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Amine GHOZLANE
shaman
Commits
335f7a16
Commit
335f7a16
authored
Aug 04, 2016
by
Amine GHOZLANE
Browse files
Debug sample name with biom files and change origin of rNVD3 package
parent
4f7fed66
Changes
5
Hide whitespace changes
Inline
Side-by-side
.gitignore
View file @
335f7a16
.Rproj.user
.Rhistory
.RData
*
.Rproj.user
*
.Rhistory
*
.RData
LoadPackages.R
View file @
335f7a16
...
...
@@ -65,7 +65,7 @@ if (!require(scatterD3)) {
if
(
!
require
(
rNVD3
))
{
library
(
devtools
)
install_github
(
'rNVD3'
,
'
ramnathv
'
)
install_github
(
'rNVD3'
,
'
aghozlane
'
)
library
(
rNVD3
)
}
...
...
internal.R
View file @
335f7a16
...
...
@@ -118,6 +118,8 @@ CheckCountsTable <- function(counts)
## Counts table
counts
=
biom_data
(
dataBIOM
)
counts
=
as.matrix
(
counts
)
## Change of - to . is risky
colnames
(
counts
)
=
gsub
(
"-"
,
"."
,
colnames
(
counts
))
counts
=
as.data.frame
(
counts
)
CheckCounts
=
CheckCountsTable
(
counts
)
counts
=
CheckCounts
$
counts
...
...
@@ -150,7 +152,6 @@ CheckCountsTable <- function(counts)
counts
=
dataC
CheckCounts
=
CheckCountsTable
(
counts
)
counts
=
CheckCounts
$
counts
## Taxonomy table
taxo
=
as.data.frame
(
dataT
)
CheckTaxo
=
CheckTaxoTable
(
taxo
,
counts
)
...
...
www/rnvd3_css/nv.d3.css
deleted
100644 → 0
View file @
4f7fed66
/********************
* HTML CSS
*/
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{
margin
:
0
;
padding
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0
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overflow
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/********************
* TOOLTIP CSS
*/
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position
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absolute
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background-color
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(
255
,
255
,
255
,
1
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padding
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solid
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box-shadow
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-webkit-border-radius
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-moz-border-radius
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6px
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border-radius
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pointer-events
:
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-webkit-touch-callout
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-webkit-user-select
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none
;
-khtml-user-select
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-moz-user-select
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-ms-user-select
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user-select
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.nvtooltip.x-nvtooltip
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.nvtooltip.y-nvtooltip
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padding
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;
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.nvtooltip
