenario",
paste("Load templates provided by openPrimeR or load your own templates?"),
"right", options = list(container = "body")
),
# selection of type of supplied templates
conditionalPanel("input.template_scenario == 'supplied'",
selectizeInput("selected_supplied_templates",
"Template type",
c("Immunology" = "immunological",
"Virology" = "virological"),
selected = "immunological"
)
),
shinyBS::bsTooltip("selected_supplied_templates",
paste("Select one of the available data sets."),
"right", options = list(container = "body"),
trigger = "focus"
),
##############
# COMPARISON TAB
################
conditionalPanel("input.primer_analysis_type == 'compare'",
############
# template selection for primer comparison
###########
conditionalPanel("input.template_scenario == 'personal'",
# personal comparison templates
fileInput("comparison_templates",
tagList(icon("file", lib = "glyphicon"),
"Template CSV"
),
multiple = TRUE, accept = "text/csv"
),
shinyBS::bsTooltip("comparison_templates",
"Upload analyzed, downloaded (raw) template files \\
in csv format corresponding to the \\
input primer sets for comparison.",
"right"
)
),
#######
# SUPPLIED TEMPLATES
#########
conditionalPanel("input.template_scenario == 'supplied'",
# SUPPLIED IMGT TEMPLATES
conditionalPanel("input.selected_supplied_templates == 'immunological'",
div(class = "one",
p("We supply functional template data for IGH,
IGK, and IGL of homo sapiens.")
),
selectizeInput("template_comparison_locus",
tagList(icon("book", lib = "glyphicon"),
"Locus"),
c("IGH", "IGK", "IGL"),
selected = NULL,
options = list(
placeholder = 'Please select one of the available template data sets',
onInitialize = I('function() { this.setValue(""); }')
)
)
),
# SUPPLIED VIRUS TEMPLATES
conditionalPanel("input.selected_supplied_templates == 'virological'",
#div(class = "one",
#p("We supply functional template data for IGH,
#IGK, and IGL of homo sapiens.")
#),
selectInput("virus_type_comparison",
"Virus",
openPrimeRui:::get.available.viruses(),
selected = "HIV-1"),
# locus to retrieve data for
selectizeInput("virus_region_comparison",
"Region",
choices = NULL,
selected = NULL,
options = list(
placeholder = 'Please select one of the available template data sets',
onInitialize = I('function() { this.setValue(""); }')
)
)
),
#######
# RESET BUTTON FOR COMPARISON TEMPLATES
#######
actionButton("reset_rv_comparison.data", "Reset",
icon = icon("refresh", lib = "glyphicon"),
class = "actionStyleSmall"),
shinyBS::bsTooltip("reset_rv_comparison.data",
"Reset uploaded primer and template sets for comparison.",
"right", options = list(container = "body")
)
)),
###########
# Analysis of primers
############
conditionalPanel("input.primer_analysis_type != 'compare'",
shinyBS::bsCollapse(id = "template_collapse_analysis",
open = "template_input_panel",
shinyBS::bsCollapsePanel(tagList(icon("book", lib = "glyphicon"),
"Template input"),
value = "template_input_panel",
style = "primary",
############
# SUPPLIED TEMPLATES: IMMUNOLOGICAL
###############
conditionalPanel("input.template_scenario == 'supplied' && input.selected_supplied_templates == 'immunological'",
# Template upload: other analysis than comparison and IMGT data are used
div(class = "one",
p("Specify the template sequences to be retrieved from ",
HTML("<a href='http://imgt.org/genedb/' target='_blank'>
IMGT Gene-DB</a>"), ".
The allowed primer binding region is automatically set
to the leader region."
)
),
# species to retrieve data for
selectInput("IMGT_DB_species",
"Species",
openPrimeRui:::get.IMGT.settings()[["model.gene.id.species.txt"]],
selected = "Homo sapiens"),
# locus to retrieve data for
selectInput("IMGT_DB_locus",
"Locus",
openPrimeRui:::get.IMGT.settings()[["model.locusLike.txt"]],
selected = "IGH"
),
# IMGT function to retrieve data for
selectInput("IMGT_DB_function",
"Function",
openPrimeRui:::get.IMGT.settings()[["model.allele.fcode.txt"]],
selected = "functional"
),
# remove partial seqs?
checkboxInput("remove_partial_seqs",
"Remove partial sequences",
TRUE
),
shinyBS::bsTooltip("remove_partial_seqs",
"Exclude sequences that are incomplete and augment IMGT data with new sequencing results (if available).",
"right", options = list(container = "body")
