diff --git a/ChangeLog.md b/ChangeLog.md
index dc719ec6..6d4f892d 100644
--- a/ChangeLog.md
+++ b/ChangeLog.md
@@ -19,6 +19,8 @@ Emperor 0.9.1 (changes since Emperor 0.9.0 go here)
* Emperor now relies on QIIME 1.7.0.
* Added option `--number_of_segments` to control the quality of all spheres
* Labels for biplots now have a color picker.
+* Add color pickers for connecting bars in coordinate comparison plots.
+* Add option to select a master set of coordinates when making a comparison plot.
*Bug Fixes*
@@ -26,6 +28,9 @@ Emperor 0.9.1 (changes since Emperor 0.9.0 go here)
* Category names are sorted alphabetically.
* Category names with non-alphanumeric characters are colored correctly now.
* Biplots checkbox now accurately reflects status of biplot visiblity rather than opposite.
+* Comparison bars checkbox now accurately reflects status of the visiblity rather than opposite.
+* Scaling by percent explained now works with vectors and coordinate comparison plots.
+* Fixed bug where only the first bars in coordinate comparison plots could be hidden.
Emperor 0.9.0 (14 May 2013)
===========================
diff --git a/emperor/format.py b/emperor/format.py
index ec3056e5..7cd22632 100755
--- a/emperor/format.py
+++ b/emperor/format.py
@@ -307,13 +307,16 @@ def format_vectors_to_js(mapping_file_data, mapping_file_headers, coords_data,
return ''.join(js_vectors_string)
-def format_comparison_bars_to_js(coords_data, coords_headers, clones):
+def format_comparison_bars_to_js(coords_data, coords_headers, clones,
+ is_serial_comparison=True):
"""Format coordinates data to create a comparison plot
Inputs:
coords_data: numpy array with the replicated coordinates
cooreds_headers: list with the headers for each of replicated coordinates
clones: number of replicates in the coords_data and coords_headers
+ is_serial_comparison: whether the samples will be connected one after the
+ other (True) or all will originate in the first set of coordinates.
Outputs:
Javascript object that contains the data for the comparison plot
@@ -323,11 +326,19 @@ def format_comparison_bars_to_js(coords_data, coords_headers, clones):
length.
AssertionError if the number of clones doesn't concord with the samples
being presented.
+
+ Unless the value of clones is > 0 this function will return an empty
+ javascript object initialization.
"""
js_comparison_string = []
js_comparison_string.append('\nvar g_comparisonPositions = new Array();\n')
+ if is_serial_comparison:
+ js_comparison_string.append('var g_isSerialComparisonPlot = true;\n')
+ else:
+ js_comparison_string.append('var g_isSerialComparisonPlot = false;\n')
+
if clones:
headers_length = len(coords_headers)
@@ -367,6 +378,9 @@ def format_emperor_html_footer_string(has_biplots=False, has_ellipses=False,
has_biplots: whether the plot has biplots or not
has_ellipses: whether the plot has ellipses or not
+ has_vectors: whether the plot has vectors or not
+ has_edges: whether the plot has edges between samples (comparison plot)
+
This function will remove unnecessary GUI elements from index.html to avoid
confusions i. e. showing an ellipse opacity slider when there are no
@@ -379,6 +393,7 @@ def format_emperor_html_footer_string(has_biplots=False, has_ellipses=False,
optional_strings.append(if_(has_biplots, _BIPLOT_VISIBILITY_SELECTOR, ''))
optional_strings.append(if_(has_biplots, _TAXA_LABELS_SELECTOR, ''))
optional_strings.append(if_(has_biplots, _TAXA_LABELS_COLOR_SELECTOR, ''))
+ optional_strings.append(if_(has_edges, _EDGES_COLOR_SELECTOR, ''))
optional_strings.append(if_(has_ellipses, _ELLIPSE_OPACITY_SLIDER, ''))
optional_strings.append(if_(has_vectors, _VECTORS_OPACITY_SLIDER, ''))
optional_strings.append(if_(has_edges, _EDGES_VISIBILITY_SELECTOR, ''))
@@ -459,10 +474,15 @@ def format_emperor_html_footer_string(has_biplots=False, has_ellipses=False,
_EDGES_VISIBILITY_SELECTOR = """
- %s%s%s
+
+
+ %s%s%s
diff --git a/emperor/sort.py b/emperor/sort.py
index 68547f47..82bacf7c 100644
--- a/emperor/sort.py
+++ b/emperor/sort.py
@@ -11,8 +11,8 @@
__email__ = "yoshiki89@gmail.com"
__status__ = "Development"
-
from numpy import zeros
+from re import compile, search
def sort_taxa_table_by_pcoa_coords(coords_header, otu_table, otu_header):
"""Sort and match the samples in the otu table and in the coordinates data
@@ -48,3 +48,40 @@ def sort_taxa_table_by_pcoa_coords(coords_header, otu_table, otu_header):
sorted_otu_headers.append(element)
return sorted_otu_headers, sorted_otu_table
+
+def sort_comparison_filenames(coord_fps):
+ """Pass in a list of file names and sort them using the suffix
+
+ Input:
+ coord_fps: list of filenames with the format something_something_qX.txt
+ where X is the index of the file.
