Fix colormap and thick_cds bugs.

pyranges · Jun 17, 2024 · f4450c4 · f4450c4
1 parent 6c2656a
commit f4450c4
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Showing 5 changed files with 19 additions and 77 deletions.
diff --git a/src/pyranges_plot/data_preparation.py b/src/pyranges_plot/data_preparation.py
@@ -339,17 +339,17 @@ def chrmd_limits(chrmd_df, limits):
     # pyranges object
     elif type(limits) is pr.PyRanges:
         # create dict to map limits
-        limits_df = limits.df
-        limits_chrmd_df = limits_df.groupby(
+        limits_chrmd_df = limits.groupby(
             CHROM_COL, group_keys=False, observed=True
         ).agg({START_COL: "min", END_COL: "max"})
-        limits_chrmd_dict = limits_chrmd_df.to_dict(orient="index")
+        # limits_chrmd_dict = limits_chrmd_df.to_dict(orient="index")
 
         # function to get matching values from limits_chrmd_df
         def make_min_max(row):
-            chromosome = str(row.name)
-            limits = limits_chrmd_dict.get(chromosome)
-            if limits:
+            chromosome = row.name[0]
+            if chromosome in limits_chrmd_df.index:
+                limits = limits_chrmd_df.loc[chromosome]
+
                 return (
                     limits[START_COL],
                     limits[END_COL],
@@ -363,7 +363,8 @@ def make_min_max(row):
     # dictionary as limits
     else:
         chrmd_df["min_max"] = [
-            limits.get(index) for index in chrmd_df.index
+            limits.get(index)
+            for index in list(chrmd_df.index.get_level_values(CHROM_COL))
         ]  # fills with None the chromosomes not specified
 
 

diff --git a/src/pyranges_plot/example_data.py b/src/pyranges_plot/example_data.py
diff --git a/src/pyranges_plot/matplotlib_base/data2plot.py b/src/pyranges_plot/matplotlib_base/data2plot.py
@@ -118,7 +118,11 @@ def apply_gene_bridge(
     # If transcript structure subtract exons
     if transcript_str:
         cds = df[df["Feature"] == "CDS"]
-        exons = df[df["Feature"] == "exon"].subtract_ranges(cds)
+        exons = df[df["Feature"] == "exon"]
+
+        # if there are exons and cds, subtract
+        if sum([cds.empty, exons.empty]) == 2:
+            exons = exons.subtract_ranges(cds)
         df = pr.concat([cds, exons])
 
     # Define depth order

diff --git a/src/pyranges_plot/plot_main.py b/src/pyranges_plot/plot_main.py
@@ -88,7 +88,7 @@ def plot(
         they do not overlap) and False for unpacked (one row per gene).
 
     color_col: str, default None
-        Name of the column used to color the genes.
+        Name of the column used to color the genes. If not specified, id_col will be used.
 
     thickness_col: str, default None
         Name of the data column with max 2 different values to plot the intervals correspondig to one value to

diff --git a/src/pyranges_plot/plotly_base/data2plot.py b/src/pyranges_plot/plotly_base/data2plot.py
@@ -127,7 +127,11 @@ def apply_gene_bridge(
     # If transcript structure subtract exons
     if transcript_str:
         cds = df[df["Feature"] == "CDS"]
-        exons = df[df["Feature"] == "exon"].subtract_ranges(cds)
+        exons = df[df["Feature"] == "exon"]
+
+        # if there are exons and cds, subtract
+        if sum([cds.empty, exons.empty]) == 2:
+            exons = exons.subtract_ranges(cds)
         df = pr.concat([cds, exons])
 
     # Define depth order