Commit 7dcaa182 authored by Liubov Chuprikova's avatar Liubov Chuprikova
Browse files

New upstream version 2019.7.0

parent 9c19f62d

q2_taxa/_version.py

+3 −3
Original line number Diff line number Diff line
@@ -23,9 +23,9 @@ def get_keywords(): 
    # setup.py/versioneer.py will grep for the variable names, so they must

    # each be defined on a line of their own. _version.py will just call

    # get_keywords().

    git_refnames = " (tag: 2019.4.0)"

    git_full = "b68f7f2cf216a6dd942c115337a4c0eaeda84006"

    git_date = "2019-05-03 04:14:42 +0000"

    git_refnames = " (tag: 2019.7.0)"

    git_full = "bc018fe8540f9f0fb4f4cf6729d840a53f5d8c31"

    git_date = "2019-07-30 18:15:55 +0000"

    keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}

    return keywords

q2_taxa/_visualizer.py

+5 −0
Original line number Diff line number Diff line
@@ -24,6 +24,11 @@ TEMPLATES = pkg_resources.resource_filename('q2_taxa', 'assets') 


def barplot(output_dir: str, table: pd.DataFrame, taxonomy: pd.Series,

            metadata: Metadata) -> None:

    ids_not_in_metadata = set(table.index) - set(metadata.ids)

    if ids_not_in_metadata:

        raise ValueError('Feature IDs found in the table are missing in the '

                         f'metadata: {ids_not_in_metadata!r}.')



    metadata = metadata.to_dataframe()

    jsonp_files, csv_files = [], []

    collapsed_tables = _extract_to_level(taxonomy, table)

q2_taxa/assets/barplot/src/init.js

+20 −9
Original line number Diff line number Diff line
@@ -2,8 +2,8 @@ import { select } from 'd3'; 


import render from './render';

import {

  availableColorSchemes,

  addTaxaPicker,

  addWidthSlider,

  addColorPicker,

  addSortByPicker,

  addDownloadLinks,
@@ -12,9 +12,20 @@ import { setupData, sort } from './data'; 
import plotLegend from './legend';





export default function init(level) {

/* Re-initializes the display.

 *

 * "state" is an object that should contain the following entries:

 *

 * level -- an integer indicating the currently selected index in the

 *          "Taxonomic Level" dropdown (starts at 0)

 *

 * colorScheme -- the name of the current color scheme

 *

 * barWidth -- an integer indicating the currently selected bar width value

 */

export default function init(state) {

  /* global d */

  const data = d[level].data;

  const data = d[state.level].data;



  // DOM

  const body = select('body .container-fluid');
@@ -47,19 +58,19 @@ export default function init(level) { 
    .style('font', '12px sans-serif')

    .text('Sample');



  const initialColorScheme = availableColorSchemes[0].name;

  const dataMeta = setupData(d[level], svgBar);

  const dataMeta = setupData(d[state.level], svgBar);

  const { sortedKeysReverse, levels } = dataMeta;



  const initialSort = sort(data, [sortedKeysReverse[0]], ['Ascending'], [false], dataMeta);

  const chartInfo = render(svgBar, initialColorScheme, initialSort, dataMeta);

  const chartInfo = render(svgBar, state.colorScheme, initialSort, dataMeta, state.barWidth);



  plotLegend(legendCol, chartInfo);



  // Controls

  const ctrlRowOne = controls.append('div').attr('class', 'row');

  addDownloadLinks(ctrlRowOne, svgBar, legendCol.select('svg'), level + 1);

  addTaxaPicker(ctrlRowOne, levels, level + 1);

  addColorPicker(ctrlRowOne, svgBar, legendCol, data, dataMeta);

  addDownloadLinks(ctrlRowOne, svgBar, legendCol.select('svg'), state.level + 1);

  addTaxaPicker(ctrlRowOne, levels, state.level + 1);

  addColorPicker(ctrlRowOne, svgBar, legendCol, data, dataMeta, state.colorScheme);

  addSortByPicker(ctrlRowOne, svgBar, data, dataMeta);

  addWidthSlider(ctrlRowOne, svgBar, data, dataMeta, state.barWidth);

}

q2_taxa/assets/barplot/src/main.js

+2 −2
Original line number Diff line number Diff line 
import init from './init';

import { getBarWidth, getColorScheme } from './toolbar';





init(0);
 
init({ level: 0, colorScheme: getColorScheme(), barWidth: getBarWidth() });

q2_taxa/assets/barplot/src/render.js

+2 −2
Original line number Diff line number Diff line
@@ -14,9 +14,9 @@ import { availableColorSchemes } from './toolbar'; 


export const transitionDur = 500;



export default function render(svg, colorScheme, xOrdering, dataMeta) {

export default function render(svg, colorScheme, xOrdering, dataMeta, barWidth) {

  const { sortMap, sortedSampleIDs } = xOrdering;

  const width = sortedSampleIDs.length * 10;

  const width = sortedSampleIDs.length * barWidth;

  const height = 600;

  const margin = { top: 20, left: 60, right: 0, bottom: 50 };

  const { keys } = dataMeta;