Brand new streamgraph API

README.md

@@ -99,11 +99,11 @@ X9,0.7232472324723247,0.7352941176470589,...,0.8066914498141264,0.0
 
 |[Stacked Barplot](https://github.com/PopovIILab/KrakenParser/wiki/Stacked-Barplot-API)|[Streamgraph](https://github.com/PopovIILab/KrakenParser/wiki/Streamgraph-API)|
 |-------|-------|
-|![kpstbar](https://github.com/user-attachments/assets/916b0164-28be-4f49-9634-707408487b85)|![kpstream](https://github.com/user-attachments/assets/5c6d930c-e85f-4e2e-9dbf-8caefca49a76)|
+|![kpstbar](https://github.com/user-attachments/assets/916b0164-28be-4f49-9634-707408487b85)|![kpstream](https://github.com/user-attachments/assets/8fc09fdb-e397-4c39-9290-ad11da5335a8)|
 
 [Stacked Barplot + Streamgraph](https://github.com/PopovIILab/KrakenParser/wiki/Combined-Stacked-Barplot-&-Streamgraph)|[Clustermap](https://github.com/PopovIILab/KrakenParser/wiki/Clustermap)|
 |-------|-------|
-|![combined_white](https://github.com/user-attachments/assets/58acea93-f079-46fd-ac4b-d2ac83098c59)|![kpclust](https://github.com/user-attachments/assets/98a4d540-7c43-4802-8f77-277a5637a7a1)|
+|![combined_white](https://github.com/user-attachments/assets/48b3f6e3-6dd5-4298-a793-23dcd549e90c)|![kpclust](https://github.com/user-attachments/assets/98a4d540-7c43-4802-8f77-277a5637a7a1)|
 
 ## Quick Start (Full Pipeline)
 To run the full pipeline, use the following command:
@@ -263,10 +263,10 @@ data/
 │  │  ├─ counts_family.txt
 │  │  ├─ ...
 │  └─ csv/                 # Total abundance CSV output
-│  │  ├─ counts_species.csv
-│  │  ├─ counts_genus.csv
-│  │  ├─ counts_family.csv
-│  │  ├─ ...
+│     ├─ counts_species.csv
+│     ├─ counts_genus.csv
+│     ├─ counts_family.csv
+│     ├─ ...
 ├─ rel_abund/              # Relative abundance CSV output
 │  ├─ ra_species.csv
 │  ├─ ra_genus.csv

krakenparser/kpplot/streamgraph.py

@@ -19,6 +19,7 @@ def streamgraph(
     sample_order: Optional[List[str]] = None,
     figsize: Tuple[int, int] = (14, 7),
     cmap: Optional[Union[str, List[str]]] = "tab20",
+    bar_width: float = 0.6,
     fill_alpha: float = 1.0,
     edgecolor: Optional[str] = None,
     edge_linewidth: float = 0.3,
@@ -137,11 +138,15 @@ def streamgraph(
 
     colors = [color_dict[col] for col in df_plot.columns]
 
+    centers = np.arange(len(df_plot.index))
+    xs = np.column_stack((centers - bar_width / 2, centers + bar_width / 2)).flatten()
+
     fig, ax = plt.subplots(figsize=figsize, facecolor=background_color)
 
+    ys = np.repeat(df_plot.values.T, 2, axis=1)
     layers = ax.stackplot(
-        df_plot.index,
-        df_plot.values.T,
+        xs,
+        ys,
         labels=df_plot.columns,
         colors=colors,
         alpha=fill_alpha,
@@ -187,10 +192,9 @@ def streamgraph(
     if grid:
         ax.grid(axis="x", linestyle=grid_linestyle, alpha=grid_alpha, zorder=0)
 
-    positions = np.arange(len(df_plot.index))
     labels = df_plot.index.tolist()
     plt.xticks(
-        positions,
+        centers,
         labels,
         rotation=xticks_rotation,
         ha=xticks_ha,

krakenparser/version.py

@@ -1 +1 @@
-__version__ = "0.6.0"
+__version__ = "0.6.1"