Merge pull request #64 from computational-cell-analytics/update_figures_chreef

The introduction of aliases was sufficient for the initial stage. Due to time constraints, improvements will be made at a later time. For now, it will be merged to reduce complications for other branches that depend on creating figures.

Author: schilling40

reproducibility/tonotopic_mapping/ChReef_GEK49L.json

@@ -0,0 +1,10 @@
+[
+    {
+		"cochlea": "G_EK_000049_L",
+		"component_list": [
+			1
+		],
+		"segmentation_channel": "SGN_v2",
+		"type": "sgn"
+	}
+]									

reproducibility/tonotopic_mapping/ChReef_GEK49R.json

@@ -0,0 +1,10 @@
+[
+    {
+		"cochlea": "G_EK_000049_R",
+		"component_list": [
+			1
+		],
+		"segmentation_channel": "SGN_v2",
+		"type": "sgn"
+	}
+]									

scripts/figures/plot_fig4.py

@@ -8,9 +8,9 @@
 import pandas as pd
 from flamingo_tools.s3_utils import BUCKET_NAME, create_s3_target
 
-from util import frequency_mapping, literature_reference_values
+from util import frequency_mapping  # , literature_reference_values
 
-INTENSITY_ROOT = "/mnt/vast-nhr/projects/nim00007/data/moser/cochlea-lightsheet/mobie_project/cochlea-lightsheet/tables/measurements"  # noqa
+INTENSITY_ROOT = "/mnt/vast-nhr/projects/nim00007/data/moser/cochlea-lightsheet/mobie_project/cochlea-lightsheet/tables/measurements2"  # noqa
 
 # The cochlea for the CHReef analysis.
 COCHLEAE = [
@@ -28,20 +28,49 @@
     "M_LR_000189_R",
 ]
 
+COCHLEAE_GERBIL = [
+    "G_EK_000049_L",
+    "G_EK_000049_R",
+]
+
+
+COCHLEAE_ALIAS = {
+    "M_LR_000143_L": "M0L",
+    "M_LR_000144_L": "M05L",
+    "M_LR_000145_L": "M06L",
+    "M_LR_000153_L": "M07L",
+    "M_LR_000155_L": "M08L",
+    "M_LR_000189_L": "M09L",
+    "M_LR_000143_R": "M0R",
+    "M_LR_000144_R": "M05R",
+    "M_LR_000145_R": "M06R",
+    "M_LR_000153_R": "M07R",
+    "M_LR_000155_R": "M08R",
+    "M_LR_000189_R": "M09R",
+    "G_EK_000049_L": "G1L",
+    "G_EK_000049_R": "G1R",
+}
+
 png_dpi = 300
 
 
-def get_chreef_data():
+def get_chreef_data(animal="mouse"):
     s3 = create_s3_target()
     source_name = "SGN_v2"
 
-    cache_path = "./chreef_data.pkl"
+    if animal == "mouse":
+        cache_path = "./chreef_data.pkl"
+        cochleae = COCHLEAE
+    else:
+        cache_path = "./chreef_data_gerbil.pkl"
+        cochleae = COCHLEAE_GERBIL
+
     if os.path.exists(cache_path):
         with open(cache_path, "rb") as f:
             return pickle.load(f)
 
     chreef_data = {}
-    for cochlea in COCHLEAE:
+    for cochlea in cochleae:
         print("Processsing cochlea:", cochlea)
         content = s3.open(f"{BUCKET_NAME}/{cochlea}/dataset.json", mode="r", encoding="utf-8")
         info = json.loads(content.read())
@@ -97,16 +126,20 @@ def group_lr(names_lr, values):
     return names, values_left, values_right
 
 
-def fig_04c(chreef_data, save_path, plot=False, plot_by_side=False):
+def fig_04c(chreef_data, save_path, plot=False, plot_by_side=False, use_alias=True):
     """Box plot showing the SGN counts of ChReef treated cochleae compared to healthy ones.
     """
     # Previous version with hard-coded values.
     # cochlea = ["M_LR_000144_L", "M_LR_000145_L", "M_LR_000151_R"]
     # alias = ["c01", "c02", "c03"]
     # sgns = [7796, 6119, 9225]
 
