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replace '_' in the clustergrammer package #36

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65 changes: 29 additions & 36 deletions clustergrammer.js
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -243,11 +243,11 @@ var Clustergrammer =
});

// process view
if (_.has(config.network_data, 'views')) {
if (underscore.has(config.network_data, 'views')) {
config.network_data.views.forEach(function (inst_view) {

underscore.each(underscore.keys(filters.possible_filters), function (inst_filter) {
if (!_.has(inst_view, inst_filter)) {
if (!underscore.has(inst_view, inst_filter)) {
inst_view[inst_filter] = default_states[inst_filter];
}
});
Expand Down Expand Up @@ -278,17 +278,11 @@ var Clustergrammer =
var col_nodes = config.network_data.col_nodes;
var row_nodes = config.network_data.row_nodes;

// console.log( config.network_data.links[0] )
// console.log( config.network_data.links[1] )
// console.log( config.network_data.links[2] )

// console.log(_.has(config.network_data,'mat'));

///////////////////////////
// convert 'mat' to links
///////////////////////////

if (_.has(config.network_data, 'mat')) {
if (underscore.has(config.network_data, 'mat')) {

var links = [];
var mat = config.network_data.mat;
Expand Down Expand Up @@ -2068,7 +2062,7 @@ var Clustergrammer =

if (inst_key != 'nodes') {

if (!_.has(filter_data, inst_key)) {
if (!underscore.has(filter_data, inst_key)) {
filter_data[inst_key] = [];
}

Expand Down Expand Up @@ -2318,13 +2312,14 @@ var Clustergrammer =

var filter_network_using_new_nodes = __webpack_require__(12);
var get_subset_views = __webpack_require__(64);
var underscore = __webpack_require__(3);

module.exports = function make_network_using_view(config, params, requested_view) {

var orig_views = config.network_data.views;

var is_enr = false;
if (_.has(orig_views[0], 'enr_score_type')) {
if (underscore.has(orig_views[0], 'enr_score_type')) {
is_enr = true;
}

Expand Down Expand Up @@ -2421,7 +2416,7 @@ var Clustergrammer =
new_network_data.views = config.network_data.views;

// add cat_colors if necessary
if (_.has(config.network_data, 'cat_colors')) {
if (underscore.has(config.network_data, 'cat_colors')) {
new_network_data.cat_colors = config.network_data.cat_colors;
}

Expand Down Expand Up @@ -13002,6 +12997,7 @@ var Clustergrammer =
var utils = __webpack_require__(2);
var get_available_filters = __webpack_require__(5);
var make_cat_params = __webpack_require__(84);
var underscore = __webpack_require__(3);

module.exports = function calc_viz_params(params, predefined_cat_colors = true) {

Expand Down Expand Up @@ -13119,14 +13115,14 @@ var Clustergrammer =
// // always make group level dict
// params.group_level = {};

if (_.has(params, 'group_level') == false) {
if (underscore.has(params, 'group_level') == false) {
if (viz.show_dendrogram) {
params.group_level = {};
}

// preventing error when un-clustered, above statement
// preserves dendro state while updating
if (_.has(params, 'group_level') == false) {
if (underscore.has(params, 'group_level') == false) {
params.group_level = {};
}

Expand Down Expand Up @@ -13306,32 +13302,34 @@ var Clustergrammer =

/***/ }),
/* 73 */
/***/ (function(module, exports) {
/***/ (function(module, exports, __webpack_require__) {

var underscore = __webpack_require__(3);

module.exports = function calc_clust_width(viz) {

viz.clust = {};
viz.clust.margin = {};

// margin on left/top of the clustergram/matrix
// margin on left/top of the clustergram/matrix
// 1) norm_label margin and width
// 2) cat_room and uni_margin
// 2) cat_room and uni_margin
viz.clust.margin.left = viz.norm_labels.margin.left + viz.norm_labels.width.row + viz.cat_room.row + viz.uni_margin;

viz.clust.margin.top = viz.norm_labels.margin.top + viz.norm_labels.width.col + viz.cat_room.col + viz.uni_margin;

