inst/shiny/ui.R
In davidsbutcher/abundancer: Determine Abundances of 12C and 14N from Protein Mass Spectra
library(abundancer)
library(magrittr)
library(dplyr)
library(assertthat)
library(glue)
library(shiny)
library(shinyBS)
library(tippy)
library(shinydashboard)
library(shinyWidgets)
library(shinyjs)
library(purrr)
library(Peptides)
library(OrgMassSpecR)
library(fs)
library(enviPat)
library(reshape2)
library(progressr)
# options(repos = BiocManager::repositories())
options(shiny.maxRequestSize = 1000*1024^2)
# UI ----------------------------------------------------------------------
shinyUI(
fluidPage(
titlePanel("abundancer"),
theme = "maglab_theme_old.css",
# theme = bslib::bs_theme(version = 4),
useShinyjs(),
setBackgroundColor(
color = c("#FFFFFF"),
gradient = "linear",
direction = "bottom"
),
tags$head(
tags$style(HTML("hr {border-top: 1px solid #A9A9A9;}")),
tags$style(
HTML(
".shiny-notification {
position:fixed;
top: calc(20%);
left: calc(40%);
}"
)
)
),
sidebarLayout(
# Sidebar -----------------------------------------------------------------
sidebarPanel(
tabsetPanel(
id = "mainpanel",
type = "pills",
tabPanel(
"Main",
hr(),
tabsetPanel(
id = "guppipanel",
type = "tabs",
tabPanel(
"Peaklist",
br(),
fileInput(
"fileInputUpload",
tippy(
"Upload peaklist",
placement = "right",
arrow = TRUE,
allowHTML = TRUE,
animation = "scale",
duration = 250,
theme = "light-border",
tooltip =
"<span style='font-size:14px;'>Upload a peaklist in CSV or XLSX format. The first column should contain m/z values and the second should contain intensities. The peaklist should contain a full isotopic distribution of a single charge state of a single protein.</span>"
),
accept = c(".xlsx", ".csv")
),
numericInput(
"scoremat_charge",
tippy(
"Charge",
placement = "right",
arrow = TRUE,
allowHTML = TRUE,
animation = "scale",
duration = 250,
theme = "light-border",
tooltip =
"<span style='font-size:14px;'>Charge state corresponding to the isotopic distribution in the peaklist. Only positive charges are supported.</span>"
),
value = 1,
min = 1,
max = 100,
step = 1
),
textAreaInput(
"scoremat_sequence",
tippy(
"Sequence",
placement = "right",
arrow = TRUE,
allowHTML = TRUE,
animation = "scale",
duration = 250,
theme = "light-border",
tooltip =
"<span style='font-size:14px;'>Sequence corresponding to the protein whose isotopic distribution is represented by the peaklist. Only single-letter codes of canonical amino acids are supported.</span>"
),
placeholder =
"Single letter canonical amino acids only",
height = "100px"
),
textInput(
"scoremat_PTM",
tippy(
"PTM formula",
placement = "right",
arrow = TRUE,
allowHTML = TRUE,
animation = "scale",
duration = 250,
theme = "light-border",
tooltip =
"<span style='font-size:14px;'>Chemical formula (in Hill notation) of post-translational modifications to the protein sequence. The formula should be provided as a delta compared to the protein's chemical formula, i.e. for a methylation the PTM formula is CH3 and not CH4. For multiple PTMs, all formulae should be combined.</span>"
),
placeholder = "Leave blank if unmodified"
),
br(),
br(),
actionButton(
"abundancer_start",
"Analyze abundance"
),
br(),
br(),
downloadButton("downloadPDFcoarse", label = "Coarse Heatmap"),
downloadButton("downloadPDFfine", label = "Fine Heatmap")
),
tabPanel(
"Settings",
# h5(em("Hover parameter names for more info")),
bsCollapse(
bsCollapsePanel(