-    # TODO map the cochlea name to its alias
-    alias = [name.replace("_", "").replace("0", "") for name in chreef_data.keys()]
+    # TODO have central function for alias for all plots?
+    if use_alias:
+        alias = [COCHLEAE_ALIAS[k] for k in chreef_data.keys()]
+    else:
+        alias = [name.replace("_", "").replace("0", "") for name in chreef_data.keys()]
+
     sgns = [len(vals) for vals in chreef_data.values()]
 
     if plot_by_side:
@@ -138,14 +171,15 @@ def fig_04c(chreef_data, save_path, plot=False, plot_by_side=False):
     plt.legend(loc="upper center", bbox_to_anchor=(0.5, 1.11),
                ncol=3, fancybox=True, shadow=False, framealpha=0.8, fontsize=legendsize)
 
-    # set range of literature values
     xmin = -0.5
     xmax = len(alias) - 0.5
     plt.xlim(xmin, xmax)
-    lower_y, upper_y = literature_reference_values("SGN")
-    plt.hlines([lower_y, upper_y], xmin, xmax)
-    plt.text(1.5, lower_y - 400, "literature", color="C0", fontsize=main_tick_size, ha="center")
-    plt.fill_between([xmin, xmax], lower_y, upper_y, color="C0", alpha=0.05, interpolate=True)
+
+    # set range of literature values
+    # lower_y, upper_y = literature_reference_values("SGN")
+    # plt.hlines([lower_y, upper_y], xmin, xmax)
+    # plt.text(1.5, lower_y - 400, "literature", color="C0", fontsize=main_tick_size, ha="center")
+    # plt.fill_between([xmin, xmax], lower_y, upper_y, color="C0", alpha=0.05, interpolate=True)
 
     sgn_values = [11153, 11398, 10333, 11820]
     sgn_value = np.mean(sgn_values)
@@ -168,11 +202,13 @@ def fig_04c(chreef_data, save_path, plot=False, plot_by_side=False):
         plt.close()
 
 
-def fig_04d(chreef_data, save_path, plot=False, plot_by_side=False, intensity=False):
+def fig_04d(chreef_data, save_path, plot=False, plot_by_side=False, intensity=False, gerbil=False, use_alias=True):
     """Transduction efficiency per cochlea.
     """
-    # TODO map the cochlea name to its alias
-    alias = [name.replace("_", "").replace("0", "") for name in chreef_data.keys()]
+    if use_alias:
+        alias = [COCHLEAE_ALIAS[k] for k in chreef_data.keys()]
+    else:
+        alias = [name.replace("_", "").replace("0", "") for name in chreef_data.keys()]
 
     values = []
     for vals in chreef_data.values():
@@ -219,7 +255,10 @@ def fig_04d(chreef_data, save_path, plot=False, plot_by_side=False, intensity=Fa
     plt.legend(loc="upper center", bbox_to_anchor=(0.5, 1.11),
                ncol=3, fancybox=True, shadow=False, framealpha=0.8, fontsize=legendsize)
     if not intensity:
-        plt.ylim(0.5, 1.05)
+        if gerbil:
+            plt.ylim(0.3, 1.05)
+        else:
+            plt.ylim(0.5, 1.05)
 
     plt.tight_layout()
     plt.savefig(save_path, bbox_inches="tight", pad_inches=0.1, dpi=png_dpi)
@@ -230,12 +269,14 @@ def fig_04d(chreef_data, save_path, plot=False, plot_by_side=False, intensity=Fa
         plt.close()
 
 
-def fig_04e(chreef_data, save_path, plot, intensity=False):
+def fig_04e(chreef_data, save_path, plot, intensity=False, gerbil=False, use_alias=True):
 
     result = {"cochlea": [], "octave_band": [], "value": []}
     for name, values in chreef_data.items():
-        # TODO map name to alias
-        alias = name.replace("_", "").replace("0", "")
+        if use_alias:
+            alias = COCHLEAE_ALIAS[name]
+        else:
+            alias = name.replace("_", "").replace("0", "")
 
         freq = values["frequency[kHz]"].values
         if intensity:
@@ -264,7 +305,10 @@ def fig_04e(chreef_data, save_path, plot, intensity=False):
         band_label_offset_y = 0.09
     else:
         band_label_offset_y = 0.07
-        ax.set_ylim(0.45, 1.05)
+        if gerbil:
+            ax.set_ylim(0.05, 1.05)
+        else:
+            ax.set_ylim(0.45, 1.05)
 