// the clustergram/matrix width is the svg width minus:
// the margin of the clustergram on the left
// the room for the spillover on the right
// ** the dendro will fit in the spillover room on the right
// the margin of the clustergram on the left
// the room for the spillover on the right
// ** the dendro will fit in the spillover room on the right
var ini_clust_width = viz.svg_dim.width - viz.clust.margin.left - viz.spillover_col_slant;

// make tmp scale to calc height of triangle col labels
var tmp_x_scale = d3.scale.ordinal().rangeBands([0, ini_clust_width]).domain(_.range(viz.num_col_nodes));
// make tmp scale to calc height of triangle col labels
var tmp_x_scale = d3.scale.ordinal().rangeBands([0, ini_clust_width]).domain(underscore.range(viz.num_col_nodes));

var triangle_height = tmp_x_scale.rangeBand() / 2;

// prevent the visualization from being unnecessarily wide
// prevent the visualization from being unnecessarily wide
if (triangle_height > viz.norm_labels.width.col) {
var reduce_width = viz.norm_labels.width.col / triangle_height;
ini_clust_width = ini_clust_width * reduce_width;
Expand Down Expand Up @@ -13498,7 +13496,7 @@ var Clustergrammer =

var possible_orders = ['clust', 'rank'];

if (_.has(inst_nodes[0], 'rankvar')) {
if (underscore.has(inst_nodes[0], 'rankvar')) {
possible_orders.push('rankvar');
}

Expand Down Expand Up @@ -13801,7 +13799,7 @@ var Clustergrammer =
ds_mat[ds_index].all_names.push(inst_row.name);

// gather row_data
if (_.has(ds_mat[ds_index], 'row_data')) {
if (underscore.has(ds_mat[ds_index], 'row_data')) {

for (x = 0; x < inst_row_data.length; x++) {
ds_mat[ds_index].row_data[x].value = ds_mat[ds_index].row_data[x].value + inst_row_data[x].value;
Expand Down Expand Up @@ -14027,7 +14025,7 @@ var Clustergrammer =
});
}

if (_.has(params.network_data, 'cat_colors') && predefined_cat_colors === true) {
if (underscore.has(params.network_data, 'cat_colors') && predefined_cat_colors === true) {
viz.cat_colors[inst_rc] = params.network_data.cat_colors[inst_rc];
}

Expand Down Expand Up @@ -14070,10 +14068,6 @@ var Clustergrammer =

viz['num_' + inst_rc + '_nodes'] = params.network_data[inst_rc + '_nodes'].length;

// if (_.has(config, 'group_level')){
// config.group_level[inst_rc] = 5;
// }

if (inst_rc === 'row') {
viz.dendro_room[inst_rc] = viz.dendro_room.symbol_width;
} else {
Expand Down Expand Up @@ -14653,7 +14647,7 @@ var Clustergrammer =
}

var keep_orig;
if (_.has(params.network_data.links[0], 'value_orig')) {
if (underscore.has(params.network_data.links[0], 'value_orig')) {
keep_orig = true;
} else {
keep_orig = false;
Expand Down Expand Up @@ -15362,7 +15356,6 @@ var Clustergrammer =
row_nodes = params.network_data.row_nodes;
} else {
underscore.each(params.network_data.row_nodes, function (inst_row) {
// if (_.contains(row_names, inst_row.name)){
if (underscore.contains(row_names, inst_row.name)) {
row_nodes.push(inst_row);
}
Expand Down Expand Up @@ -16848,7 +16841,7 @@ var Clustergrammer =

// working on tracking the 'real' number of nodes, which is only different
// if downsampling has been done
if (_.has(inst_run_count[inst_cat], 'num_nodes_ds')) {
if (underscore.has(inst_run_count[inst_cat], 'num_nodes_ds')) {
var num_nodes_ds = inst_run_count[inst_cat].num_nodes_ds;
} else {
num_nodes_ds = null;
Expand Down Expand Up @@ -20584,6 +20577,7 @@ var Clustergrammer =

var get_cat_title = __webpack_require__(143);
var d3_tip_custom = __webpack_require__(100);
var underscore = __webpack_require__(3);

module.exports = function make_row_cat_super_labels(cgm) {

Expand Down Expand Up @@ -20684,7 +20678,7 @@ var Clustergrammer =
d3.selectAll(params.root + ' .row_cat_selection_bar').call(cat_tip);
}

if (_.has(params.network_data, 'row_cat_bars')) {
if (underscore.has(params.network_data, 'row_cat_bars')) {