),
# re-load IMGT data stored on disk?
checkboxInput("update_IMGT_DB_data",
"Update existing data",
FALSE
),
shinyBS::bsTooltip("update_IMGT_DB_data",
"Reload data from IMGT?",
"right", options = list(container = "body")
),
# template retrieve button
actionButton("IMGT_template_button",
"Retrieve templates",
icon = icon("database"),
class="actionStyle btn-primary"
),
shinyBS::bsTooltip("IMGT_template_button",
"Retrieve selected templates from IMGT.",
"right", options = list(container = "body")
),
# confirm templates button
div(class="rightAligned",
shinyBS::bsButton("IMGT_template_confirm_button",
"Confirm templates",
icon = icon("check"),
class="actionStyleSmall",
disabled = TRUE)
)
), # conditional panel for IMGT template ends
########## CONDITIONAL PANEL FOR VIROLOGICAL TEMPLATES
conditionalPanel("input.template_scenario == 'supplied' && input.selected_supplied_templates == 'virological'",
# Template upload: other analysis than comparison and IMGT data are used
div(class = "one",
p("Specify the virological template sequences to be analyzed.")
),
# species to retrieve data for
selectInput("virus_type",
"Virus",
openPrimeRui:::get.available.viruses(),
selected = "HIV-1"),
# locus to retrieve data for
selectInput("virus_region",
"Region",
NULL,
),
# template retrieve button for virusees
actionButton("Virus_template_button",
"Retrieve templates",
icon = icon("database"),
class="actionStyle btn-primary"
),
shinyBS::bsTooltip("Virus_template_button",
"Retrieve selected viral templates.",
"right", options = list(container = "body")
)
),
################
###############
# PERSONAL TEMPLATES
#############
conditionalPanel("input.template_scenario == 'personal'",
########
# TEMPLATE INPUT OPTIONS
#########
#value = "config_template_header_structure",
#style = "primary",
div(p("Please customize the following settings according to the data contained in your FASTA file headers and then upload the FASTA file you want to analyze."),
class = "two"
),
shinyBS::bsCollapse(id = "personal_template_options",
open = NULL,
#####
# start of basic template options
######
shinyBS::bsCollapsePanel(
tagList(
icon("menu-hamburger", lib = "glyphicon"),
"Basic options"),
value = "basic_personal_template_options",
# header structure choice
uiOutput("header_structure", width = "50%"),
# header delimiter symbol
textInput(inputId = "template_header_delim",
label = tagList(icon("list-alt", lib = "glyphicon"),
"Header field delimiter"),
value = "|"
),
shinyBS::bsTooltip("header_structure",
"The metadata fields appearing in the headers of the template FASTA file.",
"right",
options = list(container = "body"),
trigger = "focus"
),
shinyBS::bsTooltip("template_header_delim",
"The character separating individual fields in the template headers.",
"right", options = list(container = "body")
)
),
######
# END OF basic options
###########
shinyBS::bsCollapsePanel(
tagList(
icon("menu-hamburger", lib = "glyphicon"),
"Expert options"),
value = "template_expert_panel",
# column to be used as template identifier
selectInput("template_header_ID_column",
tagList(icon("key"), "Header ID field"),
choices = c("ACCESSION", "GROUP", "SPECIES", "FUNCTION"),
selected = "ACCESSION"
),
shinyBS::bsTooltip("template_header_ID_column", "The field in the template header to be used as the identifier of the templates.",
"right", options = list(container = "body",
trigger = "focus")
),
# the character indicating gaps in the templates
textInput("gap_char",
tagList(icon("scissors"), "Alignment gap character"),
value = "-"
),
shinyBS::bsTooltip("gap_char", "The character used to indicate gaps in case of aligned input.",
"right", options = list(container = "body")
),
# remove duplicate seqs?
checkboxInput("remove_duplicated_seqs",
"Remove duplicate sequences",
FALSE
),
shinyBS::bsTooltip("remove_duplicated_seqs",
"Exclude sequences that are duplicated.",
"right", options = list(container = "body")
)
) # end of expert options
), # close options bscollapse/panel
br(),
shinyBS::bsTooltip("help_input_templates_header",
"View help on defining the template input settings.",
"right", options = list(container = "body")
),
# PESRSONAL OPTIONS END
##########
# START PERSONAL TEMPLATE INPUT
##########
# template input panel
fileInput(inputId = "sequence_file",
label = tagList(icon("file"),
"Template FASTA/CSV file"
)
),
shinyBS::bsTooltip("sequence_file", "The PCR template sequences in FASTA or CSV format.",
"right", options = list(container = "body")
),
# confirm templates button
div(class = "rightAligned",
shinyBS::bsButton("confirm_uploaded_templates",
"Confirm templates", icon = icon("check"),
class = "actionStyleSmall", disabled = TRUE,
style = "primary"
)
)
) # close conditional panel for personal input
), # close panel for template input
############ INSERT START
shinyBS::bsCollapsePanel(tagList(icon("bookmark"), "Allowed regions"),
########
# allowed regions panel
#######
value = "allowed_template_panel",
radioButtons("selected_allowed_region_definition",
label = tagList("Definition of allowed binding region"),