+
+ Output:
+ Returns a sorted version of the list that was passed in where the strings
+ are sorted according to the suffix they have, if the string doesn't have
+ a suffix it will be added to the beginning of the list.
+ """
+
+ if coord_fps == []:
+ return []
+
+ def _get_suffix(fp):
+ """Gets the number in the suffix for a string using a regex"""
+ # any alphanumeric set of characters proceeded by a 'q', a number, a dot
+ # & a txt extension at the end of the line. Take for example
+ # bray_curtis_q1.txt or unifrac_q11.txt
+ re = compile(r'(\w+)_q([0-9]+).txt$')
+ tmatch = search(re, fp)
+
+ try:
+ number = tmatch.group(2)
+ # if the regex doesn't match then put it at the beginning
+ except (IndexError, AttributeError):
+ number = -1
+
+ return float(number)
+
+ # the key function retrieves the suffix number for the function to sort
+ # according to it's floating point representation i. e. the cast to float
+ return sorted(coord_fps, key=_get_suffix)
+
diff --git a/emperor/support_files/emperor/js/emperor.js b/emperor/support_files/emperor/js/emperor.js
index 03dab67f..a5dbf70e 100644
--- a/emperor/support_files/emperor/js/emperor.js
+++ b/emperor/support_files/emperor/js/emperor.js
@@ -130,6 +130,9 @@ function toggleScaleCoordinates(element) {
var axesLen;
var operation;
+ // used only for vector and edges re-drawing
+ var currentPosition = [], currentColor = 0x000000;
+
if (!isNumeric(g_fractionExplained[g_viewingAxes[0]])) {
alert("PC" + (g_viewingAxes[0]+1) + " is too small for this feature, change your selection.");
return;
@@ -140,9 +143,6 @@ function toggleScaleCoordinates(element) {
alert("PC" + (g_viewingAxes[2]+1) + " is too small for this feature, change your selection.");
return;
}
-
- // used only for the vector re-drawing
- var currentPosition = [], currentColor;
// XOR operation for the checkbox widget, this will select an operation
// to perform over various properties, either a multiplication or a division
@@ -223,14 +223,14 @@ function toggleScaleCoordinates(element) {
for (sample_id in g_plotVectors){
// the color has to be formatted as an hex number for makeLine to work
- currentColor = "0x"+g_plotVectors[sample_id].material.color.getHexString();
+ currentColor = g_plotVectors[sample_id].material.color.getHex();
// updating the position of a vertex in a line is a really expensive
// operation, hence we just remove it from the group and create it again
g_elementsGroup.remove(g_plotVectors[sample_id]);
for (vertex in g_plotVectors[sample_id].geometry.vertices){
- currentPosition[vertex] = g_plotVectors[sample_id].geometry.vertices[vertex].position;
+ currentPosition[vertex] = g_plotVectors[sample_id].geometry.vertices[vertex];
// scale the position of each of the vertices
currentPosition[vertex].x = operation(currentPosition[vertex].x,
@@ -250,6 +250,45 @@ function toggleScaleCoordinates(element) {
currentPosition[1], currentColor, 2);
g_elementsGroup.add(g_plotVectors[sample_id]);
}
+
+ // support scaling of edges in plot comparisons
+ for(var sample_id in g_plotEdges){
+ // each edge is composed of two separate lines
+ for(var section in g_plotEdges[sample_id]){
+
+ // the color has to be formatted as an hex number for makeLine to work
+ currentColor = g_plotEdges[sample_id][section].material.color.getHex();
+
+ // remove them completely from the group and scene we no longer need
+ // these objects as re-creating them is as expensive as modifying
+ // most of their features
+ g_elementsGroup.remove(g_plotEdges[sample_id][section])
+ g_mainScene.remove(g_plotEdges[sample_id][section])
+
+ for (vertex in g_plotEdges[sample_id][section].geometry.vertices){
+ currentPosition[vertex] = g_plotEdges[sample_id][section].geometry.vertices[vertex];
+
+ // scale the position of each of the vertices
+ currentPosition[vertex].x = operation(currentPosition[vertex].x,
+ g_fractionExplained[g_viewingAxes[0]])
+ currentPosition[vertex].y = operation(currentPosition[vertex].y,
+ g_fractionExplained[g_viewingAxes[1]])
+ currentPosition[vertex].z = operation(currentPosition[vertex].z,
+ g_fractionExplained[g_viewingAxes[2]])
+
+ // create an array we can pass to makeLine
+ currentPosition[vertex] = [currentPosition[vertex].x,
+ currentPosition[vertex].y, currentPosition[vertex].z]
+ }
+
+ // add the element to the main vector array and to the group
+ g_plotEdges[sample_id][section] = makeLine(currentPosition[0],
+ currentPosition[1], currentColor, 2);
+ g_elementsGroup.add(g_plotEdges[sample_id][section]);
+ g_mainScene.add(g_plotEdges[sample_id][section]);
+
+ }
+ }
}
/* Toggle between discrete and continuous coloring for samples and labels */
@@ -753,6 +792,17 @@ function colorChangedForTaxaSpheres(color){
}
}
+/* This function is called when a new color is selected for the edges
+
+ The two input parameters are a hexadecimal formatted color and an index, the
+ index indicates which side of the edges are going to be re-colored.
