Python reference
Every function and dataset of the Python package.
Functions
GC() | A gene cluster chart |
GC.widget() | Return the chart as a Jupyter widget |
GC.to_spec() | Return the chart spec, as JSON values |
GC.labels() | Add labels to the genes |
GC.genes() | Set how the genes are drawn |
GC.transcript() | Draw the data as transcripts: exons, introns and UTRs |
GC.color() | Set the colours of the genes and the legend |
GC.pattern() | Fill the genes, exons and legend markers with a pattern per group |
GC.legend() | Set the legend |
GC.title() | Add a title and subtitle to the chart |
GC.cluster_title() | Add a title and subtitle above each cluster |
GC.sequence() | Set the line of each cluster's sequence |
GC.grid() | Set the layout of the clusters: margins, width and height |
GC.scale() | Set the scale of the clusters, and add an axis |
GC.scale_bar() | Add a scale bar to the clusters |
GC.cluster_label() | Add a label beside each cluster |
GC.cluster_footer() | Add a footer below each cluster |
GC.coordinates() | Show the start and end coordinates of the genes |
GC.cluster() | Set how genes are placed in their cluster |
GC.annotation() | Add an annotation: text, a line, an arrow, a symbol and more |
GC.track_mouse() | Show a line and the position under the mouse |
GC.events() | Make the chart report clicks, selections, drags and zooms to Shiny |
GC.toolbar() | Set the toolbar: when it shows, its buttons, icons and colours |
GC.zoom() | Add a zoom slider below the clusters |
GC.tooltip() | Set the tooltip of the genes |
GC.links() | Add links between genes of neighbouring clusters |
GC.align() | Align the clusters on a gene |
GC.normalize() | Normalise the positions of the genes: even gaps between them |
GC.element_style() | Edit or reset one element: a gene, label, title or legend entry |
GC.theme() | Set the theme of the chart |
gbk_features_to_df() | Make a table of one kind of feature of GenBank files read with read_gbk |
genbank_to_fasta() | Write the sequences of a GenBank file to a FASTA file |
geneviewer_palette() | Return the colours of a geneviewer palette, or the names of all palettes |
geneviewer_theme() | Return the settings of a built-in theme |
get_introns() | Add the introns between the exons of each transcript |
mummer_alignment() | Align neighbouring clusters with MUMmer, for links between them |
protein_blast() | Find the best hit of each gene in the query cluster's proteins |
read_bed() | Read BED files into one table |
read_fasta() | Read FASTA files into one table, a row per sequence |
read_gbk() | Read GenBank files |
read_gff() | Read GFF files into one table |
output_geneviewer() | Create a chart output in the UI, R's GC_chartOutput() |
render_geneviewer() | Draw a chart in an output, R's renderGC_chart() |
zoom_to() | Set the zoom window of a chart in a running app, R's GC_zoom_to() |
GCWidget() | A chart as a Jupyter widget |
GCWidget.on() | Call a function at each event of a kind |
GCWidget.zoom_to() | Set the zoom window of the chart, R's GC_zoom_to() |
datasets.load() | Return an example dataset |
datasets.names() | Return the names of the example datasets |
datasets.titles() | Return what each example dataset holds |
Datasets
The datasets of the R package, each loaded with datasets.load() as a pandas DataFrame.
BRCA1_splice_variants | BRCA1 Splice Variants |
coronavirus_genomes | Genes of eleven coronaviruses from the four genera |
erythromycin_BlastP | Erythromycin protein alignment results |
erythromycin_cluster | Erythromycin Gene Cluster Data |
hs_dystrophin_transcripts | Human Dystrophin Transcripts Data |
human_hox_genes | Human HOX Gene Cluster Data |
mitochondrial_gene_order | Human and Locust Mitochondrial Gene Order |
ophA_clusters | ophA Gene Cluster from Omphalotus olearius |
pQEB1_alignment | Nucleotide alignment of the pQEB1 plasmids |
pQEB1_plasmids | Genes of the blaKPC-2 plasmid pQEB1 and four of its variants |
tn7_crispr_elements | Genes of Tn7 and of Tn7-like transposons carrying a CRISPR-Cas system |