choices = c("Template-specific" = "Template-specific" ,
"Uniform" = "Uniform"
),
inline = TRUE
),
shinyBS::bsTooltip("selected_allowed_region_definition",
paste("Define the binding region either individually",
"for each template or provide uniform binding intervals"),
"right", options = list(container = "body")
),
conditionalPanel("input.selected_allowed_region_definition == 'Template-specific'",
# Template-specific binding regions
div(p("To restrict the allowed sites for primer binding for each template individually,
please input a FASTA file specifying the allowed binding regions for each template.",
openPrimeRui:::create.help.button("input_templates_allowed")),
class = "two"
),
fileInput(inputId = "leader_file", # input of fw allowed regions file
label = tagList(icon("arrow-right", lib = "glyphicon"),
"Allowed regions for forward primers (FASTA)")
),
# tooltips for fileinputs don't seem to work
shinyBS::bsTooltip("leader_file",
paste("A FASTA file with the template binding regions",
"(5\\' to 3\\' for forward primers."),
"right", options = list(container = "body")
),
fileInput(inputId = "leader_file_rev", # input of rev allowed regions file
label = tagList(icon("arrow-left", lib = "glyphicon"),
"Allowed regions for reverse primers (FASTA)")
),
shinyBS::bsTooltip("leader_file_rev",
paste("A FASTA file with the template binding regions",
"(5\\' to 3\\' for reverse primers."),
"right", options = list(container = "body")
),
##########
### CONFIRM REGIONS BUTTON:
###########
shinyBS::bsTooltip("help_input_templates_allowed",
"Help on setting the allowed regions for primer binding.",
"right", options = list(container = "body")
)
########
),
conditionalPanel("input.selected_allowed_region_definition == 'Uniform'",
# Uniform binding regions
div(p("To restrict the allowed sites for primer binding, please enter the positional range in the templates where the primers should bind. ",
openPrimeRui:::create.help.button("input_templates_uniform")),
class = "two"
),
# allowed regions fw
sliderInput("uniform_allowed_regions_fw",
label = tagList(icon("arrow-right", lib = "glyphicon"),
"5' Binding region: forward primers"),
min = 0,
max = 1000,
value = c(1,30)
),
shinyBS::bsTooltip("uniform_allowed_regions_fw",
paste("The positional range from the 5\\'",
"end of the templates where the forward",
"primers should bind."),
"right", options = list(container = "body")
),
sliderInput("uniform_allowed_regions_rev",
label = tagList(icon("arrow-left", lib = "glyphicon"),
"3' Binding region: reverse primers"),
min = 0, # if set to 0 -> primer starts with 1
max = 1000,
value = c(1,30)
),
shinyBS::bsTooltip("uniform_allowed_regions_rev",
paste("The positional range from the 5\\'",
"end of the templates where the reverse",
"primers should bind."),
"right", options = list(container = "body")
),
div(class="leftAligned",
actionButton("uniform_region_confirm_button",
"Update binding regions", icon = icon("check"),
class="actionStyle btn-primary",
)
)
), # uniform panel ends
############
# CUSTOMIZATION OF REGIONS
# -> only for template-specific / supplied templates
########
conditionalPanel("input.selected_allowed_region_definition == 'Template-specific'",
# individualization of regions
div(p("Define the binding range of forward/reverse
primers in relation to the target region."),
class = "two"
),
conditionalPanel("input.individual_allowed_regions_fw[0] != -0.99", # if leaders were loaded correctly
# modify fw binding region relative to defined binding region
sliderInput("individual_allowed_regions_fw",
label = tagList(icon("arrow-right", lib = "glyphicon"),
"Modify the allowed region for forward primers"),
min = -1,
max = 40,
value = c(-0.99, -0.99), step = 1
)
),
shinyBS::bsTooltip("individual_allowed_regions_fw",
paste("The upstream (5\\') binding region for forward primers.",
"<br>Negative positions correspond to positions",
"upstream of the target amplification site."),
"right", options = list(container = "body")
),
conditionalPanel("input.individual_allowed_regions_rev[0] != -0.99",
# modify rev binding region relative to defined binding region
sliderInput("individual_allowed_regions_rev",
label = tagList(icon("arrow-left", lib = "glyphicon"), "Modify the allowed region for reverse primers"),
min = -1, # if set to 0 -> primer starts with 1
max = 40, value = c(-0.99,-0.99),
step = 1
)
),
shinyBS::bsTooltip("individual_allowed_regions_rev",
paste("The downstream (3\\') binding region for reverse primers.",
"<br>Negative positions correspond to positions",
"downstream of the target amplification site."),
"right", options = list(container = "body")
),
# confirm button to delay updates from slides until button is pressed
div(class="leftAligned",
actionButton("individual_region_confirm_button",
"Update binding regions", icon = icon("check"),
class="actionStyle btn-primary"
)
)
) # customize conditional ends
) # allowed regions panel ends
) # template collapse ends
) # analysis conditional ends
) # template tab ends
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