Add examples with real data.

examples/pr_fig_4.py

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+import pyranges as pr
+import pyranges_plot as prp
+
+prp.set_engine("plotly")
+
+## Sars cov 2
+# http://ftp.ensemblgenomes.org/pub/viruses/gtf/sars_cov_2/Sars_cov_2.ASM985889v3.101.gtf.gz
+p = pr.read_gtf(
+    "../../performance/sars_cov_2/Sars_cov_2.ASM985889v3.101.gtf"
+)  ## modify if needed
+
+p_cds = p[p["Feature"] == "CDS"]
+
+prp.plot(p_cds, id_col="gene_name", text=False, legend=True, to_file="fig_4.png")

examples/time_test.py

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+import pyranges as pr
+import pyranges_plot as prp
+import time
+from memory_profiler import memory_usage
+
+
+prp.set_engine("plt")
+prp.set_warnings(False)
+
+# https://ftp.ensembl.org/pub/release-112/gtf/drosophila_melanogaster/Drosophila_melanogaster.BDGP6.46.112.gtf.gz
+chrom = "X"
+feat = "CDS"
+
+start_loading_t = time.time()
+start_loading_m = memory_usage()[0]
+
+path = "drosophila/Drosophila_melanogaster.BDGP6.46.112.gtf"  ## modify if needed
+d = pr.read_gtf(path)
+
+end_loading_t = time.time()
+end_loading_m = memory_usage()[0]
+
+# Get CDS
+d_cds = d[d["Feature"] == feat]
+
+# Check number of genes in each chrom
+# d_cds.groupby("Chromosome").apply(
+#     lambda x: print(
+#         "CHROM:"
+#         + str(x["Chromosome"].iloc[0])
+#         + ":   "
+#         + str(len(x.groupby("gene_id")))
+#     )
+# )
+
+# Chromosome subset
+d_cds_chrom = d_cds[d_cds["Chromosome"] == chrom]
+
+
+end_subset_t = time.time()
+end_subset_m = memory_usage()[0]
+
+prp.plot(d_cds_chrom, id_col="gene_id", to_file="_tmp.png", max_shown=3000)
+
+end_plot_t = time.time()
+end_plot_m = memory_usage()[0]
+
+print("==============================================================")
+print(f"Drosophila melanogaster | Chromosome {chrom} | Feature {feat}\n")
+
+print("Loading time: \t" + str(end_loading_t - start_loading_t) + " (s)")
+print("Loading memory:\t" + str(end_loading_m - start_loading_m) + " (MiB)")
+print()
+print("Subsetting time: \t" + str(end_subset_t - end_loading_t) + " (s)")
+print("Subsetting memory: \t" + str(end_subset_m - end_loading_m) + " (MiB)")
+print()
+print("Plotting and exporting time: \t" + str(end_plot_t - end_subset_t) + " (s)")
+print("Plotting and exporting memory: \t" + str(end_plot_m - end_subset_m) + " (MiB)")
+print("\n\n\n")