+*/
+function colorChangedForEdges(color, index){
+ for(var sample_id in g_plotEdges){
+ currentColor = g_plotEdges[sample_id][index].material.color.setHex(color);
+ }
+}
+
/*This function is called when a new value is selected in the label menu*/
function labelMenuChanged() {
if(document.getElementById('labelcombo').selectedIndex == 0){
@@ -898,12 +948,12 @@ function toggleBiplotVisibility(){
// if the element is supposed to be present; 0.5 is the default value
if(!document.biplotsvisibility.elements[0].checked){
for (index in g_plotTaxa){
- g_plotTaxa[index].material.opacity = 0;
+ g_mainScene.remove(g_plotTaxa[index]);
}
}
else{
for (index in g_plotTaxa){
- g_plotTaxa[index].material.opacity = 0.5;
+ g_mainScene.add(g_plotTaxa[index])
}
}
}
@@ -913,16 +963,16 @@ function toggleEdgesVisibility(){
// each edge is really composed of two lines and those elements are stored
// in each of the keys that are stored for each sample comparison
- if(document.edgesvisibility.elements[0].checked){
+ if(!document.edgesvisibility.elements[0].checked){
for (index in g_plotEdges){
- g_plotEdges[index][0].material.opacity = 0;
- g_plotEdges[index][1].material.opacity = 0;
+ g_mainScene.remove(g_plotEdges[index][0]);
+ g_mainScene.remove(g_plotEdges[index][1]);
}
}
else{
for (index in g_plotEdges){
- g_plotEdges[index][0].material.opacity = 1;
- g_plotEdges[index][1].material.opacity = 1;
+ g_mainScene.add(g_plotEdges[index][0]);
+ g_mainScene.add(g_plotEdges[index][1]);
}
}
}
@@ -1190,6 +1240,43 @@ function setJqueryUi() {
});
}
+ // check if the plot is a comparison plot if so, setup the elements that
+ // will allow the user to change the color of the two sides of the edges
+ if(document.getElementById('edgecolorselector_a')){
+ $('#edgecolorselector_a').css('backgroundColor',"#FFFFFF");
+ $("#edgecolorselector_a").spectrum({
+ localStorageKey: 'key',
+ color: "#FFFFFF",
+ preferredFormat: "hex6",
+ showInitial: true,
+ showInput: true,
+ change:
+ function(color) {
+ // pass a boolean flag to convert to hex6 string
+ var c = color.toHexString(true);
+ $(this).css('backgroundColor', c);
+ colorChangedForEdges(c.replace('#', '0x'), 0);
+ }
+ });
+ }
+ if(document.getElementById('edgecolorselector_b')){
+ $('#edgecolorselector_b').css('backgroundColor',"#FF0000");
+ $("#edgecolorselector_b").spectrum({
+ localStorageKey: 'key',
+ color: "#FFFFFF",
+ preferredFormat: "hex6",
+ showInitial: true,
+ showInput: true,
+ change:
+ function(color) {
+ // pass a boolean flag to convert to hex6 string
+ var c = color.toHexString(true);
+ $(this).css('backgroundColor', c);
+ colorChangedForEdges(c.replace('#', '0x'), 1);
+ }
+ });
+ }
+
$("#sopacityslider").slider({
range: "max",
min: 0,
@@ -1232,7 +1319,6 @@ function setJqueryUi() {
});
document.getElementById('labelopacity').innerHTML = $( "#lopacityslider" ).slider( "value")+"%"
-
//default color for axes labels is white
$('#axeslabelscolor').css('backgroundColor',"#FFFFFF");
$("#axeslabelscolor").spectrum({
@@ -1400,6 +1486,7 @@ function drawTaxa(){
mesh.matrixAutoUpdate = true;
// add the element to the scene and to the g_plotTaxa dictionary
+ g_elementsGroup.add(mesh)
g_mainScene.add(mesh);
g_plotTaxa[key] = mesh;
}
@@ -1443,53 +1530,104 @@ function drawVectors(){
}
}
-
/*Draw the lines that connect samples being compared (see g_comparePositiosn)
This will draw two lines between each compared sample, one with color red and
- the other one with color white, the that must be noted here is that, these two
+ the other one with color white, what must be noted here is that, these two
lines visually compose a single line and are both stored in the g_plotEdges
array in arrays of two elements where the first element is the red line and
the second element is the white line.
