metamatrix 0.1.0

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MetaMatrix

This python class provides a visual containing 3 matrices:

• [A] a heatmap
• [B] a matrix aligned on the right of the heatmap, containing metadata for each row
• [C] a matrix aligned at the bottom of the heatmap, containing metadata for each column

Usage

Minimal example:

x = MetaMatrix(df_A, df_B, df_C)
mo.Html(x.to_svg())

Interactive sorting (in marimo):

selector_column_order = mo.ui.dropdown(options=config['features']['column'])
selector_row_order = mo.ui.dropdown(options=config['features']['row'])

x = MetaMatrix(df_A, df_B, df_C,
               column_order=selector_column_order.selected_key,
               row_order=selector_row_order.selected_key,
               cell_width=5,
               features={
                    'row': {
                        'Family': 'categorical',
                        'Order': 'categorical',
                    },
                    'column': {
                        'Category': 'categorical',
                        'Location': 'categorical',
                        'Type': 'categorical',
                        'MP': 'categorical'
                    }}
              )

mo.vstack([mo.hstack([selector_column_order,selector_row_order], justify="start"), mo.Html(x.to_svg())])

Parameters

• features (default {'row': {}, 'column': {}}):
  • The metadata features to draw from matrices B (row metadata) and C (column metadata), including if they are categorical or numeric.
• column_order (default undefined):
  • Column metadata feature to sort the data columns.
• row_order (default undefined):
  • Row metadata feature to sort the data rows.
• padding_top (default 120):
  • Defines how much the complete SVG should be shifted down.
• padding_left (default 80):
  • Defines how much the complete SVG should be shifted to the right.
• cell_width (default 5):
  • Width of the heatmap cells.
• cell_height (default 15):
  • Height of the heatmap cells.
• row_metadata_cell_width (default 20):
  • Width of the row metadata cells.
• column_metadata_cell_height (default 20):
  • Height of the column metadata cells.
• column_labels (default False):
  • Whether or not to show the column labels. Useful if either is too small to show text.
• row_labels (default True):
  • Whether or not to show the row labels.

Input data

Heatmap data (dataframe df_A)

,N1,N2,N3,N4,N5,N6,N7,N8,N9,N10,N11,N12,N13,N14,N15,N16,N17,N18,N19,N20
asv1,7202,11359,26,634,2516,118,153,2179,1062,448,912,377,5376,0,208,696,0,64,210,21
asv2,3975,6078,0,271,1118,114,552,1263,469,169,298,209,802,0,23,90,60,2244,3310,31
asv3,0,0,5,0,0,0,0,47,0,0,8,2,0,0,0,674,0,20,728,0
asv4,747,1217,0,153,615,37,52,547,242,87,149,74,23,0,0,83,0,20,0,0
asv5,0,0,50,84,0,156,1140,524,291,233,37,38,0,61,0,2082,0,1252,1283,0
asv6,3364,1875,0,231,904,55,55,722,382,171,295,122,3321,96,0,21,0,14,0,110
asv7,0,0,217,71,0,44,0,0,0,0,0,46,0,2,0,26,0,50,0,0
asv8,66,358,53,145,504,0,128,410,231,135,111,94,939,211,428,1647,0,286,887,35
asv9,28,54,0,0,73,0,1457,92,91,43,0,0,104,916,20,163,79,1306,2131,71
asv10,0,0,0,0,200,0,0,209,57,0,0,0,0,0,18,59,0,0,26,0
asv11,0,132,0,31,61,0,1412,573,1152,447,129,0,37,341,57,213,1918,452,1478,0
asv12,0,0,0,45,353,25,11,388,134,24,58,23,0,4,0,207,0,0,5,0
asv13,0,0,197,80,9,0,144,82,3182,1229,4,12,0,55,0,0,0,0,0,11
asv14,0,0,0,140,407,41,0,469,158,58,123,85,0,0,0,0,0,0,0,0
asv15,0,0,683,66,0,24,797,542,776,241,0,33,0,201,43,24,58,1130,0,0
asv16,0,0,0,0,0,0,0,5,0,0,54,0,0,0,0,0,0,0,0,0
asv17,0,0,0,7,78,0,0,38,16,0,7,6,0,0,42,19,0,0,21,0
asv18,0,0,0,0,9,0,1133,367,363,175,30,67,0,24,6,57,0,1497,1641,547
asv19,0,0,160,31,0,43,236,96,0,0,0,15,0,0,0,22,0,680,0,0