     # Offsets within each octave band
     offset_map = {"L": -0.15, "R": 0.15}
@@ -336,28 +380,48 @@ def fig_04e(chreef_data, save_path, plot, intensity=False):
 def main():
     parser = argparse.ArgumentParser(description="Generate plots for Fig 4 of the cochlea paper.")
     parser.add_argument("--figure_dir", "-f", type=str, help="Output directory for plots.", default="./panels/fig4")
+    parser.add_argument("--no_alias", action="store_true")
     parser.add_argument("--plot", action="store_true")
     args = parser.parse_args()
 
+    use_alias = not args.no_alias
     os.makedirs(args.figure_dir, exist_ok=True)
 
     # Get the chreef data as a dictionary of cochlea name to measurements.
     chreef_data = get_chreef_data()
     # M_LR_00143_L is a complete outlier
     chreef_data.pop("M_LR_000143_L")
+    # remove other cochlea to have only pairs remaining
+    chreef_data.pop("M_LR_000143_R")
 
     # Create the panels:
 
     # C: The SGN count compared to reference values from literature and healthy
     # Maybe remove literature reference from plot?
-    fig_04c(chreef_data, save_path=os.path.join(args.figure_dir, "fig_04c"), plot=args.plot, plot_by_side=True)
+    fig_04c(chreef_data, save_path=os.path.join(args.figure_dir, "fig_04c"),
+            plot=args.plot, plot_by_side=True, use_alias=use_alias)
 
     # D: The transduction efficiency. We also plot GFP intensities.
-    fig_04d(chreef_data, save_path=os.path.join(args.figure_dir, "fig_04d_transduction"), plot=args.plot, plot_by_side=True)  # noqa
-    fig_04d(chreef_data, save_path=os.path.join(args.figure_dir, "fig_04d_intensity"), plot=args.plot, plot_by_side=True, intensity=True)  # noqa
-
-    fig_04e(chreef_data, save_path=os.path.join(args.figure_dir, "fig_04e_transduction"), plot=args.plot)
-    fig_04e(chreef_data, save_path=os.path.join(args.figure_dir, "fig_04e_intensity"), plot=args.plot, intensity=True)
+    fig_04d(chreef_data, save_path=os.path.join(args.figure_dir, "fig_04d_transduction"),
+            plot=args.plot, plot_by_side=True, use_alias=use_alias)
+    fig_04d(chreef_data, save_path=os.path.join(args.figure_dir, "fig_04d_intensity"),
+            plot=args.plot, plot_by_side=True, intensity=True, use_alias=use_alias)
+
+    fig_04e(chreef_data, save_path=os.path.join(args.figure_dir, "fig_04e_transduction"),
+            plot=args.plot, use_alias=use_alias)
+    fig_04e(chreef_data, save_path=os.path.join(args.figure_dir, "fig_04e_intensity"),
+            plot=args.plot, intensity=True, use_alias=use_alias)
+
+    chreef_data_gerbil = get_chreef_data(animal="gerbil")
+    fig_04d(chreef_data_gerbil, save_path=os.path.join(args.figure_dir, "fig_04d_gerbil_transduction"),
+            plot=args.plot, plot_by_side=True, gerbil=True, use_alias=use_alias)
+    fig_04d(chreef_data_gerbil, save_path=os.path.join(args.figure_dir, "fig_04d_gerbil_intensity"),
+            plot=args.plot, plot_by_side=True, intensity=True, use_alias=use_alias)
+
+    fig_04e(chreef_data_gerbil, save_path=os.path.join(args.figure_dir, "fig_04e_gerbil_transduction"),
+            plot=args.plot, gerbil=True, use_alias=use_alias)
+    fig_04e(chreef_data_gerbil, save_path=os.path.join(args.figure_dir, "fig_04e_gerbil_intensity"),
+            plot=args.plot, intensity=True, use_alias=use_alias)
 
 
 if __name__ == "__main__":