+
+ In the case of a non-serial comparison plot, all edges will originate in the
+ same point.
*/
function drawEdges(){
- var current_vector, previous = null, middle_point, index=0, line_a, line_b;
-
- for (var sampleKey in g_comparisonPositions){
- for (var edgePosition in g_comparisonPositions[sampleKey]){
+ var previous = null, origin = null, current, middle_point, index=0, line_a, line_b;
- // if we don't have a start point store it and move along
- if (previous == null) {
- previous = g_comparisonPositions[sampleKey][edgePosition];
- }
- // if we already have a start point then draw the edge
- else{
- current = g_comparisonPositions[sampleKey][edgePosition];
+ // note that this function is composed of an if-else statement with a loop
+ // that's almost identical under each case. This approach was taken as
+ // otherwise the comparison would need to happen N times instead of 1 time
+ // (N is the number of edges*2).
- // the edge is composed by two lines so calculate the middle
- // point between these two lines and end the first line in this
- // point and start the second line in this point
- middle_point = [(previous[0]+current[0])/2,
- (previous[1]+current[1])/2, (previous[2]+current[2])/2]
+ // if the comparison is serial draw one edge after the other
+ if (g_isSerialComparisonPlot == true){
+ for (var sampleKey in g_comparisonPositions){
+ for (var edgePosition in g_comparisonPositions[sampleKey]){
- line_a = makeLine(previous, middle_point, 0xFF0000, 2)
- line_b = makeLine(middle_point, current, 0xFFFFFF, 2)
-
- // index the two lines by the name of the sample plus a suffix
- g_plotEdges[sampleKey+'_'+toString(index)] = [line_a, line_b]
+ // if we don't have a start point store it and move along
+ if (previous == null) {
+ previous = g_comparisonPositions[sampleKey][edgePosition];
+ }
+ // if we already have a start point then draw the edge
+ else{
+ current = g_comparisonPositions[sampleKey][edgePosition];
+
+ // the edge is composed by two lines so calculate the middle
+ // point between these two lines and end the first line in this
+ // point and start the second line in this point
+ middle_point = [(previous[0]+current[0])/2,
+ (previous[1]+current[1])/2, (previous[2]+current[2])/2];
+
+ line_a = makeLine(previous, middle_point, 0xFFFFFF, 2);
+ line_b = makeLine(middle_point, current, 0xFF0000, 2);
+ line_a.transparent = false;
+ line_b.transparent = false;
+
+ // index the two lines by the name of the sample plus a suffix
+ g_plotEdges[sampleKey+'_'+index.toString()] = [line_a, line_b];
+
+ g_elementsGroup.add(line_a);
+ g_elementsGroup.add(line_b);
+ g_mainScene.add(line_a);
+ g_mainScene.add(line_b);
+
+ // the current line becomes the previous line for the next
+ // iteration as all samples must be connected
+ previous = g_comparisonPositions[sampleKey][edgePosition];
+ }
+ index = index+1;
+ }
- g_elementsGroup.add(line_a)
- g_elementsGroup.add(line_b)
+ // if we've finished with the connecting lines let a new line start
+ previous = null;
+ }
+ }
+ // if the comparison is not serial, originate all edges in the same coords
+ else{
+ for (var sampleKey in g_comparisonPositions){
+ for (var edgePosition in g_comparisonPositions[sampleKey]){
+ if (origin == null) {
+ origin = g_comparisonPositions[sampleKey][edgePosition];
+ }
+ else{
+ current = g_comparisonPositions[sampleKey][edgePosition];
+
+ // edges are composed of two lines so use the start and
+ // the end point to calculate the position of the vertices
+ middle_point = [(origin[0]+current[0])/2,
+ (origin[1]+current[1])/2, (origin[2]+current[2])/2];
+
+ // in the case of centered comparisons the origins are
+ // painted in color white one one side and red on the other
+ line_a = makeLine(origin, middle_point, 0xFFFFFF, 2);
+ line_b = makeLine(middle_point, current, 0xFF0000, 2);
+ line_a.transparent = false;
+ line_b.transparent = false;
+
+ // given that these are just sample repetitions just
+ // just add a suffix at the end of the sample id
+ g_plotEdges[sampleKey+'_'+index.toString()] = [line_a, line_b];
+
+ g_elementsGroup.add(line_a);
+ g_elementsGroup.add(line_b);
+ g_mainScene.add(line_a);
+ g_mainScene.add(line_b);
- // the current line becomes the previous line for the next
- // iteration as all samples must be conected
- previous = g_comparisonPositions[sampleKey][edgePosition];
+ }
+ index = index + 1;
}
- index = index+1;
+ origin = null;
}
-
- // if we've finished with the connecting lines let a new line start