// Enrichrgram title
/////////////////////
Expand Down Expand Up @@ -24158,7 +24152,6 @@ var Clustergrammer =
if (delays.run_transition) {

update_row_tiles.transition().delay(delays.update).duration(duration).attr('width', params.viz.rect_width).attr('height', params.viz.rect_height).attr('transform', function (d) {
// if (_.contains(col_nodes_names, d.col_name)){
if (underscore.contains(col_nodes_names, d.col_name)) {
return fine_position_tile(params, d);
} else {
Expand Down Expand Up @@ -25406,7 +25399,7 @@ var Clustergrammer =

var orig_nodes = params.inst_nodes[inst_rc + '_nodes'];

if (_.has(names, inst_rc)) {
if (underscore.has(names, inst_rc)) {

if (names[inst_rc].length > 0) {
var inst_names = names[inst_rc];
Expand Down
2 changes: 1 addition & 1 deletion src/categories/calc_cat_cluster_breakdown.js
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Original file line number Diff line number Diff line change
Expand Up @@ -181,7 +181,7 @@ module.exports = function calc_cat_cluster_breakdown(params, inst_data, inst_rc)

// working on tracking the 'real' number of nodes, which is only different
// if downsampling has been done
if (_.has(inst_run_count[inst_cat], 'num_nodes_ds')){
if (underscore.has(inst_run_count[inst_cat], 'num_nodes_ds')){
var num_nodes_ds = inst_run_count[inst_cat].num_nodes_ds;
} else {
num_nodes_ds = null;
Expand Down
1 change: 0 additions & 1 deletion src/enter/eeu_existing_row.js
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Original file line number Diff line number Diff line change
Expand Up @@ -47,7 +47,6 @@ module.exports = function eeu_existing_row(params, ini_inp_row_data, delays, dur
.attr('width', params.viz.rect_width)
.attr('height', params.viz.rect_height)
.attr('transform', function(d) {
// if (_.contains(col_nodes_names, d.col_name)){
if (underscore.contains(col_nodes_names, d.col_name)){
return fine_position_tile(params, d);
} else {
Expand Down
3 changes: 2 additions & 1 deletion src/labels/make_row_cat_super_labels.js
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
var get_cat_title = require('../categories/get_cat_title');
var d3_tip_custom = require('../tooltip/d3_tip_custom');
var underscore = require('underscore');

module.exports = function make_row_cat_super_labels(cgm){

Expand Down Expand Up @@ -150,7 +151,7 @@ module.exports = function make_row_cat_super_labels(cgm){
.call(cat_tip);
}

if (_.has(params.network_data, 'row_cat_bars')){
if (underscore.has(params.network_data, 'row_cat_bars')){

// Enrichrgram title
/////////////////////
Expand Down
1 change: 0 additions & 1 deletion src/labels/make_row_labels.js
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Expand Up @@ -16,7 +16,6 @@ module.exports = function make_row_labels(cgm, row_names='all', text_delay = 0){
row_nodes = params.network_data.row_nodes;
} else {
underscore.each(params.network_data.row_nodes, function(inst_row){
// if (_.contains(row_names, inst_row.name)){
if (underscore.contains(row_names, inst_row.name)){
row_nodes.push(inst_row);
}
Expand Down
12 changes: 3 additions & 9 deletions src/make_config.js
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Original file line number Diff line number Diff line change
Expand Up @@ -59,11 +59,11 @@ module.exports = function make_config(args) {
});

