Merge pull request #19 from cbib/viz-typos

Viz typos

src/dimet/config/analysis/method/abundance_plot.yaml

@@ -11,7 +11,7 @@ height_each_subfig: !!float 5.5
 palette: 'pastel'
 
 x_text_modify_as: null # or a list of float, int or str, e.g ['0h', '4h'] or [0, 4] according to the x ticks
-as_grid : False
+as_grid : False # if True will work when few (<20) metabolites by compartment
 
 do_stripplot: True
 

src/dimet/config/analysis/method/mean_enrichment_line_plot.yaml

@@ -6,10 +6,24 @@ name: Generate Mean Enrichment line plots
 figure_format: svg
 
 color_lines_by: condition # condition|metabolite
-palette_condition: muted # seaborn/matplotlib palette. Has effect if color_lines_by condition
-palette_metabolite: auto_multi_color # auto_multi_color|PATH_TO_COLOR.csv.  Has effect if color_lines_by metabolite
+palette_condition: muted # a seaborn or matplotlib palette name. Has effect if color_lines_by condition
+palette_metabolite: auto_multi_color # auto_multi_color|[or user defined key-value pairs, see below]  Has effect if color_lines_by metabolite
 xaxis_title: Time # Days|Hours|Minutes|Seconds|Time ...
 alpha: 1  # 0 for transparent, 1 max intensity
 plot_grouped_by_dict : null # cell : 0 : [Cit, Iso-cit] will display both in same plane
 height_subplot: !!float 4.8
 as_grid : False
+
+# - - keep deactivated below this line --
+# # example of palette_metabolite set as user defined key-value pairs :
+#palette_metabolite:  # missing metabolites will be internally set as gray
+#  Fumaric_acid: cadetblue
+#  Glycine: darkviolet
+#  L-Alanine: orangered
+#  L-Arginine: pink
+#  L-Asparagine: "#AFB83B"
+#  L-Aspartic_acid: "#FBF312"
+#  L-Glutamic_acid: "#FF8D85"
+#  L-Malic_acid: darkcyan
+
+

src/dimet/method/__init__.py

@@ -115,7 +115,7 @@ class MeanEnrichmentLinePlotConfig(MethodConfig):
     xaxis_title: str = "Time"
     color_lines_by: str = "condition"  # or  "metabolite"
     palette_condition: str = "paired"  # seaborn/matplotlib pals
-    palette_metabolite: str = "auto_multi_color"  # or .csv path
+    palette_metabolite: Union[str, dict] = "auto_multi_color"
     height_subplot: float = 4.3
     as_grid: Union[bool, None] = False
 

src/dimet/visualization/abundance_bars.py

@@ -53,7 +53,6 @@ def plot_one_metabolite(df: pd.DataFrame,
     returns a single object of type matplotlib.axes
     with the individual metabolite plot
     """
-    plt.rcParams.update({"font.size": 21})
     sns.barplot(
         ax=curr_ax,
         x=axisx_var,
@@ -120,7 +119,7 @@ def plot_abundance_bars_no_grid(
             output_directory,
             f"bars_{CO}_{selected_metabolites[k]}-{SMX}"
             f".{cfg.analysis.method.figure_format}")
-
+        plt.rcParams.update({"font.size": 21})
         fig_this_metabolite, axs_k = plt.subplots(
             nrows=1, ncols=1,
             figsize=(width_each_subfig, height_each_subfig))
@@ -129,6 +128,7 @@ def plot_abundance_bars_no_grid(
                                     cfg.analysis.method.palette,
                                     axs_k,
                                     cfg.analysis.method.do_stripplot)
+        axs_k = apply_advanced_param_custom_x_labs(cfg, axs_k)
         if k == 0:  # collect the legend, which is same for any plot
             thehandles, thelabels = axs_k.get_legend_handles_labels()
         axs_k.legend_.remove()
@@ -148,6 +148,17 @@ def plot_abundance_bars_no_grid(
     logger.info(f"Saved abundance plots in {output_directory}")
 