h5(strong("Peak picking parameters")),
br(),
splitLayout(
numericInput(
"peakpick_SNR",
tippy(
"SNR",
placement = "right",
arrow = TRUE,
allowHTML = TRUE,
animation = "scale",
duration = 250,
theme = "light-border",
tooltip =
"<span style='font-size:14px;'>From MSnbase documentation: \"A local maximum is considered a peak if its intensity is SNR times larger than the estimated noise.\" Noise is estimated using the MSnbase median absolute deviation method.</span>"
),
value = 25,
min = 0,
max = 100,
step = 1
),
numericInput(
"peakpick_k",
tippy(
"KNN",
placement = "right",
arrow = TRUE,
allowHTML = TRUE,
animation = "scale",
duration = 250,
theme = "light-border",
tooltip =
"<span style='font-size:14px;'>From MSnbase documentation: \"m/z values and intensities of the 2 * KNN closest signals to the centroid are used in the intensity weighted average calculation.\"</span>"
),
value = 2,
min = 1,
max = 10,
step = 1
)
),
br()
),
bsCollapsePanel(
h5(strong("Score matrix parameters")),
br(),
splitLayout(
numericInput(
"scoremat_12C",
tippy(
"<sup>12</sup>C abundance start",
placement = "top-end",
arrow = TRUE,
allowHTML = TRUE,
animation = "scale",
duration = 250,
theme = "light-border",
tooltip =
"<span style='font-size:14px;'>Starting value for <sup>12</sup>C abundance to use for calculating the coarse score matrix. <sup>12</sup>C abundance will be incremented from this value to 1 by the abundance step.</span>"
),
value = 0.987,
min = 0.9,
max = 0.999,
step = 0.001
),
numericInput(
"scoremat_14N",
tippy(
"<sup>14</sup>N abundance start",
placement = "top-end",
arrow = TRUE,
allowHTML = TRUE,
animation = "scale",
duration = 250,
theme = "light-border",
tooltip =
"<span style='font-size:14px;'>Starting value for <sup>14</sup>N abundance to use for calculating the coarse score matrix. <sup>14</sup>N abundance will be incremented from this value to 1 by the abundance step.</span>"
),
value = 0.994,
min = 0.9,
max = 0.999,
step = 0.001
)
),
splitLayout(
numericInput(
"scoremat_binSize",
tippy(
"Bin size",
placement = "top-end",
arrow = TRUE,
allowHTML = TRUE,
animation = "scale",
duration = 250,
theme = "light-border",
tooltip =
"<span style='font-size:14px;'>Prior to comparing observed and theoretical spectra, spectra are binned using this bin size value. See MSnbase documentation for more information.</span>"
),
value = 0.05,
min = 0.01,
max = 0.1,
step = 0.01
),
numericInput(
"scoremat_resolvingPower",
tippy(
"Resolving power",
placement = "top-end",
arrow = TRUE,
allowHTML = TRUE,
animation = "scale",
duration = 250,
theme = "light-border",
tooltip =
"<span style='font-size:14px;'>Resolving power to be used in generating theoretical isotopic distributions. See enviPat::envelope documentation for more information.</span>"
),
value = 300000,
min = 1000,
max = 1000000,
step = 1000
)
),
splitLayout(
numericInput(
"scoremat_coarseMult",
tippy(
"Coarse step mult.",
placement = "top-end",
arrow = TRUE,
allowHTML = TRUE,
animation = "scale",
duration = 250,
theme = "light-border",
tooltip =
"<span style='font-size:14px;'>Value by which coarse step is multiplied to determine range for calculating fine matrix.</span>"
),
value = 1,
min = 1,
max = 10,
step = 1
),
selectInput(
"scoremat_compfunc",
tippy(
"Spec. comp. func.",
placement = "right",
arrow = TRUE,
allowHTML = TRUE,
animation = "scale",
duration = 250,
theme = "light-border",
tooltip =
