msiUI <- function() {
dashboardPage(skin="red",
dashboardHeader(
title="Cardinal",
titleWidth=200
),
dashboardSidebar(
width=200,
sidebarMenuOutput("tab_menu")
),
dashboardBody(
get_dashboard_bg_color(),
tags$style(type="text/css",
".shiny-input-container
{padding: 0px !important;}"),
uiOutput("tab_display")
)
)
}
helpUI <- function() {
fluidRow(
box(title="Getting started",
"Welcome to ", tags$i("CardinalVis"), "!",
br(), br(),
"Before using ", tags$i("CardinalVis"), " you need to load
a dataset as a ", tags$code("MSImagingExperiment"),
"object by using ", tags$code("readMSIData()"), " in R.",
br(), br(),
"See ", tags$code("?readMSIData"), " for help loading data into R.",
br(), br(),
"Once a dataset is loaded in R, you can use ", tags$i("CardinalVis"),
" to explore and visualize it.",
br(), br(),
"Use the ", tags$strong("Data"), " tab on the left
to select a loaded dataset, and click ", tags$strong("+"),
"to open a new view of the data.",
br(), br(),
"The dataset will open in a new tab. You can
open multiple datasets and switch
between views of them by using the tabs
in the sidebar.",
width=4),
box(title="Navigation",
"When viewing a ", tags$code("MSImagingExperiment"),
"you can navigate between images and spectra
by brushing and clicking on the plots.",
br(), br(),
"Double-click a pixel on the image to see the
corresponding mass spectrum.",
br(), br(),
"Double-click an m/z value on the spectrum to see the
corresponding image.",
br(), br(),
"Brush the plots by clicking and dragging
to zoom in on the selected region.",
br(), br(),
"Use the buttons on the side of the plots
to zoom in, zoom out, or zoom-to-fit.",
width=4),
box(title="Viewing options",
"Use the ", tags$strong("Navigation"), "box to control
the current m/z value, pixel coordinates,
and selected experimental runs. Multiple runs
can be plotted at the same time.",
br(), br(),
"Use the ", tags$strong("Overlay"), "box to overlay
the current plots with images from additional m/z values
or spectra from additional pixels. (Use the checkbox
to toggle which overlays are active.)",
br(), br(),
"Use the ", tags$strong("Intensity range"), "box to
control the intensity range for the current
image and spectrum. By default, the intensity range
automatically scales to the current pixel or m/z value.",
br(), br(),
"Use the ", tags$strong("Image options"), "box to control
image processing options such as spatial smoothing
and contrast enhancement.",
br(), br(),
"Use the ", tags$strong("Variables"), "box to display
a column from the object's", tags$code("pixelData()"),
"or", tags$code("featureData()"), "instead of the intensity.",
width=4)
)
}
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