 
+def apply_advanced_param_custom_x_labs(cfg, curr_axs):
+    if cfg.analysis.method.x_text_modify_as is not None:
+        xticks_text_l: list = cfg.analysis.method.x_text_modify_as
+        try:
+            xticks_text_l = [str(i) for i in xticks_text_l]
+            curr_axs.set_xticklabels(xticks_text_l)
+        except Exception as e:
+            print(e, "The argument 'x_text_modify_as' is incorrectly set")
+    return curr_axs
+
+
 def plot_as_grid_of_bars(
         piled_sel_df: pd.DataFrame, selected_metabolites: List[str],
         CO: str, SMX: str,
@@ -166,7 +177,7 @@ def plot_as_grid_of_bars(
     corrector_factor = 0.7
     total_height_grid = height_each_subfig * len(selected_metabolites) + \
         (corrector_factor * 7 * len(selected_metabolites))
-
+    plt.rcParams.update({"font.size": 21})
     fig, axs = plt.subplots(
         nrows=len(selected_metabolites), ncols=1,
         sharey=False, figsize=(width_each_subfig, total_height_grid))
@@ -182,13 +193,7 @@ def plot_as_grid_of_bars(
                                      axs[i],
                                      cfg.analysis.method.do_stripplot)
 
-        if cfg.analysis.method.x_text_modify_as is not None:
-            xticks_text_l: list = cfg.analysis.method.x_text_modify_as
-            try:
-                xticks_text_l = [str(i) for i in xticks_text_l]
-                axs[i].set_xticklabels(xticks_text_l)
-            except Exception as e:
-                print(e, "The argument 'x_text_modify_as' is incorrectly set")
+        axs[i] = apply_advanced_param_custom_x_labs(cfg, axs[i])
 
     thehandles, thelabels = axs[-1].get_legend_handles_labels()
     for i in range(len(selected_metabolites)):

src/dimet/visualization/distr_fit_plot.py

@@ -176,5 +176,5 @@ def run_distr_fit_plot(
                 run_dist_fit_plot_pairwise(df, dataset, cfg, comparison,
                                            test, out_file_path)
         # elif mode == "time_course":
-        #     pass  # not implemented to date, evaluate if worthed
+        #     pass  # not implemented to date, evaluate if worth it
         logger.info(f"saved plots to {out_plot_dir}")

src/dimet/visualization/mean_enrichment_line_plot.py

@@ -123,21 +123,24 @@ def plot_one_metabolite(metabolite_name: str,
     If several metabolites in input dataframes,
     they will be plotted sharing axes in same plane.
     """
-    sns.lineplot(
-        ax=axs_z,  # starts in 1 (after the empty row index 0)
-        x="timenum",
-        y="Fractional Contribution (%)",
-        hue=color_lines_by,
-        style="condition",
-        err_style=None,
-        alpha=alpha_conf,
-        linewidth=4.5,
-        palette=palette_option[color_lines_by],
-        zorder=1,
-        data=metabolite_df,
-
-        legend=True,
-    )
+    if len(list(metabolite_df['timenum'].unique())) > 1:
+        sns.lineplot(
+            ax=axs_z,  # starts in 1 (after the empty row index 0)
+            x="timenum",  y="Fractional Contribution (%)",
+            hue=color_lines_by,
+            style="condition",
+            err_style=None,
+            alpha=alpha_conf,
+            linewidth=4.5,
+            palette=palette_option[color_lines_by],
+            zorder=1, data=metabolite_df,
+            legend=True)
+    else:  # when only one time point line is impossible, do scatter (dots)
+        sns.scatterplot(
+            ax=axs_z, x="timenum", y="Fractional Contribution (%)",
+            hue=color_lines_by, style="condition", alpha=alpha_conf, s=40,
+            palette=palette_option[color_lines_by], zorder=1, legend=True,
+            data=metabolite_df)
     axs_z.set_xticks([float(i) for i in time_ticks])
 