"<span style='font-size:14px;'>Sepctrum comparison function to be used for comparing observed and theoretical isotopic envelopes.</span>"
),
choices =
list(
"Cosine similarity" = "dotproduct",
"Cor" = "cor",
"ScoreMFA" = "scoremfa",
"ScoreMFA (C++)" = "scoremfacpp"
),
selected = "Cosine similarity"
)
),
# div(
# style="display: inline-block;vertical-align:top; width: 150px;",
# selectInput(
# "scoremat_compfunc",
# tippy(
# "Spectrum comparison function",
# placement = "right",
# arrow = TRUE,
# allowHTML = TRUE,
# animation = "scale",
# duration = 250,
# theme = "light-border",
# tooltip =
# "<span style='font-size:14px;'>Function to be used for comparing observed and theoretical isotopic envelopes.</span>"
# ),
# choices =
# list(
# "Cosine similarity" = "dotproduct",
# "Cor" = "cor",
# "ScoreMFA" = "scoremfa",
# "ScoreMFA (C++)" = "scoremfacpp"
# ),
# selected = "Cosine similarity"
# )
# ),
br()
),
bsCollapsePanel(
h5(strong("Heatmap parameters")),
br(),
div(
style="display: inline-block;vertical-align:top; width: 125px;",
selectInput(
"heatmap_fill",
tippy(
"Heatmap fill",
placement = "right",
arrow = TRUE,
allowHTML = TRUE,
animation = "scale",
duration = 250,
theme = "light-border",
tooltip =
"<span style='font-size:14px;'>Color palette to use for score matrix heatmap. All palettes are from the viridis R package and are accessible to colorblind readers.</span>"
),
choices =
c(
"magma",
"inferno",
"plasma",
"viridis",
"cividis"
),
selected = "plasma"
)
),
div(
style="display: inline-block;vertical-align:top; width: 125px;"
),
div(
style="display: inline-block;vertical-align:top; width: 125px;",
numericInput(
"heatmap_scale_coarse_start",
tippy(
"Coarse heatmap fill range, start",
placement = "right",
arrow = TRUE,
allowHTML = TRUE,
animation = "scale",
duration = 250,
theme = "light-border",
tooltip =
"<span style='font-size:14px;'>xxx</span>"
),
value = 0,
min = 0,
max = 1,
step = 0.01
)
),
div(
style="display: inline-block;vertical-align:top; width: 125px;",
numericInput(
"heatmap_scale_coarse_end",
tippy(
"Coarse heatmap fill range, end",
placement = "right",
arrow = TRUE,
allowHTML = TRUE,
animation = "scale",
duration = 250,
theme = "light-border",
tooltip =
"<span style='font-size:14px;'>xxx</span>"
),
value = 1,
min = 0.01,
max = 1,
step = 0.01
)
),
div(
style="display: inline-block;vertical-align:top; width: 125px;",
numericInput(
"heatmap_scale_fine_start",
tippy(
"Fine heatmap fill range, start",
placement = "right",
arrow = TRUE,
allowHTML = TRUE,
animation = "scale",
duration = 250,
theme = "light-border",
tooltip =
"<span style='font-size:14px;'>xxx</span>"
),
value = 0,
min = 0,
max = 1,
step = 0.001
)
),
div(
style="display: inline-block;vertical-align:top; width: 125px;",
numericInput(
"heatmap_scale_fine_end",
tippy(
"Fine heatmap fill range, end",
placement = "right",
arrow = TRUE,
allowHTML = TRUE,
animation = "scale",
duration = 250,
theme = "light-border",
tooltip =
"<span style='font-size:14px;'>xxx</span>"
),
value = 1,
min = 0.001,
max = 1,
step = 0.001
)
),
br()
)
)
)
)
),
tabPanel(
"About",
hr(),
includeMarkdown("about.md")
)
)
),
# Main Panel --------------------------------------------------------------
mainPanel(
textOutput("output_test"),
splitLayout(
plotOutput("output_plot_MS"),
uiOutput("output_html_MS")
),
br(),
splitLayout(
plotOutput("output_plot_scoremat1"),
plotOutput("output_plot_scoremat2")
)
),
fluid = FALSE
)
)
)
