notebook prototype v4

index.pug

- let counter = 1
- let cells = [{group: 1, type: 'text', fold: true, heading: 'Common plotting pitfalls with large data', paragraph: 'When working with large datasets, visualizations are often the only way available to understand the properties of that dataset -- there are simply too many data points to examine each one!  Thus it is very important to be aware of some common plotting problems that are minor inconveniences with small datasets but very serious problems with larger ones.', git: 'modified'},{group: 1, type: 'text', paragraph: 'We\'ll first load the plotting libraries and set up some defaults:', git: 'modified'},{group: 1, type: 'code', string: 'conda install -c bokeh -c ioam holoviews colorcet matplotlib scikit-image', time: '0.1'},{group: 1, type: 'code', string: 'import numpy as np \n np.random.seed(42) \n \n import holoviews as hv \n hv.notebook_extension(\'matplotlib\') \n \n %opts Points [color_index=2] (cmap="bwr" edgecolors=\'k\' s=50 alpha=1.0) \n %opts Scatter3D [color_index=3 fig_size=250] (cmap=\'bwr\' edgecolor=\'k\' s=50 alpha=1.0) \n %opts Image (cmap="gray_r") {+axiswise} \n %opts RGB [bgcolor="black" show_grid=False] \n \n import holoviews.plotting.mpl \n holoviews.plotting.mpl.MPLPlot.fig_alpha = 0 \n holoviews.plotting.mpl.ElementPlot.bgcolor = \'white\' \n \n from holoviews.operation.datashader import datashade \n from colorcet import fire \n datashade.cmap=fire[50:] \n', time: '0.1'},{group: 2, type: 'text', fold: true, heading: '1. Overplotting', paragraph: 'Let\'s consider plotting some 2D data points that come from two separate categories, here plotted as blue and red in **A** and **B** below.  When the two categories are overlaid, the appearance of the result can be very different depending on which one is plotted first:'},{group: 2, type: 'code', string: 'def blues_reds(offset=0.5,pts=300):\n    blues = (np.random.normal( offset,size=pts), np.random.normal( offset,size=pts), -1*np.ones((pts)))\n    reds  = (np.random.normal(-offset,size=pts), np.random.normal(-offset,size=pts),  1*np.ones((pts)))\n    return hv.Points(blues, vdims=["c"]), hv.Points(reds, vdims=["c"])\n\nblues,reds = blues_reds()\nblues + reds + reds*blues + blues*reds', time: '2.5', image: 'https://s3-us-west-2.amazonaws.com/s.cdpn.io/61037/notebooks-scatter-plot.png'},{group: 3,type: 'text', fold: true, heading: '2. Oversaturation', paragraph: 'You can reduce problems with overplotting by using transparency/opacity, via the alpha parameter provided to control opacity in most plotting programs.  E.g. if alpha is 0.1, full color saturation will be achieved only when 10 points overlap, reducing the effects of plot ordering but making it harder to see individual points:'},{group: 3,type: 'code', string: '%%opts Points (s=50 alpha=0.1)\nblues + reds + reds*blues + blues*reds', image: 'https://s3-us-west-2.amazonaws.com/s.cdpn.io/61037/scatter-plot-2.png', git: 'added'},]

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playground.json

{
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script.js

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hljs.initHighlightingOnLoad();

$("#theme").click(function(){
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scripts

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style.sass

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  --borderSelection: rgba(255, 255, 255, 0.12)
  --shadow: rgba(0, 0, 0, 0.8)
  --code: #D4D4D4
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.light
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  --iconHighlight: #388a34
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  --code: #000
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*
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body
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  padding: 0
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  color: var(--fontColor)
  background-color: var(--editor)
  display: flex
  height: 100%
  overflow: hidden
  flex-direction: column
  align-items: center
  // justify-content: center
#theme
  width: 100%
  padding: 4px 16px
  display: block
  text-align: right
  text-decoration: none
  color: var(--fontColor)

