diff --git a/.nojekyll b/.nojekyll index 08cd278..8f69b98 100644 --- a/.nojekyll +++ b/.nojekyll @@ -1 +1 @@ -1979e0f7 \ No newline at end of file +ecd3a40b \ No newline at end of file diff --git a/figures/action-checkboxes.gif b/figures/action-checkboxes.gif new file mode 100644 index 0000000..936ab9e Binary files /dev/null and b/figures/action-checkboxes.gif differ diff --git a/figures/data-parameters-reduced-dimension-plot.png b/figures/data-parameters-reduced-dimension-plot.png new file mode 100644 index 0000000..312d5e4 Binary files /dev/null and b/figures/data-parameters-reduced-dimension-plot.png differ diff --git a/search.json b/search.json index 6b967b0..2258dc7 100644 --- a/search.json +++ b/search.json @@ -13,12 +13,33 @@ "section": "", "text": "iSEE is a Bioconductor package designed to produce interactive web applications for the visualisation of biological assays (Figure 2.1).\n\n\n\nFigure 1.1: The iSEE app interface.\n\n\nInitiated in 2017 with single-cell RNA-sequencing in mind, iSEE was designed in such a way that it naturally handles any biological assay that can be stored in a rectangular matrix of features (in rows) and samples (in columns).\nWhat makes iSEE stand out from other interactive web-application is its focus on the SummarizedExperiment class (Figure 1.2), a data structure is widely used throughout the Bioconductor project, from bulk to single-cell experiments.\n\n\n\nFigure 1.2: Schematic representation of the SummarizedExperiment class (reproduced from the vignette of the SummarizedExperiment package).\n\n\nThe well-defined and stable SummarizedExperiment data structure makes it easy for iSEE to automatically detect information commonly stored in dedicated components of SummarizedExperiment objects and display that information in a range of interactive panels, including tables and plots." }, + { + "objectID": "ui.html#overview", + "href": "ui.html#overview", + "title": "2  The user interface", + "section": "2.1 Overview", + "text": "2.1 Overview\nIn this chapter, we describe the contents and layout of a standard iSEE app.\nSpecifically, we focus on the appearance of the interactive point-and-click interface presented to end-users who come to simply explore the data set without any programming knowledge required.\nIllustrative screenshots are taken from the iSEE app produced by the example code given in the help page of the iSEE() function, which can be access from an R console by typing either help(iSEE) or ?iSEE." + }, + { + "objectID": "ui.html#panels", + "href": "ui.html#panels", + "title": "2  The user interface", + "section": "2.2 Panels", + "text": "2.2 Panels\nUnder entirely default settings, data sets loaded into the iSEE app are automatically parsed for standard information stored in SummarizedExperiment objects. Based on the information available and a set of eight core panel types designed to display different pieces of information, the iSEE() function automatically populates the interface with one panel of each type for which the relevant information is available.\n\n\n\nFigure 2.1: First row of panel in the iSEE app interface, for an example data set.\n\n\nThe example code given in the help page of the iSEE() function produces an iSEE app that showcases all eight core panel types:\n\n\n\n\n\n\n\n(a) Reduced dimension plot\n\n\n\n\n\n\n\n(b) Row data table\n\n\n\n\n\n\n\n(c) Feature assay plot\n\n\n\n\n\n\n\n\n\n(d) Column data plot\n\n\n\n\n\n\n\n(e) Row data plot\n\n\n\n\n\n\n\n(f) Sample assay plot\n\n\n\n\n\n\n\n\n\n(g) Column data table\n\n\n\n\n\n\n\n(h) Complex heatmap plot\n\n\n\n\nFigure 2.2: Core panel types in the iSEE package, in their default configuration.\n\n\nEach core panel type is designed to display a different piece of information stored in the object. The purpose of each panel will be discussed in a separate chapter." + }, { "objectID": "ui.html#actions", "href": "ui.html#actions", "title": "2  The user interface", - "section": "2.1 Actions", - "text": "2.1 Actions\nOnce the panels are loaded into the interface, users are free to interact with the interface in any way they see fit.\n\n2.1.1 Scrolling\nScroll up and down the interface, to bring panels in view.\n\n\n\nFigure 2.3: Scrolling up and down the app interface.\n\n\n\n\n2.1.2 Collabsible boxes\nClick on the header of collapsible boxes located under the panel output, to reveal interactive elements controlling the contents displayed in each panel.\n\n\n\nFigure 2.4: Expanding collapsible boxes.\n\n\n\n\n2.1.3 Selection inputs\nClick on dropdown elements to reveal their choices. Click a different choice to see the panel output change accordingly.\n\n\n\nFigure 2.5: Changing the selected choice in dropdown menus." + "section": "2.3 Actions", + "text": "2.3 Actions\nOnce the panels are loaded into the interface, users are free to interact with the interface in any way they see fit.\n\n2.3.1 Scrolling\nUse the mouse wheel, trackpad, or directional arrows (up and down), to scroll up and down the interface, to bring panels into view.\n\n\n\nFigure 2.3: Scrolling up and down the app interface.\n\n\n\n\n2.3.2 Collabsible boxes\nClick on the header of collapsible boxes located under the panel output, to reveal interactive elements controlling various aspects of the contents displayed in each panel.\n\n\n\nFigure 2.4: Expanding collapsible boxes.\n\n\n\n\n2.3.3 Selection inputs\nClick on dropdown elements to reveal their choices. Click a different choice to see the panel output change accordingly.\n\n\n\nFigure 2.5: Changing the selected choice in dropdown menus.\n\n\n\n\n2.3.4 Checkboxes\nClick on checkboxes to toggle any number of mutually-compatible parameters.\n\n\n\nFigure 2.6: Toggling checkboxes." + }, + { + "objectID": "ui.html#collapsible-boxes-of-parameters", + "href": "ui.html#collapsible-boxes-of-parameters", + "title": "2  The user interface", + "section": "2.4 Collapsible boxes of parameters", + "text": "2.4 Collapsible boxes of parameters\n\n2.4.1 Data parameters\nThe Data parameters collapsible box contains interactive elements that control the nature of the observations displayed in each panel.\nFor plots, that is typically the choice of variables shown along each axis.\nFor tables, that is typically the subset of columns hidden in the panel.\n\n\n\nFigure 2.7: The Data parameters box of the Reduced dimension plot panel, expanded to reveal its contents." }, { "objectID": "references.html", diff --git a/ui.html b/ui.html index 5410857..10f414d 100644 --- a/ui.html +++ b/ui.html @@ -133,11 +133,18 @@

