pavlin-policar/openTSNE

How to download 'macosko_2015.pkl.gz' & How to save plot result as figures file

buaalyx opened this issue · 0 comments

question one :
I'm running the openTSNE/examples/01_simple_usage.ipynb, and get the follow error message
`FileNotFoundError: [Errno 2] No such file or directory: 'data/macosko_2015.pkl.gz'
How to download the example datasets?

question two :
I want to fit my own dataset, I wrote the following code snippets:

    logits = model.get_embedding(G, feat_key, target).cpu()
    logit_array = logits.detach().numpy()
    tsne = TSNE(
        perplexity=50,
        metric="euclidean",
        n_jobs=8,
        random_state=42,
        verbose=True
    )
    embedding_train = tsne.fit(logit_array)
    fig, ax = plt.subplots(1, 1, figsize=(15, 15))
    utils.plot(embedding_train, labels, colors=utils.MACOSKO_COLORS)
    plt.tight_layout()
    plt.savefig('tsne.jpeg')

it seems embedding_train fits well, the shape is (n,2),and I change key of the colors dict of MASCO as the labels value, something like
MACOSKO_COLORS = { 0: "#A5C93D", 1: "#8B006B", 2: "#2000D7", 3: "#538CBA", 4: "#8B006B" }

But there is no point in tsne.jpeg, only the colors label
image

sorry I can't find the problem, and will you provide an simple example to save figure? Hope to get reply.