Row metadata (dataframe df_B)

"","Kingdom","Phylum","Class","Order","Family","Genus","Species"
"asv1","Bacteria","Proteobacteria","Gammaproteobacteria","Burkholderiales","T34",NA,NA
"asv2","Bacteria","Bacteroidota","Bacteroidia","Flavobacteriales","Flavobacteriaceae","Flavobacterium","terrigena"
"asv3","Bacteria","Proteobacteria","Gammaproteobacteria","Pseudomonadales","Moraxellaceae","Acinetobacter",NA
"asv4","Bacteria","Firmicutes","Bacilli",NA,NA,NA,NA
"asv5","Bacteria","Actinobacteriota","Actinobacteria","Micrococcales","Microbacteriaceae","Candidatus Limnoluna",NA
"asv6","Bacteria","Proteobacteria","Gammaproteobacteria","Burkholderiales","Comamonadaceae","Limnohabitans",NA
"asv7","Bacteria","Proteobacteria","Alphaproteobacteria","SAR11 clade","Clade III",NA,NA
"asv8","Bacteria","Proteobacteria","Gammaproteobacteria","Burkholderiales","Comamonadaceae",NA,NA
"asv9","Bacteria","Bacteroidota","Bacteroidia","Cytophagales","Spirosomaceae","Pseudarcicella",NA
"asv10","Bacteria","Firmicutes","Bacilli",NA,NA,NA,NA
"asv11","Bacteria","Bacteroidota","Bacteroidia","Flavobacteriales","Flavobacteriaceae","Flavobacterium",NA
"asv12","Bacteria","Firmicutes","Bacilli","Mycoplasmatales","Mycoplasmataceae","Candidatus Bacilloplasma",NA
"asv13","Bacteria","Bacteroidota","Bacteroidia","Flavobacteriales","Crocinitomicaceae","Fluviicola",NA
"asv14","Bacteria","Bacteroidota","Bacteroidia","Flavobacteriales","Flavobacteriaceae","Flavobacterium",NA
"asv15","Bacteria","Bacteroidota","Bacteroidia","Chitinophagales","Chitinophagaceae","Sediminibacterium",NA
"asv16","Bacteria","Verrucomicrobiota","Verrucomicrobiae","Verrucomicrobiales","DEV007",NA,NA
"asv17","Bacteria","Proteobacteria","Alphaproteobacteria","Sphingomonadales","Sphingomonadaceae","Sphingomonas",NA
"asv18","Bacteria","Bacteroidota","Bacteroidia","Sphingobacteriales","NS11-12 marine group",NA,NA
"asv19","Bacteria","Actinobacteriota","Actinobacteria","Frankiales","Sporichthyaceae","Candidatus Planktophila",NA

Column metadata (dataframe df_C)

sample_name;Category;Location;Type;MP
N1;Natural pond;LRV;Daphnia;Low
N2;Natural pond;LRV;Daphnia;Low
N3;Natural pond;LRV;Daphnia;Low
N4;Natural pond;LRV;Daphnia;Low
N5;Natural pond;LRV;Daphnia;Low
N6;Natural pond;LRV;Daphnia;Low
N7;Natural pond;LRV;Daphnia;Low
N8;Natural pond;LRV;Daphnia;Low
N9;Natural pond;LRV;Daphnia;Low
N10;Natural pond;LRV;Daphnia;Low
N11;Natural pond;LRV;Daphnia;Low
N12;Natural pond;LRV;Daphnia;Low
N13;Natural pond;LRV;Daphnia;Low
N14;Natural pond;LRV;Daphnia;Low
N15;Natural pond;LRV;Daphnia;Low
N16;Natural pond;LRV;Daphnia;Low
N17;Natural pond;LRV;Daphnia;Low
N18;Natural pond;LRV;Daphnia;Low
N19;Natural pond;LRV;Daphnia;Low
N20;Natural pond;LRV;Daphnia;Low

Dataframe requirements

• The index of df_B (row metadata) should be the same as the index of df_A (heatmap data). It is allowed that some index values in df_B are not present in the index of df_A.
• The index of df_C (column metadata) should be the same as the column names of df_A (heatmap data). It is allowed that some column names in df_C are not present in the column names of df_A.