add example scripts

examples/create_tsv.py

+from wela.dataloader import dataloader
+
+datasets = ["Pdr5_3_11_22", "Pdr5_flc_10ugml_1676"]
+for dataname in datasets:
+    dl = dataloader(
+        h5dir="/Users/pswain/ecdf/swainlab/aliby_datasets/ivan",
+        wdir="/Users/pswain/wip/tsv_data",
+    )
+    dl.load(dataname, key_index="median_GFP")
+    dl.save()

examples/plot_kymograph.py

+from wela.dataloader import dataloader
+from wela.plotting import kymograph, plot_lineage
+
+# from genutils import figs2pdf
+import matplotlib.cm
+
+
+datasets = ["Pdr5_3_11_22", "Pdr5_flc_10ugml_1676"]
+for dataname in datasets:
+    dl = dataloader(".", "/Users/pswain/wip/tsv_data")
+    dl.load(dataname, use_tsv=True)
+    df = dl.get_sorted_df("median_GFP")
+
+    title = dataname.split(".")[0]
+    kymograph(df, hue="buddings", title=title)
+    kymograph(df, hue="median_GFP", title=title)
+    kymograph(
+        df,
+        hue="bud_growth_rate",
+        title=title,
+        vmin=-50,
+        vmax=50,
+        cmap=matplotlib.cm.Spectral,
+    )
+    # df.id = df.id.astype("object")
+    # df.to_csv(dataname + ".tsv", sep="\t", index=False)
+# figs2pdf("fluconazole")
+
+if False:
+    plot_lineage(dl.ids[34], dl.df)

examples/run_gr.py

+from wela.growth_rate import find_all_grs, add_to_dataloader
+from wela.dataloader import dataloader
+
+run_GP = False
+
+wdir = "/Users/pswain/wip/tsv_data"
+datasets = ["Pdr5_3_11_22", "Pdr5_flc_10ugml_1676"]
+
+# it is better to run dataloader first to generate a tsv file
+# to run directly on h5 files, add use_tsv=False
+
+for dataname in datasets:
+    if run_GP:
+        # generate pkl files and pdf files for inspection
+        # run first with max_no_cells=2 to check the results
+        find_all_grs(dataname, max_no_cells=None, wdir=wdir)
+    else:
+        # add pkl files to df
+        dl = dataloader(wdir=wdir)
+        dl.load(dataname, use_tsv=True)
+        add_to_dataloader(dl, wdir)