h3
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margin
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0
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padding
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14px
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line-height
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18px
;
font-weight
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normal
;
background-color
:
#f7f7f7
;
text-align
:
center
;
border-bottom
:
1px
solid
#ebebeb
;
-webkit-border-radius
:
5px
5px
0
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;
-moz-border-radius
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5px
0
0
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border-radius
:
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5px
0
0
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}
.nvtooltip
p
{
margin
:
0
;
padding
:
5px
14px
;
text-align
:
center
;
}
.nvtooltip
span
{
display
:
inline-block
;
margin
:
2px
0
;
}
.nvtooltip-pending-removal
{
position
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absolute
;
pointer-events
:
none
;
}
/********************
* SVG CSS
*/
svg
{
-webkit-touch-callout
:
none
;
-webkit-user-select
:
none
;
-khtml-user-select
:
none
;
-moz-user-select
:
none
;
-ms-user-select
:
none
;
user-select
:
none
;
/* Trying to get SVG to act like a greedy block in all browsers */
display
:
block
;
width
:
100%
;
height
:
100%
;
}
svg
text
{
font
:
normal
12px
Arial
;
}
svg
.title
{
font
:
bold
14px
Arial
;
}
.nvd3
.nv-background
{
fill
:
white
;
fill-opacity
:
0
;
/*
pointer-events: none;
*/
}
.nvd3.nv-noData
{
font-size
:
18px
;
font-weight
:
bold
;
}
/**********
* Brush
*/
.nv-brush
.extent
{
fill-opacity
:
.125
;
shape-rendering
:
crispEdges
;
}
/**********
* Legend
*/
.nvd3
.nv-legend
.nv-series
{
cursor
:
pointer
;
}
.nvd3
.nv-legend
.disabled
circle
{
fill-opacity
:
0
;
}
/**********
* Axes
*/
.nvd3
.nv-axis
path
{
fill
:
none
;
stroke
:
#000
;
stroke-opacity
:
.75
;
shape-rendering
:
crispEdges
;
}
.nvd3
.nv-axis
path
.domain
{
stroke-opacity
:
.75
;
}
.nvd3
.nv-axis.nv-x
path
.domain
{
stroke-opacity
:
0
;
}
.nvd3
.nv-axis
line
{
fill
:
none
;
stroke
:
#000
;
stroke-opacity
:
.25
;
shape-rendering
:
crispEdges
;
}
.nvd3
.nv-axis
line
.zero
{
stroke-opacity
:
.75
;
}
.nvd3
.nv-axis
.nv-axisMaxMin
text
{
font-weight
:
bold
;
}
.nvd3
.x
.nv-axis
.nv-axisMaxMin
text
,
.nvd3
.x2
.nv-axis
.nv-axisMaxMin
text
,
.nvd3
.x3
.nv-axis
.nv-axisMaxMin
text
{
text-anchor
:
middle
}
/**********
* Brush
*/
.nv-brush
.resize
path
{
fill
:
#eee
;
stroke
:
#666
;
}
/**********
* Bars
*/
.nvd3
.nv-bars
.negative
rect
{
zfill
:
brown
;
}
.nvd3
.nv-bars
rect
{
zfill
:
steelblue
;
fill-opacity
:
.75
;
transition
:
fill-opacity
250ms
linear
;
-moz-transition
:
fill-opacity
250ms
linear
;
-webkit-transition
:
fill-opacity
250ms
linear
;
}
.nvd3
.nv-bars
rect
:hover
{
fill-opacity
:
1
;
}
.nvd3
.nv-bars
.hover
rect
{
fill
:
lightblue
;
}
.nvd3
.nv-bars
text
{
fill
:
rgba
(
0
,
0
,
0
,
0
);
}
.nvd3
.nv-bars
.hover
text
{
fill
:
rgba
(
0
,
0
,
0
,
1
);
}
/**********
* Bars
*/
.nvd3
.nv-multibar
.nv-groups
rect
,