davidsbutcher/abundancer documentation built on Feb. 21, 2022, 2:13 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
library(abundancer)
library(magrittr)
library(dplyr)
library(assertthat)
library(glue)
library(shiny)
library(shinyBS)
library(tippy)
library(shinydashboard)
library(shinyWidgets)
library(shinyjs)
library(purrr)
library(Peptides)
library(OrgMassSpecR)
library(fs)
library(enviPat)
library(reshape2)
library(progressr)
# options(repos = BiocManager::repositories())
options(shiny.maxRequestSize = 1000*1024^2)
# UI ----------------------------------------------------------------------
shinyUI(
fluidPage(
titlePanel("abundancer"),
theme = "maglab_theme_old.css",
# theme = bslib::bs_theme(version = 4),
useShinyjs(),
setBackgroundColor(
color = c("#FFFFFF"),
gradient = "linear",
direction = "bottom"
),
tags$head(
tags$style(HTML("hr {border-top: 1px solid #A9A9A9;}")),
tags$style(
HTML(
".shiny-notification {
position:fixed;
top: calc(20%);
left: calc(40%);
}"
)
)
),
sidebarLayout(
# Sidebar -----------------------------------------------------------------
sidebarPanel(
tabsetPanel(
id = "mainpanel",
type = "pills",
tabPanel(
"Main",
hr(),
tabsetPanel(
id = "guppipanel",
type = "tabs",
tabPanel(
"Peaklist",
br(),
fileInput(
"fileInputUpload",
tippy(
"Upload peaklist",
placement = "right",
arrow = TRUE,
allowHTML = TRUE,
animation = "scale",
duration = 250,
theme = "light-border",
tooltip =
"<span style='font-size:14px;'>Upload a peaklist in CSV or XLSX format. The first column should contain m/z values and the second should contain intensities. The peaklist should contain a full isotopic distribution of a single charge state of a single protein.</span>"
),
accept = c(".xlsx", ".csv")
),
numericInput(
"scoremat_charge",
tippy(
"Charge",
placement = "right",
arrow = TRUE,
allowHTML = TRUE,
animation = "scale",
duration = 250,
theme = "light-border",
tooltip =
"<span style='font-size:14px;'>Charge state corresponding to the isotopic distribution in the peaklist. Only positive charges are supported.</span>"
),
value = 1,
min = 1,
max = 100,
step = 1
),
textAreaInput(
"scoremat_sequence",
tippy(
"Sequence",
placement = "right",
arrow = TRUE,
allowHTML = TRUE,
animation = "scale",
duration = 250,
theme = "light-border",
tooltip =
"<span style='font-size:14px;'>Sequence corresponding to the protein whose isotopic distribution is represented by the peaklist. Only single-letter codes of canonical amino acids are supported.</span>"
),
placeholder =
"Single letter canonical amino acids only",
height = "100px"
),
textInput(
"scoremat_PTM",
tippy(
"PTM formula",
placement = "right",
arrow = TRUE,
allowHTML = TRUE,
animation = "scale",
duration = 250,
theme = "light-border",
tooltip =
"<span style='font-size:14px;'>Chemical formula (in Hill notation) of post-translational modifications to the protein sequence. The formula should be provided as a delta compared to the protein's chemical formula, i.e. for a methylation the PTM formula is CH3 and not CH4. For multiple PTMs, all formulae should be combined.</span>"
),
placeholder = "Leave blank if unmodified"
),
br(),
br(),
actionButton(
"abundancer_start",
"Analyze abundance"
),
br(),
br(),
downloadButton("downloadPDFcoarse", label = "Coarse Heatmap"),
downloadButton("downloadPDFfine", label = "Fine Heatmap")
),
tabPanel(
"Settings",
# h5(em("Hover parameter names for more info")),
bsCollapse(
bsCollapsePanel(
h5(strong("Peak picking parameters")),
