Plotting different samples in the same bubble plot

User Questions
1

Hi Daniel!
I want to make my bubble plot as in the photo, but after importing the file i get to plot only the taxonomy as part of one big sample even though i have different (photo 2. My import file)

I’ve already tried to separate the samples in different files, each one including the taxonomy, and compared them but i didn’t work.
P.s I’m new at using MEGAN so I don’t fully understand how my import file must looks like in order to let know the program that i have different samples or how fuse them in one file.

Captura de Pantalla 2020-01-24 a la(s) 22.21.46
Captura de Pantalla 2020-01-24 a la(s) 22.21.46387×714 147 KB

Captura de Pantalla 2020-01-24 a la(s) 22.02.08
Captura de Pantalla 2020-01-24 a la(s) 22.02.08782×199 11.6 KB

2

You need to transpose your file so that each line represents a different taxon and each column represents a different sample.

Example:

Samples <tab> T0.S01<tab> T0.S02 <tab> T.S03 <tab> …
Phaeococcomyces mexicanus <tab> 0 <tab> 0 <tab> 0 <tab> 15 <tab> 0 <tab>…

3

Hi Daniel,

I’d like to plot different samples in the same bubble plot too, but using KEGG pathways not taxonomy.

I prepared my table as you specified for taxonomy.

samples CT NT SF CM
Cell Growth and Death 7870 9368 3640 2138
Cell Motility 22034 21218 6020 3822
Transport and Catabolism 4310 5602 1790 914
Membrane Transport 88016 112146 41542 20963
Signal Transduction 13189 16945 6040 3442
Signaling Molecules and Interaction 4844 3646 1227 562
Folding, Sorting and Degradation 28414 40188 14720 7430
Replication and Repair 168614 170593 59893 29708
Transcription 22175 24093 8144 4409
Translation 42190 56274 18826 9746
Cancers 1502 2132 756 440
Immune System Diseases 282 262 82 60
Infectious Diseases 5529 6322 2089 1041
Metabolic Diseases 1220 1586 513 204
Neurodegenerative Diseases 970 680 186 86
Amino Acid Metabolism 122760 148594 55943 30118
Biosynthesis of Other Secondary Metabolites 20835 20847 8469 4275
Carbohydrate Metabolism 135326 155343 56424 29276
Energy Metabolism 56881 73705 27109 14544
Enzyme Families 35507 37466 13262 7259
Glycan Biosynthesis and Metabolism 55340 47590 15744 8707
Lipid Metabolism 42575 37617 12320 6277
Metabolism of Cofactors and Vitamins 40250 42813 14895 7259
Metabolism of Other Amino Acids 35740 29275 10472 5156
Metabolism of Terpenoids and Polyketides 12173 14432 5025 2692
Nucleotide Metabolism 63922 71684 26700 14008
Xenobiotics Biodegradation and Metabolism 8383 11214 4066 2199
Digestive System 4047 2924 961 476
Endocrine System 6231 8742 2715 1309
Environmental Adaptation 2109 2790 982 516
Excretory System 128 116 28 14
Immune System 1336 2012 714 412
Nervous System 1670 2628 870 388

4

Unfortunately, MEGAN doesn’t current parse KEGG names. Please replace the names by the corresponding id numbers defined in the attached file.
kegg.map (1.5 MB)

For example, your first line should then be:

2000023 7870 9368 3640 2138

Note that the numbers defined in the mapping file are not part of KEGG but rather are internal MEGAN-assigned identifiers.

5

I have this information, Please, check the attached table.

kegg_enzymes_counts.csv (82.4 KB)