.nvd3
.nv-multibarHorizontal
.nv-groups
rect
,
.nvd3
.nv-discretebar
.nv-groups
rect
{
stroke-opacity
:
0
;
transition
:
fill-opacity
250ms
linear
;
-moz-transition
:
fill-opacity
250ms
linear
;
-webkit-transition
:
fill-opacity
250ms
linear
;
}
.nvd3
.nv-multibar
.nv-groups
rect
:hover
,
.nvd3
.nv-multibarHorizontal
.nv-groups
rect
:hover
,
.nvd3
.nv-discretebar
.nv-groups
rect
:hover
{
fill-opacity
:
1
;
}
.nvd3
.nv-discretebar
.nv-groups
text
,
.nvd3
.nv-multibarHorizontal
.nv-groups
text
{
font-weight
:
bold
;
fill
:
rgba
(
0
,
0
,
0
,
1
);
stroke
:
rgba
(
0
,
0
,
0
,
0
);
}
/***********
* Pie Chart
*/
.nvd3.nv-pie
path
{
stroke-opacity
:
0
;
transition
:
fill-opacity
250ms
linear
,
stroke-width
250ms
linear
,
stroke-opacity
250ms
linear
;
-moz-transition
:
fill-opacity
250ms
linear
,
stroke-width
250ms
linear
,
stroke-opacity
250ms
linear
;
-webkit-transition
:
fill-opacity
250ms
linear
,
stroke-width
250ms
linear
,
stroke-opacity
250ms
linear
;
}
.nvd3.nv-pie
.nv-slice
text
{
stroke
:
#000
;
stroke-width
:
0
;
}
.nvd3.nv-pie
path
{
stroke
:
#fff
;
stroke-width
:
1px
;
stroke-opacity
:
1
;
}
.nvd3.nv-pie
.hover
path
{
fill-opacity
:
.7
;
/*
stroke-width: 6px;
stroke-opacity: 1;
*/
}
.nvd3.nv-pie
.nv-label
rect
{
fill-opacity
:
0
;
stroke-opacity
:
0
;
}
/**********
* Lines
*/
.nvd3
.nv-groups
path
.nv-line
{
fill
:
none
;
stroke-width
:
2.5px
;
/*
stroke-linecap: round;
shape-rendering: geometricPrecision;
transition: stroke-width 250ms linear;
-moz-transition: stroke-width 250ms linear;
-webkit-transition: stroke-width 250ms linear;
transition-delay: 250ms
-moz-transition-delay: 250ms;
-webkit-transition-delay: 250ms;
*/
}
.nvd3
.nv-groups
path
.nv-area
{
stroke
:
none
;
/*
stroke-linecap: round;
shape-rendering: geometricPrecision;
stroke-width: 2.5px;
transition: stroke-width 250ms linear;
-moz-transition: stroke-width 250ms linear;
-webkit-transition: stroke-width 250ms linear;
transition-delay: 250ms
-moz-transition-delay: 250ms;
-webkit-transition-delay: 250ms;
*/
}
.nvd3
.nv-line.hover
path
{
stroke-width
:
6px
;
}
/*
.nvd3.scatter .groups .point {
fill-opacity: 0.1;
stroke-opacity: 0.1;
}
*/
.nvd3.nv-line
.nvd3.nv-scatter
.nv-groups
.nv-point
{
fill-opacity
:
0
;
stroke-opacity
:
0
;
}
.nvd3.nv-scatter.nv-single-point
.nv-groups
.nv-point
{
fill-opacity
:
.5
!important
;
stroke-opacity
:
.5
!important
;
}
.nvd3
.nv-groups
.nv-point
{
transition
:
stroke-width
250ms
linear
,
stroke-opacity
250ms
linear
;
-moz-transition
:
stroke-width
250ms
linear
,
stroke-opacity
250ms
linear
;
-webkit-transition
:
stroke-width
250ms
linear
,
stroke-opacity
250ms
linear
;
}
.nvd3.nv-scatter
.nv-groups
.nv-point.hover
,
.nvd3
.nv-groups
.nv-point.hover
{
stroke-width
:
20px
;
fill-opacity
:
.5
!important
;
stroke-opacity
:
.5
!important
;
}
.nvd3
.nv-point-paths
path
{
stroke
:
#aaa
;
stroke-opacity
:
0
;
fill
:
#eee
;
fill-opacity
:
0
;
}
.nvd3
.nv-indexLine
{
cursor
:
ew-resize
;
}
/**********
* Distribution
*/
.nvd3
.nv-distribution
{
pointer-events
:
none
;
}
/**********
* Scatter
*/
/* **Attempting to remove this for useVoronoi(false), need to see if it's required anywhere
.nvd3 .nv-groups .nv-point {
pointer-events: none;
}
*/