br(),
splitLayout(
numericInput(
"peakpick_SNR",
tippy(
"SNR",
placement = "right",
arrow = TRUE,
allowHTML = TRUE,
animation = "scale",
duration = 250,
theme = "light-border",
tooltip =
"<span style='font-size:14px;'>From MSnbase documentation: \"A local maximum is considered a peak if its intensity is SNR times larger than the estimated noise.\" Noise is estimated using the MSnbase median absolute deviation method.</span>"
),
value = 25,
min = 0,
max = 100,
step = 1
),
numericInput(
"peakpick_k",
tippy(
"KNN",
placement = "right",
arrow = TRUE,
allowHTML = TRUE,
animation = "scale",
duration = 250,
theme = "light-border",
tooltip =
"<span style='font-size:14px;'>From MSnbase documentation: \"m/z values and intensities of the 2 * KNN closest signals to the centroid are used in the intensity weighted average calculation.\"</span>"
),
value = 2,
min = 1,
max = 10,
step = 1
)
),
br()
),
bsCollapsePanel(
h5(strong("Score matrix parameters")),
br(),
splitLayout(
numericInput(
"scoremat_12C",
tippy(
"<sup>12</sup>C abundance start",
placement = "top-end",
arrow = TRUE,
allowHTML = TRUE,
animation = "scale",
duration = 250,
theme = "light-border",
tooltip =
"<span style='font-size:14px;'>Starting value for <sup>12</sup>C abundance to use for calculating the coarse score matrix. <sup>12</sup>C abundance will be incremented from this value to 1 by the abundance step.</span>"
),
value = 0.987,
min = 0.9,
max = 0.999,
step = 0.001
),
numericInput(
"scoremat_14N",
tippy(
"<sup>14</sup>N abundance start",
placement = "top-end",
arrow = TRUE,
allowHTML = TRUE,
animation = "scale",
duration = 250,
theme = "light-border",
tooltip =
"<span style='font-size:14px;'>Starting value for <sup>14</sup>N abundance to use for calculating the coarse score matrix. <sup>14</sup>N abundance will be incremented from this value to 1 by the abundance step.</span>"
),
value = 0.994,
min = 0.9,
max = 0.999,
step = 0.001
)
),
splitLayout(
numericInput(
"scoremat_binSize",
tippy(
"Bin size",
placement = "top-end",
arrow = TRUE,
allowHTML = TRUE,
animation = "scale",
duration = 250,
theme = "light-border",
tooltip =
"<span style='font-size:14px;'>Prior to comparing observed and theoretical spectra, spectra are binned using this bin size value. See MSnbase documentation for more information.</span>"
),
value = 0.05,
min = 0.01,
max = 0.1,
step = 0.01
),
numericInput(
"scoremat_resolvingPower",
tippy(
"Resolving power",
placement = "top-end",
arrow = TRUE,
allowHTML = TRUE,
animation = "scale",
duration = 250,
theme = "light-border",
tooltip =
"<span style='font-size:14px;'>Resolving power to be used in generating theoretical isotopic distributions. See enviPat::envelope documentation for more information.</span>"
),
value = 300000,
min = 1000,
max = 1000000,
step = 1000
)
),
splitLayout(
numericInput(
"scoremat_coarseMult",
tippy(
"Coarse step mult.",
placement = "top-end",
arrow = TRUE,
allowHTML = TRUE,
animation = "scale",
duration = 250,
theme = "light-border",
tooltip =
"<span style='font-size:14px;'>Value by which coarse step is multiplied to determine range for calculating fine matrix.</span>"
),
value = 1,
min = 1,
max = 10,
step = 1
),
selectInput(
"scoremat_compfunc",
tippy(
"Spec. comp. func.",
placement = "right",
arrow = TRUE,
allowHTML = TRUE,
animation = "scale",
duration = 250,
theme = "light-border",
tooltip =