// process view
if (_.has(config.network_data, 'views')){
if (underscore.has(config.network_data, 'views')){
config.network_data.views.forEach(function(inst_view){

underscore.each( underscore.keys(filters.possible_filters), function(inst_filter){
if ( !_.has(inst_view, inst_filter) ){
if (!underscore.has(inst_view, inst_filter) ){
inst_view[inst_filter] = default_states[inst_filter];
}
});
Expand Down Expand Up @@ -97,17 +97,11 @@ module.exports = function make_config(args) {
var col_nodes = config.network_data.col_nodes;
var row_nodes = config.network_data.row_nodes;

// console.log( config.network_data.links[0] )
// console.log( config.network_data.links[1] )
// console.log( config.network_data.links[2] )

// console.log(_.has(config.network_data,'mat'));

///////////////////////////
// convert 'mat' to links
///////////////////////////

if (_.has(config.network_data, 'mat')){
if (underscore.has(config.network_data, 'mat')){

var links = [];
var mat = config.network_data.mat;
Expand Down
2 changes: 1 addition & 1 deletion src/matrix/calc_downsampled_matrix.js
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Original file line number Diff line number Diff line change
Expand Up @@ -44,7 +44,7 @@ module.exports = function calc_downsampled_matrix(params, mat, ds_level){
ds_mat[ds_index].all_names.push(inst_row.name);

// gather row_data
if (_.has(ds_mat[ds_index], 'row_data')){
if (underscore.has(ds_mat[ds_index], 'row_data')){

for (x=0; x < inst_row_data.length; x++){
ds_mat[ds_index].row_data[x].value = ds_mat[ds_index].row_data[x].value + inst_row_data[x].value;
Expand Down
2 changes: 1 addition & 1 deletion src/matrix/make_simple_rows.js
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Expand Up @@ -19,7 +19,7 @@ module.exports = function make_simple_rows(params, inst_data, tip, row_selection
}

var keep_orig;
if (_.has(params.network_data.links[0], 'value_orig')) {
if (underscore.has(params.network_data.links[0], 'value_orig')) {
keep_orig = true;
} else {
keep_orig = false;
Expand Down
2 changes: 1 addition & 1 deletion src/network/filter_network_using_new_nodes.js
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Expand Up @@ -63,7 +63,7 @@ module.exports = function filter_network_using_new_nodes(config, new_nodes) {
new_network_data.views = config.network_data.views;

// add cat_colors if necessary
if (_.has(config.network_data, 'cat_colors')){
if (underscore.has(config.network_data, 'cat_colors')){
new_network_data.cat_colors = config.network_data.cat_colors;
}

Expand Down
2 changes: 1 addition & 1 deletion src/network/filter_viz_using_names.js
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Expand Up @@ -22,7 +22,7 @@ module.exports = function filter_viz_using_names(names, external_cgm = false){

var orig_nodes = params.inst_nodes[inst_rc+'_nodes'];

if (_.has(names, inst_rc)){
if (underscore.has(names, inst_rc)){

if (names[inst_rc].length > 0){
var inst_names = names[inst_rc];
Expand Down
3 changes: 2 additions & 1 deletion src/network/make_network_using_view.js
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@@ -1,12 +1,13 @@
var filter_network_using_new_nodes = require('./filter_network_using_new_nodes');
var get_subset_views = require('../filters/get_subset_views');
var underscore = require('underscore');

module.exports = function make_network_using_view(config, params, requested_view) {

var orig_views = config.network_data.views;

var is_enr = false;
if (_.has(orig_views[0], 'enr_score_type')){
if (underscore.has(orig_views[0], 'enr_score_type')){
is_enr = true;
}

Expand Down
4 changes: 0 additions & 4 deletions src/params/calc_cat_params.js
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Expand Up @@ -20,10 +20,6 @@ module.exports = function calc_cat_params(params, viz){

viz['num_'+inst_rc+'_nodes'] = params.network_data[inst_rc+'_nodes'].length;

// if (_.has(config, 'group_level')){
// config.group_level[inst_rc] = 5;
// }

if(inst_rc === 'row'){
viz.dendro_room[inst_rc] = viz.dendro_room.symbol_width;
} else {
Expand Down
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