Table of contents

@@ -162,9 +169,14 @@

2  +

2.1 Overview

In this chapter, we describe the contents and layout of a standard iSEE app.

Specifically, we focus on the appearance of the interactive point-and-click interface presented to end-users who come to simply explore the data set without any programming knowledge required.

Illustrative screenshots are taken from the iSEE app produced by the example code given in the help page of the iSEE() function, which can be access from an R console by typing either help(iSEE) or ?iSEE.

+ +
+

2.2 Panels

Under entirely default settings, data sets loaded into the iSEE app are automatically parsed for standard information stored in SummarizedExperiment objects. Based on the information available and a set of eight core panel types designed to display different pieces of information, the iSEE() function automatically populates the interface with one panel of each type for which the relevant information is available.

@@ -249,12 +261,13 @@

2  -

2.1 Actions

+

+
+

2.3 Actions

Once the panels are loaded into the interface, users are free to interact with the interface in any way they see fit.

-
-

2.1.1 Scrolling

-

Scroll up and down the interface, to bring panels in view.

+
+

2.3.1 Scrolling

+

Use the mouse wheel, trackpad, or directional arrows (up and down), to scroll up and down the interface, to bring panels into view.

@@ -262,9 +275,9 @@

-
-

2.1.2 Collabsible boxes

-

Click on the header of collapsible boxes located under the panel output, to reveal interactive elements controlling the contents displayed in each panel.

+
+

2.3.2 Collabsible boxes

+

Click on the header of collapsible boxes located under the panel output, to reveal interactive elements controlling various aspects of the contents displayed in each panel.

@@ -272,8 +285,8 @@

-
-

2.1.3 Selection inputs

+
+

2.3.3 Selection inputs

Click on dropdown elements to reveal their choices. Click a different choice to see the panel output change accordingly.

@@ -281,6 +294,31 @@

Figure 2.5: Changing the selected choice in dropdown menus.

+
+
+

2.3.4 Checkboxes

+

Click on checkboxes to toggle any number of mutually-compatible parameters.

+
+
+

+
Figure 2.6: Toggling checkboxes.
+
+
+
+
+
+

2.4 Collapsible boxes of parameters

+
+

2.4.1 Data parameters

+

The Data parameters collapsible box contains interactive elements that control the nature of the observations displayed in each panel.

+

For plots, that is typically the choice of variables shown along each axis.

+

For tables, that is typically the subset of columns hidden in the panel.

+
+
+

+
Figure 2.7: The Data parameters box of the Reduced dimension plot panel, expanded to reveal its contents.
+
+