.nvd3
.nv-groups
.nv-point.hover
{
stroke-width
:
20px
;
stroke-opacity
:
.5
;
}
.nvd3
.nv-scatter
.nv-point.hover
{
fill-opacity
:
1
;
}
/*
.nv-group.hover .nv-point {
fill-opacity: 1;
}
*/
/**********
* Stacked Area
*/
.nvd3.nv-stackedarea
path
.nv-area
{
fill-opacity
:
.7
;
/*
stroke-opacity: .65;
fill-opacity: 1;
*/
stroke-opacity
:
0
;
transition
:
fill-opacity
250ms
linear
,
stroke-opacity
250ms
linear
;
-moz-transition
:
fill-opacity
250ms
linear
,
stroke-opacity
250ms
linear
;
-webkit-transition
:
fill-opacity
250ms
linear
,
stroke-opacity
250ms
linear
;
/*
transition-delay: 500ms;
-moz-transition-delay: 500ms;
-webkit-transition-delay: 500ms;
*/
}
.nvd3.nv-stackedarea
path
.nv-area.hover
{
fill-opacity
:
.9
;
/*
stroke-opacity: .85;
*/
}
/*
.d3stackedarea .groups path {
stroke-opacity: 0;
}
*/
.nvd3.nv-stackedarea
.nv-groups
.nv-point
{
stroke-opacity
:
0
;
fill-opacity
:
0
;
}
.nvd3.nv-stackedarea
.nv-groups
.nv-point.hover
{
stroke-width
:
20px
;
stroke-opacity
:
.75
;
fill-opacity
:
1
;
}
/**********
* Line Plus Bar
*/
.nvd3.nv-linePlusBar
.nv-bar
rect
{
fill-opacity
:
.75
;
}
.nvd3.nv-linePlusBar
.nv-bar
rect
:hover
{
fill-opacity
:
1
;
}
/**********
* Bullet
*/
.nvd3.nv-bullet
{
font
:
10px
sans-serif
;
}
.nvd3.nv-bullet
.nv-measure
{
fill-opacity
:
.8
;
}
.nvd3.nv-bullet
.nv-measure
:hover
{
fill-opacity
:
1
;
}
.nvd3.nv-bullet
.nv-marker
{
stroke
:
#000
;
stroke-width
:
2px
;
}
.nvd3.nv-bullet
.nv-markerTriangle
{
stroke
:
#000
;
fill
:
#fff
;
stroke-width
:
1.5px
;
}
.nvd3.nv-bullet
.nv-tick
line
{
stroke
:
#666
;
stroke-width
:
.5px
;
}
.nvd3.nv-bullet
.nv-range.nv-s0
{
fill
:
#eee
;
}
.nvd3.nv-bullet
.nv-range.nv-s1
{
fill
:
#ddd
;
}
.nvd3.nv-bullet
.nv-range.nv-s2
{
fill
:
#ccc
;
}
.nvd3.nv-bullet
.nv-title
{
font-size
:
14px
;
font-weight
:
bold
;
}
.nvd3.nv-bullet
.nv-subtitle
{
fill
:
#999
;
}
.nvd3.nv-bullet
.nv-range
{
fill
:
#999
;
fill-opacity
:
.4
;
}
.nvd3.nv-bullet
.nv-range
:hover
{
fill-opacity
:
.7
;
}
/**********
* Sparkline
*/
.nvd3.nv-sparkline
path
{
fill
:
none
;
}
.nvd3.nv-sparklineplus
g
.nv-hoverValue
{
pointer-events
:
none
;
}
.nvd3.nv-sparklineplus
.nv-hoverValue
line
{
stroke
:
#333
;
stroke-width
:
1.5px
;
}
.nvd3.nv-sparklineplus
,
.nvd3.nv-sparklineplus
g
{
pointer-events
:
all
;
}
.nvd3
.nv-hoverArea
{
fill-opacity
:
0
;
stroke-opacity
:
0
;
}
.nvd3.nv-sparklineplus
.nv-xValue
,
.nvd3.nv-sparklineplus
.nv-yValue
{
/*
stroke: #666;
*/
stroke-width
:
0
;
font-size
:
.9em
;
font-weight
:
normal
;
}
.nvd3.nv-sparklineplus
.nv-yValue
{
stroke
:
#f66
;
}
.nvd3.nv-sparklineplus
.nv-maxValue
{
stroke
:
#2ca02c
;
fill
:
#2ca02c
;
}
.nvd3.nv-sparklineplus
.nv-minValue
{
stroke
:
#d62728
;
fill
:
#d62728
;
}
.nvd3.nv-sparklineplus
.nv-currentValue
{
/*
stroke: #444;
fill: #000;
*/
font-weight
:
bold
;
font-size
:
1.1em
;
}
/**********
* historical stock
*/
.nvd3.nv-ohlcBar
.nv-ticks
.nv-tick
{
stroke-width
:
2px
;
}
.nvd3.nv-ohlcBar
.nv-ticks
.nv-tick.hover
{
stroke-width
:
4px
;
}
.nvd3.nv-ohlcBar
.nv-ticks
.nv-tick.positive
{
stroke
:
#2ca02c
;
}
.nvd3.nv-ohlcBar
.nv-ticks
.nv-tick.negative
{
stroke
:
#d62728
;
}
.nvd3.nv-historicalStockChart
.nv-axis
.nv-axislabel
{
font-weight
:
bold
;
}