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microarray percentile summary from dcallan #229

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200 changes: 200 additions & 0 deletions View/lib/perl/GraphPackage/GGLinePlot.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -1407,6 +1407,206 @@ myPlotly <- myPlotly %>% onRender(annotationJS)
# ),
# myPlotly
# )
";
$self->setPlotlyCustomConfig($plotlyConfig);

return $self;
}
#--------------------------------------------------------------------------------

package EbrcWebsiteCommon::View::GraphPackage::GGLinePlot::MicroarrayPercentileSummary;
use base qw( EbrcWebsiteCommon::View::GraphPackage::GGLinePlot );
use strict;

sub new {
my $class = shift;
my $self = $class->SUPER::new(@_);
my $id = $self->getId();

$self->setPartName('microarray.summary');
$self->setYaxisLabel('');
$self->setPlotTitle("Microarray Percentile Summary - $id");
$self->setForceNoLines(1);
my $projectId = $self->getProject();
my $exprMetric = "Percentile";

my $adjust = "
arrayTypes <- lapply(unique(profile.df.full\$DISPLAY_NAME), FUN = function(name) {ifelse(data.table::uniqueN(profile.df.full\$PROFILE_TYPE[profile.df.full\$DISPLAY_NAME == name]) > 1, 'Two Channel Array', 'One Channel Array')})
names(arrayTypes) <- unique(profile.df.full\$DISPLAY_NAME)
getArrayType <- function(name) {arrayTypes[[name]]}
profile.df.full\$LEGEND <- unlist(lapply(profile.df.full\$DISPLAY_NAME, getArrayType))
suffix <- ifelse(profile.df.full\$LEGEND == 'Two Channel Array', ifelse(profile.df.full\$PROFILE_TYPE == 'channel2_percentiles', '- channel 2', '- channel 1'), '')
profile.df.full\$LEGEND <- as.factor(paste0(profile.df.full\$LEGEND, suffix))

profile.df.full\$TOOLTIP <- paste(profile.df.full\$ELEMENT_NAMES, profile.df.full\$VALUE)
profile.df.full\$DISPLAY_NAME <- factor(profile.df.full\$DISPLAY_NAME, levels = rev(levels(as.factor(profile.df.full\$DISPLAY_NAME))))
the.colors <- rep('black', data.table::uniqueN(profile.df.full\$LEGEND))

truncatedSamplesTable <- function(x,y) {
numSamples <- length(x)
if (numSamples > 10) { x <- x[1:10]; y <- y[1:10] }
tableText <- paste(paste0(x, \": \", y), collapse=\"<br>\")
if (numSamples > 10) { tableText <- paste0(tableText, \"<br>...<br><i>(Click on points in graph to see all samples.<br> Zoom may also be necessary.)</i>\")}

return(tableText)
}

table.df <- profile.df.full %>%
group_by(DISPLAY_NAME) %>%
summarize(TABLE=truncatedSamplesTable(ELEMENT_NAMES, VALUE))
table.df\$TABLE <- paste0(\"<b>Sample: $exprMetric</b><br>\", table.df\$TABLE)
profile.df.full <- merge(profile.df.full, table.df, by = 'DISPLAY_NAME')
";

$self->addAdjustProfile($adjust);

my $plotlyConfig = "
x.max <- 100

myYShift <- 15
if (uniqueN(profile.df.full\$DISPLAY_NAME) < 6) {
myYShift <- 25
}

#reimplement w different colors once i have something working
myColors <- ifelse(profile.df.full\$LEGEND == 'One Channel Array', \"#009988\", ifelse(profile.df.full\$LEGEND == 'Two Channel Array- channel 1', \"#33BBEE\", \"#0077BB\"))
myOpaqueColors <- ifelse(profile.df.full\$LEGEND == 'One Channel Array', \"#44AA99\", ifelse(profile.df.full\$LEGEND == 'Two Channel Array- channel 1', \"#88CCEE\", \"#4A96C2\"))
myTextColors <- rep(\"black\", uniqueN(profile.df.full\$LEGEND))
colors.df <- data.table(\"LEGEND\" = unique(profile.df.full\$LEGEND), \"COLOR\" = paste0(myOpaqueColors, \"|\", myTextColors))
profile.df.full <- merge(profile.df.full, colors.df, by = \"LEGEND\")
profile.df.full\$COLOR <- paste0(profile.df.full\$COLOR, \"|\", profile.df.full\$DATASET_PRESENTER_ID)

