bokulich-lab / q2-coordinates Goto Github PK

adjust plugin to newest qiime2 version (2020.11.1 -> 2021.2.0)

Steps to reproduce:

• use the attached metadata file to draw an interactive map as follows:

  qiime coordinates draw-interactive-map \ 
     --m-metadata-file meta_sample.txt \           
     --p-latitude Latitude \
     --p-longitude Longitude \
     --p-column Depth \            
     --o-visualization test-viz.qzv 
  

• open the visualization

Expected behaviour:
Map is displayed correctly.

Actual behaviour:
Map is missing - see the screenshot.

they should be larger, and dimensions should be fixed, or at least fixed height? Currently fixed width (I think), which results in lots of white space if maps are longer than wide.

Enhance visualisation of multiple samples from identical location, e.g. by adding jitter to scatter plot (inspiration) or aggregating values of same location. Currently samples from same location with differing values are not distinguishable.

This is a followup question/issue related to #10

I note that the quadtree is output as a Phylogeny[Rooted], but the README shows some provenance-breaking reformatting necessary to use with q2-empress. Is a new transformer needed? Or why is this reformatting not just done in the first place?

If reformatting is necessary for this to be used as a normal Phylogeny[Rooted], then a quadtree should have its own special type (maybe Phylogeny[quadtree]), and we can add a transformer or an action to perform this conversion.

Any thoughts @zoechallacombe @wasade ? Thanks!

automatically adjust scale to sensible unit, size, and intervals (e.g., 1 km intervals)

automatically locate to unused corner or outside of plot beneath legend.

they point to nbokulich/q2-coordinates instead of bokulich-lab/q2-coordinates

also the dependencies, etc might need updating.

hence distances between points would take elevation into account.

column should be optional in draw-interactive-map and draw-map, i.e., if no column is selected, all points should be colored uniformly. Currently, it is optional but omitting a column raises an error:

Test data: metadata.txt

Command:

qiime coordinates draw-interactive-map \
    --m-metadata-file metadata.txt \
    --p-latitude lat \
    --p-longitude lon \
    --o-visualization map.qzv

Full traceback:

Traceback (most recent call last):
  File "/Users/nbokulich/miniconda3/envs/q2coord/lib/python3.6/site-packages/q2cli/commands.py", line 329, in __call__
    results = action(**arguments)
  File "/Users/nbokulich/miniconda3/envs/q2coord/lib/python3.6/site-packages/decorator.py", line 232, in fun
    return caller(func, *(extras + args), **kw)
  File "/Users/nbokulich/miniconda3/envs/q2coord/lib/python3.6/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
    output_types, provenance)
  File "/Users/nbokulich/miniconda3/envs/q2coord/lib/python3.6/site-packages/qiime2/sdk/action.py", line 452, in _callable_executor_
    ret_val = self._callable(output_dir=temp_dir, **view_args)
  File "/Users/nbokulich/miniconda3/envs/q2coord/lib/python3.6/site-packages/q2_coordinates/mapper.py", line 129, in draw_interactive_map
    ['column', 'latitude', 'longitude'], missing_data)
  File "/Users/nbokulich/miniconda3/envs/q2coord/lib/python3.6/site-packages/q2_coordinates/_utilities.py", line 27, in _load_and_validate
    metadata = metadata[columns]
  File "/Users/nbokulich/miniconda3/envs/q2coord/lib/python3.6/site-packages/pandas/core/frame.py", line 2912, in __getitem__
    indexer = self.loc._get_listlike_indexer(key, axis=1, raise_missing=True)[1]
  File "/Users/nbokulich/miniconda3/envs/q2coord/lib/python3.6/site-packages/pandas/core/indexing.py", line 1254, in _get_listlike_indexer
    self._validate_read_indexer(keyarr, indexer, axis, raise_missing=raise_missing)
  File "/Users/nbokulich/miniconda3/envs/q2coord/lib/python3.6/site-packages/pandas/core/indexing.py", line 1304, in _validate_read_indexer
    raise KeyError(f"{not_found} not in index")
KeyError: '[None] not in index'

However, selecting a column causes this to work. E.g., command:

qiime coordinates draw-interactive-map \
    --m-metadata-file metadata.txt \
    --p-latitude lat \
    --p-longitude lon \
    --p-column language \
    --o-visualization map.qzv

Looks like draw-map raises the same error as draw-interactive-map so column is not being handled appropriately by either...

The readme is quite outdated. Should be updated to:

1. patch up the text and visuals
2. include links to view/download example data/qzvs
3. some methods need a little more description (or links to better description), e.g., for quadtrees.

Choropleth maps would be a useful feature, e.g., for plotting average values within a region, or even density of sampling within a region.

input: metadata
required params: latitude, longitude
output: interactive chloropleth map

optional inputs: metadata column to average per area [otherwise plot density by default]

Some examples and relevant projects:
https://plotly.com/python/choropleth-maps/
https://github.com/pysal/mapclassify
https://geopandas.org/en/stable/community/ecosystem.html

zoom, box selection, hover tools, drag

Currently the map resolution is autoscaled by default. Expose the resolution setting to the user.

allowing plugin to support python 3.8 and be compatible with newest QIIME2 version (2021.2.0 -> 2021.4.0 )