- previous = null;
}
}
@@ -1566,7 +1704,7 @@ function saveSVG(button){
$('body').css('cursor','default');
}
-/*Utility function to draw two vertices lines at a time
+/*Utility function to draw two-vertices lines at a time
This function allows you to create a line with only two vertices i. e. the
start point and the end point, plus the color and width of the line. The
@@ -1589,7 +1727,7 @@ function makeLine(coords_a, coords_b, color, width){
geometry.vertices.push(new THREE.Vector3(coords_a[0], coords_a[1], coords_a[2]));
geometry.vertices.push(new THREE.Vector3(coords_b[0], coords_b[1], coords_b[2]));
- // the line will contain the two vertices and the describecd material
+ // the line will contain the two vertices and the described material
line = new THREE.Line(geometry, material);
return line;
@@ -1601,18 +1739,30 @@ function makeLine(coords_a, coords_b, color, width){
displayed uses.
*/
function drawAxisLines() {
+ var axesColorFromColorPicker;
+
// removing axes, if they do not exist the scene doesn't complain
g_mainScene.remove(g_xAxisLine);
g_mainScene.remove(g_yAxisLine);
g_mainScene.remove(g_zAxisLine);
-
+
+ // value should be retrieved from the picker every time the axes are drawn
+ axesColorFromColorPicker = $("#axescolor").spectrum("get").toHexString(true);
+ axesColorFromColorPicker = axesColorFromColorPicker.replace('#','0x')
+ axesColorFromColorPicker = parseInt(axesColorFromColorPicker, 16)
+
// one line for each of the axes
g_xAxisLine = makeLine([g_xMinimumValue, g_yMinimumValue, g_zMinimumValue],
- [g_xMaximumValue, g_yMinimumValue, g_zMinimumValue], 0xFFFFFF, 3);
+ [g_xMaximumValue, g_yMinimumValue, g_zMinimumValue], axesColorFromColorPicker, 3);
g_yAxisLine = makeLine([g_xMinimumValue, g_yMinimumValue, g_zMinimumValue],
- [g_xMinimumValue, g_yMaximumValue, g_zMinimumValue], 0xFFFFFF, 3);
+ [g_xMinimumValue, g_yMaximumValue, g_zMinimumValue], axesColorFromColorPicker, 3);
g_zAxisLine = makeLine([g_xMinimumValue, g_yMinimumValue, g_zMinimumValue],
- [g_xMinimumValue, g_yMinimumValue, g_zMaximumValue], 0xFFFFFF, 3);
+ [g_xMinimumValue, g_yMinimumValue, g_zMaximumValue], axesColorFromColorPicker, 3);
+
+ // axes shouldn't be transparent
+ g_xAxisLine.material.transparent = false;
+ g_yAxisLine.material.transparent = false;
+ g_zAxisLine.material.transparent = false;
g_mainScene.add(g_xAxisLine)
g_mainScene.add(g_yAxisLine)
@@ -1624,7 +1774,7 @@ function changePointCount() {
document.getElementById('pointCount').innerHTML = g_visiblePoints+'/'+g_plotIds.length+' points'
}
-/* Validating and modifying the view axes */
+/* Validating and modifying the view axes */
function changeAxesDisplayed() {
if (!jQuery.isEmptyObject(g_vectorPositions) || !jQuery.isEmptyObject(g_taxaPositions) ||
!jQuery.isEmptyObject(g_ellipsesDimensions) || g_number_of_custom_axes!=0) {
@@ -2026,7 +2176,7 @@ $(document).ready(function() {
var labelCoordinates;
- // reposistion the labels for the axes in the 3D plot
+ // reposition the labels for the axes in the 3D plot
labelCoordinates = toScreenXY(new THREE.Vector3(g_xMaximumValue, g_yMinimumValue, g_zMinimumValue), g_sceneCamera,$('#main_plot'));
$("#pc1_label").css('left', labelCoordinates['x'])
$("#pc1_label").css('top', labelCoordinates['y'])
diff --git a/scripts/make_emperor.py b/scripts/make_emperor.py
index 4ed93edf..0a2172ab 100755
--- a/scripts/make_emperor.py
+++ b/scripts/make_emperor.py
@@ -23,6 +23,7 @@
from qiime.biplots import make_biplot_scores_output
from emperor.biplots import preprocess_otu_table
+from emperor.sort import sort_comparison_filenames
from emperor.filter import keep_samples_from_pcoa_data
from emperor.util import (copy_support_files, preprocess_mapping_file,
preprocess_coords_file, fill_mapping_field_from_mapping_file,
@@ -62,14 +63,15 @@
" to use for the missing values: ", "%prog -i unweighted_unifrac_pc.txt -m "
"Fasting_Map_modified.txt -a DOB -o pcoa_dob_with_missing_custom_axes_value"
"s -x 'DOB:20060000'"),
- ("PCoA plot with an explicit axis and using --missing_custom_axes_values but "
- "setting different values based on another column", "Create a PCoA plot with an "
- "axis of the plot representing the 'DOB' of the samples and defining the position "
- "over the gradient of those samples missing a numeric value but using as reference "
- "another column of the mapping file. In this case we are going to plot the samples "
- "that are Control on the Treatment column on 20080220 and on 20080240 those that "
