Table of contents

  1. Introduction
  2. Objects menu
  3. Global features
  4. Loading and saving
  5. Figure legend
  6. Additional views
  7. Zooming
  8. Using templates

Introduction

Data format

The software accepts data in comma-separate values (csv) format. Columns should represent features/variables and rows should represent conditions or samples, see Table 1. Data should have a column header indicating feature names (shaded blue in Table 1) and row header indicating condition names (shaded grey in Table 1). The data in ShapoGraphy should be scaled between 0 and 1.0. Dimensional data (i.e. length, width, ..) should be scaled between 0.1 and 1.0 to avoid diminishing of the smallest object. Dimensional data should be scaled in a way that their ratios (w/l) before and after normalization is equal. For example, if the largest object length is l1=100 and width w1=50, then l1'=1 and w1=.5. You can also normalize your data in our app using the Normalise data sub-menu on the right. There, you can select the dimensional variables if applicable.

Table 1: Example on the format of the data that can be uploaded to ShapoGraphy
Condition Cell length Cell width Number of nuclei Nucleus length Nucleus width
Control 0.5 0.4 2 0.4 0.3
Condition 1 0.9 0.5 4 0.5 0.35
Condition 2 0.6 0.45 5 0.3 0.3
Condition 3 0.8 0.5 7 0.5 0.45
Condition 4 0.4 0.2 6 0.2 0.2

To plot your data using ShapoGraphy you need to first upload data. Currently ShapoGraphy support comma separated files (i.e. csv files, see File format). Add objects to represent map your data to using the shapes on the left menu (e.g. an ellipse for a cell or tumour, a square for a well, or draw your own shape).

gesture
Draw square
Draw circle
Draw hexagon
Draw triangle
Draw rounded rectangle
Draw semi-circle
Draw custom

The added objects will be displayed on right menu (see Objects menu) where their names, locations relative to each other and initial size can be customized in the Global features menu.

The color of an object can be static (fixed for all samples) or dynamic (vary across samples depending on a selected variable value). If you wish to use a static color, you can adjust it from the color picker in the left menu where you can also adjust the object stroke color.

Features

Several features can be mapped to each object as detailed below. The user can show/hide a certain visual element by clicking on the eye icon.

  • Object dimensions:
  • Length: object length or height
  • Width: object width. If you only have one dimensional variable (e.g. area, or radius) then select the same feature for length and width.
  • Fill gradient: this element assigns a color for each object instance based on the value of the selected variable and the chosen gradient as in a heat map
  • Fill Symbols: this element fills the object with symbols propotional to the selected variable value.
  • Border overlay: this element plots part of object border as a thick line. The extent of the thick line is propotional to the selected feature value. The color of the thick line can be specified. This element can be used to represent the extent of cell crowding or adhesion
  • Border overlay symbols: this element plots symbols on the border of the object propotional to the selected variable value. You can sepcify the symbole (e.g. dashes, star or dots).
  • Spikes: this element can represent irregularity in the object shape or spread of the object (e.g. spread of tumour). It extends around the object border proportional to the selected variable value.
  • Mesh: this element can represent selected feature values as the density of mesh. The user have a choice of vertical, horizontal, radial, grid, or random grid mesh. For example the density of horizontal lines can represent fiber density
  • Rotation: the object will be rotated depending on the variable value.
  • Opacity: the transperency of the object will be depending on the variable value.
  • ShapoGraphy requirements

    For best experience, run ShapoGraphy using Google Chrome.

    Positional mapping

    This section allows you to sort glyphs based on a certain variable, or arrange them in a scatter plot by choosing X and Y variabless

    Sorting

    You can select variables To sort plotted glyph sets based on the value of a designated variable.

    Scatter plot

    To arrange plotted glyph sets in a scatter plot, you can select variables to position them on the x- and y-axis. This help sorting the glyphs or further group them and effectively add additional dimensions.

    Objects menu

    The object menu contains a list of the objects you have created

    From here, you can manipulate your objects as follows:

    Global features

    The global features menu contain features that will be equally applied to the object across all data points (rows in the data file)

    Available global features include:

    Loading and saving

    An additional option to load your data to our page is selecting the load project option from the file menu
    this will open a window where you can select your data.csv file and any previous template.json file you worked on earlier
    this will load the dataset and apply the template to it at the same time
    Please notice that the template.json file must contain values with similar feature names. If you load a dataset with different feature names then you need to map your features to the object elements again.

    Additional saving options include:

    1. Save template: to save the design and data mapping as a json file select File -> save template.
    2. Save Svg: to save the plot as a SVG file, select File -> save SVG.
    3. Save PNG: to save the plot as a PNG file, select File -> save PNG.

    Figure legend

    You can view the legend specifying the feature mapping to different glyph objects by clicking the legend button in the top menu

    You can also save this legend as a SVG file or a PNG image by selecting the save legend option from the file menu

    Additional views

    Addition views in ShapoGraphy include:

    Heat map

    Accessed by clicking the heatmap button in the top menu.

    Data table

    Shows the dataset values in a table for ease of access
    Accessed by clicking the Table icon option in the top menu*.
    *The dataset option becomes visible only after loading a data file

    Zooming

    The user can zoom in or zoom out on any point on the canvas

    This is done by clicking the Zoom in icon and then moving the mouse pointer to the desired point and scrolling the mouse wheel to zoom in or out

    To cancel the zooming operation, simply click the Zoom out icon which will revert the canvas to it's original state

    Using templates

    Shapography introduces pre-designed templates which the user can use with their own datasets

    On the homepage, you can find them in the templates section, click on the template that you like to see and it will be rendered on the canvas before you

    At that point, the template will be using a mock dataset for the sake of demonstration, you can load one of our datasets to apply the template to them, or simply use your own

    At the moment most templates have their own tutorials which would be indicated at the top of the rendered canvas, you can also access them through the 'Help' tab in the navbar