Description:

makimono 0.1.4

Makimono is a python package wrapping (mostly) around the matplotlib and bokeh
packages and providing convenient plotting tools to visualize RNA-Seq expression in sets
of interest. Optionally, GO and/or KEGG enrichment (“interfacing” with the R packages topGO
and GOstats) reports for those sets of interest can also be generated from topGO/GOstats results and incorporated into the makimono package outputs.

Current release: 0.1.4 (alpha)
Provides basic functionality and basic documentation. Methods and functions are working provided the inputs
are within the expected formats and constraints (onus is on the user – see more at the end).
TODO:

Write tests
Improve documentation
Increment/improve exception handling
Extend functionality with new features
Re-write old code to integrate as new modules


Installation:
# pip install makimono-0.1.4.tar.gz
or
# pip install makimono
Usage:
Refer to the included jupyter python notebooks (see docs folder) for usage examples of the methods and functions in the makimono package.
Additionally, the makimono package ships with a command line utility, makisu
that allows access to part of the functionally of the package.
To use makisu on the command line just type:
$ makisu [arguments]


makisu
usage: makisu [-h] -p {mpl,bokeh,bokehplus} -e EXPRESSION -r REPLICATES -t
TIMEPOINTS [TIMEPOINTS ...] -i INPUT [-a ALPHA]
[-xk XTICKS [XTICKS ...]] [-m {all,web,batch}] [-o OUTPUTFOLDER]

Required arguments:

[-p] plotting mode (options: mpl, bokeh, bokehplus)
[-e] path to file with RNA-Seq expression counts
[-r] number of replicates in expression counts file
[-t] list of experimental time points
[-i] path [or folder] to file(s) containing lists of genes/transcripts of interest

Optional arguments:

[-a] level of significance (to filter enrichment results) -- [defaults to 0.05]
[-xk] list of ticks for the plot's x-axis -- [defaults to timepoints]
[-m] plot portability (for bokeh/bokehplus -- options: all, web[default] and batch)
[-o] folder where to output your plots/reports [defaults to user's home directory]

Input files requirements:
To use makimono the following files are required:

RNA-Seq expression counts.
List(s) of subsets of genes/transcripts of interest.

The RNA-Seq expression file should be a tab-separated file where the first column corresponds a gene/transcript identifier with the following columns being the counts for each replicate at each experimental time point.
e.g.
Cre14.g622075.t1.1 10 5 75 77 39 34 18 25 15 22 21 6 19 13 17 32

(...)

Cre10.g467200.t1.1 21 36 320 293 114 111 37 80 63 68 49 61 53 66 66 86
In the example above comes from an experiment with 8 time points and 2 replicates, thus for transcript Cre14.g622075.t1.1 10 and 5 are the counts for the two replicates at the first time point, 75 and 77 are the counts for the two replicates at the second time point and so on.
The file(s) with the genes/transcripts of interest must list one identifier per line and optionally can have additional (tab-separated) annotations on their respective line.
e.g.
Cre01.g053250.t1.1 RING/FYVE/PHD zinc finger superfamily protein
Cre02.g147150.t1.1

(...)

Cre03.g173800.t1.2 PDX2 Pyridoxal kinase Pyridoxal kinase, involved in vitamin B6 biosynthesis.


Term enrichment reports:
(available with the ‘bokehplus’ plotting mode)

Term enrichment reports for GO term enrichment and KEGG pathway enrichment can be incorporated into the bokeh interactive plots. Makimono uses the enrichment result files as produced by the R packages topGO (for GO term enrichments) and GOstats (for KEGG pathways enrichments) to generate these reports. To use these R modules (these need to be installed on the system and) and one should refer to their original documentation or alternatively use (see example in docs folder) the limited and experimental “interface” provided by the module enricher packaged with makimono.

e.g.
GO term enrichment file sample (produced by topGO)
GO.ID Term Annotated Significant Expected Rank in classicFisher classicFisher elimFisher
GO:0034450 ubiquitin-ubiquitin ligase activity 2 2 0 1 3.3e-06 3.3e-06
GO:0004360 glutamine-fructose-6-phosphate transamin... 1 1 0 4 0.0019 0.0019
GO:0008478 pyridoxal kinase activity 2 1 0 6 0.0038 0.0038
GO term enrichment file sample (produced by topGO)
e.g.
KEGGID Pvalue OddsRatio ExpCount Count Size Term
00790 0.00540248514316588 Inf 0.00540248514316586 1 10 Folate biosynthesis
WARNING: The current implementation of the enricher module relies on a rigid folder/filename structure and convention.


Enrichment result files must be of the form: <basename>_enrichment.tsv
Enrichment files must be placed on a rigid folder hierarchy relative to the location of the files with the sets of interest, as in the example shown below.


e.g.
.
├── 002_{0h=2h=8h=12h=24h=48h}GT{30min=4h}.txt
├── 026_{30min}GT{2h}GT{4h=8h=12h=24h=48h}GT{0h}.txt
├── 053_{8h=12h=24h=48h}GT{30min=2h=4h}GT{0h}.txt
├── 317_{30min=2h=4h=8h=12h=24h=48h}GT{0h}.txt
├── goenrich
│ ├── BP
│ │ ├── 002_{0h=2h=8h=12h=24h=48h}GT{30min=4h}_enrichment.tsv
│ │ ├── 026_{30min}GT{2h}GT{4h=8h=12h=24h=48h}GT{0h}_enrichment.tsv
│ │ ├── 053_{8h=12h=24h=48h}GT{30min=2h=4h}GT{0h}_enrichment.tsv
│ │ └── 317_{30min=2h=4h=8h=12h=24h=48h}GT{0h}_enrichment.tsv
│ ├── CC
│ │ ├── 002_{0h=2h=8h=12h=24h=48h}GT{30min=4h}_enrichment.tsv
│ │ ├── 026_{30min}GT{2h}GT{4h=8h=12h=24h=48h}GT{0h}_enrichment.tsv
│ │ ├── 053_{8h=12h=24h=48h}GT{30min=2h=4h}GT{0h}_enrichment.tsv
│ │ └── 317_{30min=2h=4h=8h=12h=24h=48h}GT{0h}_enrichment.tsv
│ └── MF
│ ├── 002_{0h=2h=8h=12h=24h=48h}GT{30min=4h}_enrichment.tsv
│ ├── 026_{30min}GT{2h}GT{4h=8h=12h=24h=48h}GT{0h}_enrichment.tsv
│ ├── 053_{8h=12h=24h=48h}GT{30min=2h=4h}GT{0h}_enrichment.tsv
│ └── 317_{30min=2h=4h=8h=12h=24h=48h}GT{0h}_enrichment.tsv
└── keggenrich
├── 026_{30min}GT{2h}GT{4h=8h=12h=24h=48h}GT{0h}_enrichment.tsv
├── 053_{8h=12h=24h=48h}GT{30min=2h=4h}GT{0h}_enrichment.tsv
└── 317_{30min=2h=4h=8h=12h=24h=48h}GT{0h}_enrichment.tsv
In the example above, the files listing the four sets of interest are at the root directory. Sub-directory keggenrich/ holds the respective KEGG pathway enrichment result files (for each of the four sets of interest). The goenrich/ sub-directory holds the enrichment result files for the GO term enrichments for the same four sets of interest. However, there they are further split into three different sub-directories reflecting each orthogonal ontology comprising the GeneOntology.

License

For personal and professional use. You cannot resell or redistribute these repositories in their original state.

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