- "are Fast:", "%prog -i unweighted_unifrac_pc.txt -m Fasting_Map_modified.txt -a DOB "
- "-o pcoa_dob_with_missing_custom_axes_with_multiple_values -x "
+ ("PCoA plot with an explicit axis and using --missing_custom_axes_values "
+ "but setting different values based on another column", "Create a PCoA plot"
+ " with an axis of the plot representing the 'DOB' of the samples and "
+ "defining the position over the gradient of those samples missing a numeric"
+ " value but using as reference another column of the mapping file. In this "
+ "case we are going to plot the samples that are Control on the Treatment "
+ "column on 20080220 and on 20080240 those that are Fast:", "%prog -i "
+ "unweighted_unifrac_pc.txt -m Fasting_Map_modified.txt -a DOB -o "
+ "pcoa_dob_with_missing_custom_axes_with_multiple_values -x "
"'DOB:Treatment==Control=20080220' -x 'DOB:Treatment==Fast=20080240'"),
("Jackknifed principal coordinates analysis plot", "Create a jackknifed "
"PCoA plot (with confidence intervals for each sample) passing as the input"
@@ -178,25 +180,30 @@
' the "--taxa_fp" file to display. Passing "-1" will cause to display all '
'the taxonomic groups, this option is only used when creating BiPlots. '
'[default=%default]', default=10, type='int'),
- make_option('-s', '--master_pcoa', help='Used only when plotting ellipsoids'
- ' for jackknifed beta diversity (i.e. using a directory of coord files'
- ' instead of a single coord file). The coordinates in this file will be the'
- ' center of each ellipisoid. [default: arbitrarily selected file from the '
- 'input directory]', default=None, type='existing_filepath'),
+ make_option('-s', '--master_pcoa', help='Used only when the input is a '
+ 'directory of coordinate files i. e. for jackknifed beta diversity plot or'
+ ' for a coordinate comparison plot (procrustes analysis). The coordinates '
+ 'in this file will be the center of each ellipsoid in the case of a '
+ 'jackknifed PCoA plot or the center where the connecting arrows originate '
+ 'from for a comparison plot. [default: arbitrarily selected file from the '
+ 'input directory for a jackknifed plot or None for a comparison plot in '
+ 'this case one file will be connected to the next one and so on]',
+ default=None, type='existing_filepath'),
make_option('-t', '--taxa_fp', help='Path to a summarized taxa file (i. '
'e. the output of summarize_taxa.py). This option is only used when '
'creating BiPlots. [default=%default]', default=None, type=
'existing_filepath'),
make_option('-x', '--missing_custom_axes_values', help='Option to override '
- 'the error shown when the catergory used in \'--custom_axes\' has non-numeric '
- 'values in the mapping file. The basic format is custom_axis:new_value. For '
- 'example, if you want to plot in time 0 all the samples that do not have a numeric '
- 'value in the column Time. you would pass -x "Time:0". Additionally, you can pass '
- 'this format custom_axis:other_column==value_in_other_column=new_value, with this '
- 'format you can specify different values (new_value) to use in the substitution '
- 'based on other column (other_column) value (value_in_other_column); see example '
- 'above. This option could be used in all explicit axes.',action='append',
- default=None),
+ 'the error shown when the catergory used in \'--custom_axes\' has '
+ 'non-numeric values in the mapping file. The basic format is '
+ 'custom_axis:new_value. For example, if you want to plot in time 0 all the '
+ 'samples that do not have a numeric value in the column Time. you would '
+ 'pass -x "Time:0". Additionally, you can pass this format '
+ 'custom_axis:other_column==value_in_other_column=new_value, with this '
+ 'format you can specify different values (new_value) to use in the '
+ 'substitution based on other column (other_column) value '
+ '(value_in_other_column); see example above. This option could be used in '
+ 'all explicit axes.',action='append', default=None),
make_option('-o','--output_dir',type="new_dirpath", help='path to the '
'output directory that will contain the PCoA plot. [default: %default]',
default='emperor'),
@@ -230,7 +237,7 @@ def main():
number_of_axes = opts.number_of_axes
compare_plots = opts.compare_plots
number_of_segments = opts.number_of_segments
-
+
# verifying that the number of axes requested is greater than 3
if number_of_axes<3:
option_parser.error(('You need to plot at least 3 axes.'))