#activity-bar
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  height: 100vh
  background-color: var(--activity)
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      align-items: center
      justify-content: space-between
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      svg:active
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      #run:hover, .fold:hover,.folded:hover
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      .fold
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      .fold,.folded
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        width: 20px
        height: 20px
      .folded
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    &:hover
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    &:active,
    &:focus
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    padding: 2px 4px
    top: -12px
    right: 44px
    border: 1px solid rgba(white, .16)
    background-color: var(--editor)
    svg
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      color: var(--fontColor)
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      border-top: none
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      display: flex
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        align-items: center
        svg
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      .right
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      font-family: -apple-system, BlinkMacSystemFont, sans-serif
      padding: 16px
      background-color: var(--output)
      img
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        height: auto
  &:hover:not(.new-cell)
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    .execution
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    #actions
      display: flex
      .fold
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    .editor
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    .code:hover
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  position: fixed
  width: 100%
  height: 100%
  top: 0
  left: 0
#menu
  z-index: 999
  position: absolute
  list-style-type: none
  padding: 4px 0
  color: var(--fontColor)
  background-color: var(--sidebar)
  box-shadow: var(--shadow) 0px 4px 8px
  @at-root
    .light #menu
      background-color: var(--editor)
      li:hover
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  li
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    align-items: center
    min-width: 200px
    margin: 0
    padding: 8px 24px
    text-transform: capitalize
    &.border
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      pointer-events: none
      padding: 1px 0 0 0
      background-color: var(--borderColor)
    &:hover
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      background-color: #094771
      cursor: pointer
    span
      font-family: -apple-system,BlinkMacSystemFont,Segoe UI,Helvetica,Arial,sans-serif,Apple Color Emoji,Segoe UI Emoji
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    span.shortcut
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.new-cell
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  margin: 0
  padding: 4px 0
  position: relative
  display: flex
  align-items: center
  transition: opacity .2s ease-in
  transition-delay: .1s
  background: transparent
  &:hover
    opacity: 1
  .border
    z-index: 0
    position: absolute
    width: calc(100% - 48px)
    height: 1px
    left: 24px
    right: 0
    margin: auto
    background-color: var(--borderColor)
  .button
    z-index: 1
    font-size: 12px
    font-family: -apple-system, BlinkMacSystemFont, sans-serif
    padding: 4px 8px
    background-color: var(--editor)
    margin: 0 8px
    display: flex
    align-items: center
    &:hover
      cursor: pointer
    svg
      width: 14px
      height: 14px
      margin-right: 4px
      &, & *
        fill: var(--icon)



pre
  margin: 0
  padding: 0

.hljs
  padding: 0
  background-color: transparent

.hljs
  font-size: 12px
  line-height: 1.2rem
  font-family: 'Input Mono', monospace
  display: block
  overflow-x: auto
  color: var(--code)

.hljs-keyword, .hljs-literal, .hljs-symbol, .hljs-name
  color: #C586C0

.hljs-link
  color: #569CD6
  text-decoration: underline

.hljs-built_in, .hljs-type
  color: #4EC9B0

.hljs-number, .hljs-class
  color: #B8D7A3

.hljs-string, .hljs-meta-string
  color: #D69D85

.hljs-regexp, .hljs-template-tag
  color: #9A5334

.hljs-title
  color: #DCDCAA

.hljs-subst, .hljs-function, .hljs-params
  color: #DCDCDC

.hljs-comment, .hljs-quote
  color: #57A64A
  font-style: italic

.hljs-doctag
  color: #608B4E

.hljs-meta, .hljs-meta-keyword, .hljs-tag
  color: #9B9B9B

.hljs-variable, .hljs-template-variable
  color: #BD63C5

.hljs-attr, .hljs-attribute, .hljs-builtin-name
  color: #9CDCFE

.hljs-section
  color: gold

.hljs-emphasis
  font-style: italic

.hljs-strong
  font-weight: bold

.hljs-bullet, .hljs-selector-tag, .hljs-selector-id, .hljs-selector-class, .hljs-selector-attr, .hljs-selector-pseudo
  color: #D7BA7D

.hljs-addition
  background-color: #144212
  display: inline-block
  width: 100%

.hljs-deletion
  background-color: #600
  display: inline-block
  width: 100%

.light
  .hljs-keyword, .hljs-literal, .hljs-symbol, .hljs-name
    color: #af00db

  .hljs-link
    color: #569CD6
    text-decoration: underline

  .hljs-built_in, .hljs-type
    color: #4EC9B0

  .hljs-number, .hljs-class
    color: #098658

  .hljs-string, .hljs-meta-string
    color: #a31515

  .hljs-regexp, .hljs-template-tag
    color: #9A5334

  .hljs-title
    color: #795e26

  .hljs-subst, .hljs-function, .hljs-params
    color: #001080

  .hljs-comment, .hljs-quote
    color: #57A64A
    font-style: italic

  .hljs-doctag
    color: #608B4E

  .hljs-meta, .hljs-meta-keyword, .hljs-tag
    color: #9B9B9B

  .hljs-variable, .hljs-template-variable
    color: #BD63C5

  .hljs-attr, .hljs-attribute, .hljs-builtin-name
    color: #9CDCFE

  .hljs-section
    color: gold

  .hljs-emphasis
    font-style: italic

  .hljs-strong
    font-weight: bold

  .hljs-bullet, .hljs-selector-tag, .hljs-selector-id, .hljs-selector-class, .hljs-selector-attr, .hljs-selector-pseudo
    color: #D7BA7D

  .hljs-addition
    background-color: #144212
    display: inline-block
    width: 100%

  .hljs-deletion
    background-color: #600
    display: inline-block
    width: 100%