As Lars showed, getting the graph to look the way you want is just a matter of removing the missing values from your data arrays.
However, you wouldn't normally want to do that by hand, deleting all the rows with missing values. You need to use an array filter function to remove the missing values from your data arrays.
Once you have the complete data array as an array of series objects, each with an array of values, this code should work:
//to remove the missing values, so that the graph
//will just connect the valid points,
//filter each data array:
data.forEach(function(series) {
series.values = series.values.filter(
function(d){return d.y||(d.y === 0);}
);
//the filter function returns true if the
//data has a valid y value
//(either a "true" value or the number zero,
// but not null or NaN)
});
Updated fiddle here: http://jsfiddle.net/xammamax/8Kk8v/
Of course, when you are constructing the data array from a csv where each series is a separate column, you can do the filtering at the same time as you create the array:
var chartdata = [];//initialize as empty array
d3.csv("top_1_L-shaped.csv", function(error, csv) {
if (error)
return console.log("there was an error loading the csv: " + error);
var columndata = ["Germany", "Switzerland", "Portugal",
"Japan", "Italy", "Spain", "France",
"Finland", "Sweden", "Denmark", "Netherlands"];
for (var i = 0; i < columndata.length; i++) {
chartdata[i].key = columndata[i];
chartdata[i].values = csv.map(function(d) {
return [+d["year"], +d[ columndata[i] ] ];
})
.filter(function(d){
return d[1]||(d[1] === 0);
});
//the filter is applied to the mapped array,
//and the results are assigned to the values array.
}
});