@@ -244,6 +251,8 @@ def main():
offending_fields = []
non_numeric_categories = []
+ serial_comparison = True
+
# can't do averaged pcoa plots _and_ custom axes in the same plot
if custom_axes!=None and len(custom_axes.split(','))>1 and\
isdir(input_coords):
@@ -254,7 +263,7 @@ def main():
# make sure the flag is not misunderstood from the command line interface
if isdir(input_coords) == False and compare_plots:
option_parser.error('Cannot use the \'--compare_plots\' flag unless the'
- ' input input path is a directory.')
+ ' input path is a directory.')
# before creating any output, check correct parsing of the main input files
try:
@@ -290,6 +299,31 @@ def main():
if master_pcoa in coord_fps: # remove it if duplicated
coord_fps.remove(master_pcoa)
coord_fps = [master_pcoa] + coord_fps # prepend it to the list
+ # passing a master file means that the comparison is not serial
+ elif master_pcoa and compare_plots:
+ serial_comparison = False
+
+ # guarantee that the master is the first and is not repeated
+ if master_pcoa in coord_fps:
+ coord_fps.remove(master_pcoa)
+ coord_fps = [master_pcoa] + sort_comparison_filenames(coord_fps)
+
+ # QIIME generates folders of transformed coordinates for the specific
+ # purpose of connecting all coordinates to a set of origin coordinates.
+ # The name of this file is suffixed as _transformed_reference.txt
+ elif master_pcoa == None and len([f for f in coord_fps if f.endswith(
+ '_transformed_reference.txt')]):
+ master_pcoa = [f for f in coord_fps if f.endswith(
+ '_transformed_reference.txt')][0]
+ serial_comparison = False
+
+ # Note: the following steps are to guarantee consistency.
+ # remove the master from the list and re-add it as a first element
+ # the rest of the files must be sorted alphabetically so the result
+ # will be: ['unifrac_transformed_reference.txt',
+ # 'unifrac_transformed_q1.txt', 'unifrac_transformed_q2.txt'] etc
+ coord_fps.remove(master_pcoa)
+ coord_fps = [master_pcoa] + sort_comparison_filenames(coord_fps)
for fp in coord_fps:
try:
@@ -344,7 +378,7 @@ def main():
# other exeptions should be catched here; code will be updated then
except ValueError:
option_parser.error(('The PCoA file \'%s\' does not seem to be a '
- 'coordinates formatted file, verify by manuall inspecting '
+ 'coordinates formatted file, verify by manually inspecting '
'the contents.') % input_coords)
# number of samples ids that are shared between coords and mapping files
@@ -410,18 +444,16 @@ def main():
header, mapping_data = filter_mapping_file(mapping_data, header,
sids_intersection, include_repeat_cols=True)
-
-
- # catch the errors that could ocurr when filling the mapping file values
+ # catch the errors that could occur when filling the mapping file values
if missing_custom_axes_values:
try:
# the fact that this uses parse_metadata_state_descriptions makes
- # the follwoing option '-x Category:7;PH:12' to work as well as the
+ # the following option '-x Category:7;PH:12' to work as well as the
# script-interface-documented '-x Category:7 -x PH:12' option
for val in missing_custom_axes_values:
if ':' not in val:
- option_parser.error("Not valid missing value for custom axes: %s"
- % val)
+ option_parser.error("Not valid missing value for custom "
+ "axes: %s" % val)
mapping_data = fill_mapping_field_from_mapping_file(mapping_data,
header, ';'.join(missing_custom_axes_values))
@@ -563,14 +595,14 @@ def main():
fp_out.write(format_vectors_to_js(mapping_data, header, coords_data,
