Commit 335f7a16 authored by Amine  GHOZLANE's avatar Amine GHOZLANE
Browse files

Debug sample name with biom files and change origin of rNVD3 package

parent 4f7fed66
.Rproj.user
.Rhistory
.RData
*.Rproj.user
*.Rhistory
*.RData
......@@ -65,7 +65,7 @@ if (!require(scatterD3)) {
if (!require(rNVD3)) {
library(devtools)
install_github('rNVD3', 'ramnathv')
install_github('rNVD3', 'aghozlane')
library(rNVD3)
}
......
......@@ -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)
......
/********************
* HTML CSS
*/
.chartWrap {
margin: 0;
padding: 0;
overflow: hidden;
}
/********************
* TOOLTIP CSS
*/
.nvtooltip {
position: absolute;
background-color: rgba(255,255,255,1);
padding: 1px;
border: 1px solid rgba(0,0,0,.2);
z-index: 10000;
font-family: Arial;
font-size: 13px;
transition: opacity 500ms linear;
-moz-transition: opacity 500ms linear;
-webkit-transition: opacity 500ms linear;
transition-delay: 500ms;
-moz-transition-delay: 500ms;
-webkit-transition-delay: 500ms;
-moz-box-shadow: 0 5px 10px rgba(0,0,0,.2);
-webkit-box-shadow: 0 5px 10px rgba(0,0,0,.2);
box-shadow: 0 5px 10px rgba(0,0,0,.2);
-webkit-border-radius: 6px;
-moz-border-radius: 6px;
border-radius: 6px;
pointer-events: none;
-webkit-touch-callout: none;
-webkit-user-select: none;
-khtml-user-select: none;
-moz-user-select: none;
-ms-user-select: none;
user-select: none;
}
.nvtooltip.x-nvtooltip,
.nvtooltip.y-nvtooltip {
padding: 8px;
}
.nvtooltip h3 {
margin: 0;
padding: 4px 14px;
line-height: 18px;
font-weight: normal;
background-color: #f7f7f7;
text-align: center;
border-bottom: 1px solid #ebebeb;
-webkit-border-radius: 5px 5px 0 0;
-moz-border-radius: 5px 5px 0 0;
border-radius: 5px 5px 0 0;
}
.nvtooltip p {
margin: 0;
padding: 5px 14px;
text-align: center;
}
.nvtooltip span {
display: inline-block;
margin: 2px 0;
}
.nvtooltip-pending-removal {
position: 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;
<