#some bs about dual axes
profile.df.full.1 <- profile.df.full[profile.df.full\$DISPLAY_NAME == profile.df.full\$DISPLAY_NAME[length(profile.df.full\$DISPLAY_NAME)],]
if (uniqueN(profile.df.full\$DISPLAY_NAME) == 1) {
profile.df.full.2 <- profile.df.full.1
} else {
profile.df.full.2 <- profile.df.full[profile.df.full\$DISPLAY_NAME != profile.df.full\$DISPLAY_NAME[length(profile.df.full\$DISPLAY_NAME)],]
}

myPlotly <- plot_ly(type = \"box\", data = profile.df.full.2, x = ~VALUE, y = ~DISPLAY_NAME, color = ~LEGEND, colors = myColors, text = ~TOOLTIP, customdata = ~COLOR, hoverinfo = \"none\", boxpoints = \"all\", jitter = 0.3, pointpos = 0, showlegend = TRUE, opacity = .6, marker=list(color=\"black\")) %>%
add_trace(type = \"box\", data = profile.df.full.1, x = ~VALUE, y = ~DISPLAY_NAME, color = ~LEGEND, colors = myColors, text = ~TOOLTIP, customdata = ~COLOR, hoverinfo = \"none\", boxpoints = \"all\", jitter = 0.3, pointpos = 0, showlegend = FALSE, opacity = .6, marker=list(color=\"black\"), xaxis = \"x2\") %>%
layout(xaxis = list(title = \"Percentile\",
range = c(0, x.max),
dtick = 10,
zerolinecolor = \"#eee\"),
xaxis2 = list(range = c(0, x.max),
dtick = 10,
zerolinecolor = \"#eee\",
overlaying = \"x\",
side = \"top\"),
yaxis = list(visible = FALSE),
margin = list(l = 75,
r = 30,
b = 75,
t = 60,
pad = 1),
boxgap = .6,
boxmode = 'group'
) %>%
add_annotations(yref=\"paper\",
xref=\"paper\",
y=1.075,
x=-0.05,
text=\"<b><i>Gene:</i></b>\",
showarrow=F,
font=list(size=14,
color=\"black\")) %>%
add_annotations(yref=\"paper\",
xref=\"paper\",
y=1.075,
x=0,
text=\"<i>$id</i>\",
showarrow=F,
font=list(size=14,
color=\"darkred\")) %>%
highlight(on = \"plotly_selected\") %>%
add_annotations(x = -.05,
y = unique(profile.df.full\$DISPLAY_NAME),
text = unique(profile.df.full\$DISPLAY_NAME),
hovertext = unique(profile.df.full\$TABLE),
xref = \"paper\",
yref = \"y\",
xanchor = \"left\",
showarrow = FALSE,
font=list(size=10),
yshift = myYShift,
valign = \"top\",
name = unique(profile.df.full\$DATASET_PRESENTER_ID)) %>%
config(displaylogo = FALSE,
collaborate = FALSE)

annotationJS <- \"function(el) {
var updatemenus =[{
buttons: [
{
args: [{annotations: el.layout.annotations}],
label: '<i>click to remove sample labels</i>',
method: 'relayout'
}
],
showactive: false,
active: 0,
type: 'buttons',
y: -0.1,
x: 0.85,
xanchor: 'center',
yanchor: 'bottom',
bgcolor: 'lightgray',
borderwidth: 0
}];

Plotly.relayout(el.id, {updatemenus: updatemenus});

el.on('plotly_click', function(d) {
var ptsData = d.points[0].data;

var i;
var annArray = [];
var foundDup = false;
for (i = 0; i < ptsData.x.length; i++) {
if (!(Array.isArray(ptsData.text))) {
ptsData.text = [ptsData.text];
}
var ann = {
bgcolor: ptsData.customdata[i].split('|')[0],
bordercolor: 'black',
arrowsize: .5,
ay: 30,
ax: ptsData.x[i],
axref: 'x',
clicktoshow: 'onoff',
font: {size: 12,
color: ptsData.customdata[i].split('|')[1]},
textangle: 60,
text: ptsData.text[i],
x: ptsData.x[i],
y: ptsData.y[i],
xref: 'x',
yref: 'y',
xanchor: 'left',
showarrow: true
};

// delete instead if already exists
el.layout.annotations.forEach(
function(oldAnn, index) {
if (ann.x === oldAnn.x && ann.y === oldAnn.y) {
Plotly.relayout(el.id, 'annotations[' + index + ']', 'remove');
foundDup = true;
}
});
annArray.push(ann);
}
if (foundDup) return;

Plotly.relayout(el.id, {annotations: el.layout.annotations.concat(annArray)});
})

}\"

myPlotly <- myPlotly %>% onRender(annotationJS)

";
$self->setPlotlyCustomConfig($plotlyConfig);

Expand Down