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Boutros lab style guide for plots and figures material of published manuscripts

This Style guide should serve as a general guideline.

The Rmarkdown file serves as template for creating tidy graphics of the most used data visualizations. The general color scheme should be used for highlights in figures. The interaction scheme, for everything related to genetic interactions.

General advice on color and data visualization

Consider Gestalt principles:

  1. figure-ground
    The figure-ground principle states that people instinctively perceive objects as either being in the foreground or the background.

  2. similarity
    The principle of similarity states that when things appear to be similar to each other, we group them together. And we also tend to think they have the same function.

  3. proximity
    The principle of proximity states that things that are close together appear to be more related than things that are spaced farther apart.

  4. common region
    The principle of common region is highly related to proximity. It states that when objects are located within the same closed region, we perceive them as being grouped together.

  5. continuity
    The principle of continuity states that elements that are arranged on a line or curve are perceived to be more related than elements not on the line or curve.

  6. closure
    The principle of closure states that when we look at a complex arrangement of visual elements, we tend to look for a single, recognizable pattern.

  7. focal point The focal point principle states that whatever stands out visually will capture and hold the viewer’s attention first.

Color Coding by Bang Wong

R Styles

General color scheme.

b110_grey   = '#808080'
b110_grey_light   = '#909090'
b110_transparent_black = alpha('#000000',0.5)

b110_blue= '#4285f4'
b110_green= '#008744'
b110_yellow= '#ffa700'
b110_red= '#d62d20'

Genetic interaction color scheme.

sgi_blue    = '#5087C8'
sgi_yellow1 = '#F2EE35'
sgi_yellow2 = '#FED98E'

General plotting style.

theme_b110<-function(){
  theme_classic() +
  theme(
    axis.text=element_text(size = 16), 
    axis.title=element_text(size = 16),
    plot.title = element_text(size = 22,hjust = 0.5,face="bold"),
    legend.title = element_text(size = 22),
    legend.text = element_text(size =16),
    legend.position = "bottom"
    )
}

CSS styles for web-pages and apps

#allcontent {
      font-family: 'Open Sans', sans-serif;
      width: 800px;
      text-align: left;
      /*font-family: Verdana, Arial, sans-serif;*/
      font-size: 12px;
      margin-left: auto;
      margin-right: auto;
}

td.header{      border:0px;
                        background-color: #2662C3;
                        font-family: 'Open Sans', sans-serif;
                font-size: 16px;
                text-align: center;
                border-radius: 5px
        }
td.header:hover{background-color: #5692F3;}

a:link {
      color: #333;
      font-family: 'Open Sans', sans-serif;
      /*font-family: Verdana;*/
      text-decoration: underline;
}

a:visited {
      color: #333;
      font-family: 'Open Sans', sans-serif;
      /*font-family: Verdana;*/
      text-decoration: underline;
}

And more to be added...

Gestalt list was adapted from Usertesting