     axs_z.scatter(
@@ -149,10 +152,7 @@ def plot_one_metabolite(metabolite_name: str,
         mean_and_sd_metabolite_df["timenum"],
         mean_and_sd_metabolite_df["mean"],
         yerr=mean_and_sd_metabolite_df["sd"],
-        fmt="none",
-        capsize=3.5,
-        ecolor="black",
-        zorder=2
+        fmt="none", capsize=3.5, ecolor="black", zorder=2
     )
     axs_z.set_ylabel("Fractional Contribution (%)", size=19),
     axs_z.set(xlabel=xaxis_title)
@@ -300,34 +300,48 @@ def give_colors_by_metabolite(cfg: DictConfig,
                    "mediumturquoise", "darkcyan", "teal", "cadetblue",
                    "slategrey", "steelblue", "navy", "darkslateblue",
                    "blueviolet",
-                   "darkochid", "purple", "mediumvioletred", "crimson"]
+                   "darkorchid", "purple", "mediumvioletred", "crimson"]
 
     colors_dict = dict()
 
+    tmp = set()
+    for co in metabolites_numbered_dict.keys():
+        for k in metabolites_numbered_dict[co].keys():
+            tmp.update(set(metabolites_numbered_dict[co][k]))
+    metabolites = sorted(list(tmp))
+
     if cfg.analysis.method.palette_metabolite == "auto_multi_color":
-        tmp = set()
-        for co in metabolites_numbered_dict.keys():
-            for k in metabolites_numbered_dict[co].keys():
-                tmp.update(set(metabolites_numbered_dict[co][k]))
-        metabolites = sorted(list(tmp))
         if len(metabolites) <= 12:
             # default Paired palette for coloring individual metabolites
             palettecols = sns.color_palette("Paired", 12)
             for i in range(len(metabolites)):
                 colors_dict[metabolites[i]] = palettecols[i]
-        else:  # more than 12 colors obliges to set them manually
+        elif (len(metabolites) > 12) and (
+                len(metabolites) <= len(handycolors)):
             for i in range(len(metabolites)):
                 colors_dict[metabolites[i]] = handycolors[i]
-    else:  # argument_color_metabolites is a csv file
+        elif len(metabolites) > 30:
+            logger.error(
+                "Error: > %s metabolites: wrong combination of params "
+                " color_lines_by and palette_metabolite options. Please set  "
+                "color_lines_by as 'condition'; or alternatively give key-"
+                "value pairs in palette_metabolite", (len(handycolors)))
+            raise ValueError
+    else:  # argument_color_metabolites is a key-value dict (set in yaml)
         try:
-            file_containing_colors = cfg.analysis.method.palette_metabolite
-            df = pd.read_csv(file_containing_colors, header=0)
-            for i, row in df.iterrows():
-                metabolite = df.iloc[i, 0]  # first column metabolite
-                color = df.iloc[i, 1]  # second column is color
-                colors_dict[metabolite] = color
+            # fill the user blanks with dimgray color by default
+            for metabolite in metabolites:
+                try:
+                    colors_dict[metabolite] = (
+                        cfg.analysis.method.palette_metabolite[metabolite])
+                except KeyError:
+                    colors_dict[metabolite] = "dimgray"
+                except Exception as e:
+                    colors_dict[metabolite] = "dimgray"
+                    logger.info(e, "user color not readable, continuing")
+
         except Exception as e:
-            logger.info(e, f"\n could not assign color, wrong csv file: \
+            logger.info(e, f"\n could not assign color : \
                    {cfg.analysis.method.palette_metabolite}")
             colors_dict = None
 

tests/test_abundance_bars.py

@@ -76,6 +76,7 @@ def test_plot_abundance_bars_no_grid(self):
         cfg_m = DictConfig({'analysis': {
             'method': {'palette': 'dark',
                        'do_stripplot': False,
+                       'x_text_modify_as': None,
                        'figure_format': 'svg'}
             }
         })