Plot ty data for each rep

Author: phuongho43

fluoressential/main.py

@@ -8,8 +8,8 @@
 from skimage import img_as_float
 from skimage.io import imread
 
-from fluoressential.plot import plot_bgd, plot_img
-from fluoressential.process import calc_imgs_cmax, list_img_fps, subtract_bgd
+from fluoressential.plot import plot_bgd, plot_img, plot_ty
+from fluoressential.process import calc_dF_F0, calc_imgs_cmax, list_img_fps, subtract_bgd
 
 
 def img_task(img_fp, results_dp, sub_bgd_kwargs, plot_img_kwargs):
@@ -41,6 +41,7 @@ def analyze_imgs(rep_dp, gau_scale=1, vert_scale=2, ct_cutoff=0.1, cmax=None, sh
     df = pd.DataFrame(data)
     y_csv_fp = results_dp / "y.csv"
     df.to_csv(y_csv_fp, index=False)
+    return df
 
 
 def main():
@@ -80,7 +81,12 @@ def main():
     for class_dp in [Path(class_dp) for class_dp in class_dps]:
         for rep_dp in [dp for dp in natsorted(class_dp.glob("*")) if dp.is_dir()]:
             print(rep_dp)
-            analyze_imgs(rep_dp, gau_scale=4, vert_scale=2, ct_cutoff=0.05, cmax=None, show_cbar=True, sbar_microns=22, t_unit="s")
+            ty_df = analyze_imgs(rep_dp, gau_scale=4, vert_scale=2, ct_cutoff=0.05, cmax=None, show_cbar=True, sbar_microns=22, t_unit="s")
+            ty_df = calc_dF_F0(ty_df.astype(float))
+            fig_fp = rep_dp / "results" / "y.png"
+            xlabel = "Time (s)"
+            ylabel = r"$\mathbf{\Delta F/F_{0}}$"
+            plot_ty(fig_fp, ty_df, xlabel=xlabel, ylabel=ylabel)
 
     ## RFP Reporter Expression ##
     ## 293T Input Intensity ##

fluoressential/plot.py

@@ -99,8 +99,24 @@ def plot_bgd(fig_fp, img, bgd):
         bg_rows = np.argsort(np.var(img, axis=1))[-100:-1:10]
         row_i = np.random.choice(bg_rows.shape[0])
         bg_row = bg_rows[row_i]
-        fig, ax = plt.subplots(figsize=(24, 20))
+        fig, ax = plt.subplots(figsize=(24, 16))
         ax.plot(img[bg_row, :], color="#648FFF")
         ax.plot(bgd[bg_row, :], color="#785EF0")
         fig.savefig(fig_fp, dpi=100)
     plt.close("all")
+
+
+def plot_ty(fig_fp, ty_df, xlabel, ylabel):
+    fig_fp = Path(fig_fp)
+    fig_fp.parent.mkdir(parents=True, exist_ok=True)
+    with sns.axes_style("whitegrid"), mpl.rc_context(STYLE):
+        fig, ax = plt.subplots(figsize=(24, 16))
+        sns.lineplot(ax=ax, data=ty_df, x="t", y="y", color="#785EF0")
+        ax.set_xlabel(xlabel)
+        ax.set_ylabel(ylabel)
+        ax.locator_params(axis="x", nbins=10)
+        ax.locator_params(axis="y", nbins=10)
+        fig.tight_layout()
+        fig.canvas.draw()
+        fig.savefig(fig_fp, dpi=100)
+    plt.close("all")

fluoressential/process.py

@@ -72,3 +72,10 @@ def calc_imgs_cmax(imgs_dp, sub_bgd_kwargs):
     max_img = subtract_bgd(img_as_float(imread(max_img_fp)), **sub_bgd_kwargs)[0]
     cmax = np.percentile(max_img, 99.99)
     return cmax
+
+
+def calc_dF_F0(y_df):
+    F0 = y_df["y"].iloc[:5].mean()
+    dF = y_df["y"] - F0
+    y_df["y"] = dF / F0
+    return y_df

fluoressential/style.py

@@ -1,7 +1,7 @@
 PALETTE = ["#8069EC", "#EA822C", "#2ECC71", "#D143A4", "#F1C40F", "#34495E", "#648FFF"]
 
 STYLE = {
-    "figure.figsize": (24, 20),
+    "figure.figsize": (24, 16),
     "lines.linewidth": 16,
     "lines.markersize": 24,
     "lines.markeredgecolor": "#212121",
@@ -28,10 +28,10 @@
     "ytick.major.size": 36,
     "xtick.major.width": 12,
     "ytick.major.width": 12,
-    "xtick.minor.size": 12,
-    "ytick.minor.size": 12,
-    "xtick.minor.width": 4,
-    "ytick.minor.width": 4,
+    "xtick.minor.size": 18,
+    "ytick.minor.size": 18,
+    "xtick.minor.width": 6,
+    "ytick.minor.width": 6,
     "legend.fontsize": 64,
     "legend.handletextpad": 0.4,
     "legend.labelspacing": 0.4,