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Plotting

Use plot_results to visualize colony results as:

  • heatmap
  • bubble
from gitter_py import gitter, plot_results

df = gitter("examples/extdata/sample.jpg", plate_format=1536, verbose="n")

heatmap = plot_results(df, kind="heatmap", title="Colony size heatmap")
heatmap.savefig("heatmap.png", dpi=200)

bubble = plot_results(df, kind="bubble", title="Colony size bubble plot")
bubble.savefig("bubble.png", dpi=200)

Flagged colonies are overlaid when show_flags=True (default) and flag data exists.

Optional CLI example

gitter run examples/extdata/sample.jpg --out sample.csv
gitter plot sample.csv --plot-type heatmap --out heatmap.png
gitter plot sample.csv --plot-type bubble --out bubble.png