coords_headers, add_vectors[0], add_vectors[1]))
fp_out.write(format_comparison_bars_to_js(coords_data, coords_headers,
- clones))
+ clones, is_serial_comparison=serial_comparison))
fp_out.write(format_emperor_html_footer_string(taxa_fp != None,
isdir(input_coords) and not compare_plots, add_vectors != [None, None],
clones>0))
fp_out.close()
copy_support_files(output_dir)
- # write the bilot coords in the output file if a path is passed
+ # write the biplot coords in the output file if a path is passed
if biplot_fp and taxa_fp:
# make sure this file can be created
try:
diff --git a/tests/test_format.py b/tests/test_format.py
index 47389d78..d2584923 100755
--- a/tests/test_format.py
+++ b/tests/test_format.py
@@ -162,14 +162,31 @@ def test_format_comparison_bars_to_js(self):
# empty string generation for comparison i. e. no clones
out_js_comparison_string = format_comparison_bars_to_js(
- self.comparison_coords_data, self.comparison_coords_headers, 0)
+ self.comparison_coords_data, self.comparison_coords_headers, 0,
+ True)
self.assertEquals(out_js_comparison_string, '\nvar '
- 'g_comparisonPositions = new Array();\n')
+ 'g_comparisonPositions = new Array();\nvar g_isSerialComparisonPlot'
+ ' = true;\n')
out_js_comparison_string = format_comparison_bars_to_js(
- self.comparison_coords_data, self.comparison_coords_headers, 3)
+ self.comparison_coords_data, self.comparison_coords_headers, 3,
+ True)
self.assertEquals(out_js_comparison_string, COMPARISON_JS_STRING)
+ # empty string generation for comparison i. e. no clones
+ out_js_comparison_string = format_comparison_bars_to_js(
+ self.comparison_coords_data, self.comparison_coords_headers, 0,
+ False)
+ self.assertEquals(out_js_comparison_string, '\nvar '
+ 'g_comparisonPositions = new Array();\nvar g_isSerialComparisonPlot'
+ ' = false;\n')
+
+ out_js_comparison_string = format_comparison_bars_to_js(
+ self.comparison_coords_data, self.comparison_coords_headers, 3,
+ False)
+ self.assertEquals(out_js_comparison_string,
+ COMPARISON_JS_STRING_NON_SERIAL)
+
def test_format_comparison_bars_to_js_exceptions(self):
"""Check the correct exceptions are raised for incorrect inputs"""
@@ -400,6 +417,18 @@ def test_format_emperor_html_footer_string(self):
COMPARISON_JS_STRING = """
var g_comparisonPositions = new Array();
+var g_isSerialComparisonPlot = true;
+g_comparisonPositions['sampa'] = [[-0.0677, -2.036, 0.2726], [-0.972, 0.551, 1.144], [0.2339, -0.88, -1.753]];
+g_comparisonPositions['sampb'] = [[-1.782, -0.972, 0.1582], [1.438, -2.603, -1.39], [0.436, 2.12, -0.935]];
+g_comparisonPositions['sampc'] = [[-0.659, -0.2566, 0.514], [-0.356, 0.0875, 0.772], [-0.88, 1.069, 1.069]];
+g_comparisonPositions['sampd'] = [[-1.179, -0.968, 2.525], [1.512, -1.239, -0.0365], [0.294, 0.2988, 0.0467]];
+g_comparisonPositions['sampe'] = [[-0.896, -1.765, 0.274], [1.17, 1.31, -1.407], [1.64, 0.2485, -0.354]];
+g_comparisonPositions['sampf'] = [[-0.0923, 1.414, -0.622], [2.618, 0.739, -0.01295], [0.821, -1.13, -1.794]];
+"""
+
+COMPARISON_JS_STRING_NON_SERIAL = """
+var g_comparisonPositions = new Array();
+var g_isSerialComparisonPlot = false;
g_comparisonPositions['sampa'] = [[-0.0677, -2.036, 0.2726], [-0.972, 0.551, 1.144], [0.2339, -0.88, -1.753]];
g_comparisonPositions['sampb'] = [[-1.782, -0.972, 0.1582], [1.438, -2.603, -1.39], [0.436, 2.12, -0.935]];
g_comparisonPositions['sampc'] = [[-0.659, -0.2566, 0.514], [-0.356, 0.0875, 0.772], [-0.88, 1.069, 1.069]];
@@ -518,14 +547,14 @@ def test_format_emperor_html_footer_string(self):