"<span style='font-size:14px;'>Sepctrum comparison function to be used for comparing observed and theoretical isotopic envelopes.</span>"
),
choices =
list(
"Cosine similarity" = "dotproduct",
"Cor" = "cor",
"ScoreMFA" = "scoremfa",
"ScoreMFA (C++)" = "scoremfacpp"
),
selected = "Cosine similarity"
)
),
# div(
# style="display: inline-block;vertical-align:top; width: 150px;",
# selectInput(
# "scoremat_compfunc",
# tippy(
# "Spectrum comparison function",
# placement = "right",
# arrow = TRUE,
# allowHTML = TRUE,
# animation = "scale",
# duration = 250,
# theme = "light-border",
# tooltip =
# "<span style='font-size:14px;'>Function to be used for comparing observed and theoretical isotopic envelopes.</span>"
# ),
# choices =
# list(
# "Cosine similarity" = "dotproduct",
# "Cor" = "cor",
# "ScoreMFA" = "scoremfa",
# "ScoreMFA (C++)" = "scoremfacpp"
# ),
# selected = "Cosine similarity"
# )
# ),
br()
),
bsCollapsePanel(
h5(strong("Heatmap parameters")),
br(),
div(
style="display: inline-block;vertical-align:top; width: 125px;",
selectInput(
"heatmap_fill",
tippy(
"Heatmap fill",
placement = "right",
arrow = TRUE,
allowHTML = TRUE,
animation = "scale",
duration = 250,
theme = "light-border",
tooltip =
"<span style='font-size:14px;'>Color palette to use for score matrix heatmap. All palettes are from the viridis R package and are accessible to colorblind readers.</span>"
),
choices =
c(
"magma",
"inferno",
"plasma",
"viridis",
"cividis"
),
selected = "plasma"
)
),
div(
style="display: inline-block;vertical-align:top; width: 125px;"
),
div(
style="display: inline-block;vertical-align:top; width: 125px;",
numericInput(
"heatmap_scale_coarse_start",
tippy(
"Coarse heatmap fill range, start",
placement = "right",
arrow = TRUE,
allowHTML = TRUE,
animation = "scale",
duration = 250,
theme = "light-border",
tooltip =
"<span style='font-size:14px;'>xxx</span>"
),
value = 0,
min = 0,
max = 1,
step = 0.01
)
),
div(
style="display: inline-block;vertical-align:top; width: 125px;",
numericInput(
"heatmap_scale_coarse_end",
tippy(
"Coarse heatmap fill range, end",
placement = "right",
arrow = TRUE,
allowHTML = TRUE,
animation = "scale",
duration = 250,
theme = "light-border",
tooltip =
"<span style='font-size:14px;'>xxx</span>"
),
value = 1,
min = 0.01,
max = 1,
step = 0.01
)
),
div(
style="display: inline-block;vertical-align:top; width: 125px;",
numericInput(
"heatmap_scale_fine_start",
tippy(
"Fine heatmap fill range, start",
placement = "right",
arrow = TRUE,
allowHTML = TRUE,
animation = "scale",
duration = 250,
theme = "light-border",
tooltip =
"<span style='font-size:14px;'>xxx</span>"
),
value = 0,
min = 0,
max = 1,
step = 0.001
)
),
div(
style="display: inline-block;vertical-align:top; width: 125px;",
numericInput(
"heatmap_scale_fine_end",
tippy(
"Fine heatmap fill range, end",
placement = "right",
arrow = TRUE,
allowHTML = TRUE,
animation = "scale",
duration = 250,
theme = "light-border",
tooltip =
"<span style='font-size:14px;'>xxx</span>"
),
value = 1,
min = 0.001,
max = 1,
step = 0.001
)
),
br()
)
)
)
)
),
tabPanel(
"About",
hr(),
includeMarkdown("about.md")
)
)
),
# Main Panel --------------------------------------------------------------
mainPanel(
textOutput("output_test"),
splitLayout(
plotOutput("output_plot_MS"),
uiOutput("output_html_MS")
),
br(),
splitLayout(
plotOutput("output_plot_scoremat1"),
plotOutput("output_plot_scoremat2")
)
),
fluid = FALSE
)
)
)
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