From 47aac80b584754d360fc20b60afaa2c9aeabb6d4 Mon Sep 17 00:00:00 2001
From: "Abolfazl (Abe)" <abea@arcinstitute.org>
Date: Tue, 21 May 2024 13:07:52 -0700
Subject: [PATCH 01/27] add option to only highlight dots

---
 screenpro/plotting.py | 54 ++++++++++++++++++++++++-------------------
 1 file changed, 30 insertions(+), 24 deletions(-)

diff --git a/screenpro/plotting.py b/screenpro/plotting.py
index 99f2f56..df33575 100644
--- a/screenpro/plotting.py
+++ b/screenpro/plotting.py
@@ -106,7 +106,7 @@ def plot_volcano(ax, df_in, threshold, up_hit='resistance_hit', down_hit='sensit
     ax.legend()
 
 
-def label_as_black(ax, df_in, label, threshold, size=2, size_txt=None, 
+def label_as_black(ax, df_in, label, threshold, size=2, size_txt="auto",
                    ctrl_label = 'no-targeting',
                    t_x=.5, t_y=-0.1):
     df = prep_data(df_in, threshold, ctrl_label)
@@ -117,17 +117,19 @@ def label_as_black(ax, df_in, label, threshold, size=2, size_txt=None,
     ax.scatter(target_data['score'], target_data['-log10(pvalue)'],
                s=size, linewidth=0.5, edgecolors='black', facecolors='black', label='target')
 
-    if not size_txt:
+    if size_txt == None:
+        pass
+    elif size_txt == 'auto':
         size_txt = size * 2
+    else:
+        # Annotate the points
+        for i, _ in enumerate(target_data['target']):
+            txt = target_data['target'].iloc[i]
+            ax.annotate(txt, (target_data['score'].iloc[i] + t_x, target_data['-log10(pvalue)'].iloc[i] + t_y),
+                        color='black', size=size_txt)
 
-    # Annotate the points
-    for i, _ in enumerate(target_data['target']):
-        txt = target_data['target'].iloc[i]
-        ax.annotate(txt, (target_data['score'].iloc[i] + t_x, target_data['-log10(pvalue)'].iloc[i] + t_y),
-                    color='black', size=size_txt)
 
-
-def label_sensitivity_hit(ax, df_in, label, threshold, size=2, size_txt=None,
+def label_sensitivity_hit(ax, df_in, label, threshold, size=2, size_txt="auto",
                           ctrl_label = 'no-targeting',
                           t_x=.5, t_y=-0.1):
     df = prep_data(df_in, threshold, ctrl_label)
@@ -138,17 +140,19 @@ def label_sensitivity_hit(ax, df_in, label, threshold, size=2, size_txt=None,
     ax.scatter(target_data['score'], target_data['-log10(pvalue)'],
                s=size, linewidth=0.5, edgecolors='black', facecolors='#3182bd', label='target')
 
-    if not size_txt:
+    if size_txt == None:
+        pass
+    elif size_txt == 'auto':
         size_txt = size * 2
-
-    # Annotate the points
-    for i, _ in enumerate(target_data['target']):
-        txt = target_data['target'].iloc[i]
-        ax.annotate(txt, (target_data['score'].iloc[i] + t_x, target_data['-log10(pvalue)'].iloc[i] + t_y),
-                    color='black', size=size_txt)
+    else:
+        # Annotate the points
+        for i, _ in enumerate(target_data['target']):
+            txt = target_data['target'].iloc[i]
+            ax.annotate(txt, (target_data['score'].iloc[i] + t_x, target_data['-log10(pvalue)'].iloc[i] + t_y),
+                        color='black', size=size_txt)
 
 
-def label_resistance_hit(ax, df_in, label, threshold, size=2, size_txt=None, 
+def label_resistance_hit(ax, df_in, label, threshold, size=2, size_txt="auto",
                          ctrl_label = 'no-targeting',
                          t_x=.5, t_y=-0.1):
     df = prep_data(df_in, threshold, ctrl_label)
@@ -159,14 +163,16 @@ def label_resistance_hit(ax, df_in, label, threshold, size=2, size_txt=None,
     ax.scatter(target_data['score'], target_data['-log10(pvalue)'],
                s=size, linewidth=0.5, edgecolors='black', facecolors='#de2d26', label='target')
 
-    if not size_txt:
+    if size_txt == None:
+        pass
+    elif size_txt == 'auto':
         size_txt = size * 2
-
-    # Annotate the points
-    for i, _ in enumerate(target_data['target']):
-        txt = target_data['target'].iloc[i]
-        ax.annotate(txt, (target_data['score'].iloc[i] + t_x, target_data['-log10(pvalue)'].iloc[i] + t_y),
-                    color='black', size=size_txt)
+    else:
+        # Annotate the points
+        for i, _ in enumerate(target_data['target']):
+            txt = target_data['target'].iloc[i]
+            ax.annotate(txt, (target_data['score'].iloc[i] + t_x, target_data['-log10(pvalue)'].iloc[i] + t_y),
+                        color='black', size=size_txt)
 
 
 def plotReplicateScatter(ax, adat_in, x, y, title, min_val=None, max_val=None, log_transform=True):

From 8340fef9a1c9dc4ae004c72a9b14d6f1aba2c167 Mon Sep 17 00:00:00 2001
From: "Abolfazl (Abe)" <abea@arcinstitute.org>
Date: Wed, 22 May 2024 00:01:17 -0700
Subject: [PATCH 02/27] add `getAnnotatedTable` function

---
 screenpro/assays.py | 44 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)

diff --git a/screenpro/assays.py b/screenpro/assays.py
index 3ffb958..cebc303 100644
--- a/screenpro/assays.py
+++ b/screenpro/assays.py
@@ -216,6 +216,50 @@ def getPhenotypeScores(self, run_name, score_name, threshold=5, ctrl_label='negC
 
         return out
 
+    def getAnnotatedTable(self, run_name, threshold=5, ctrl_label='negCtrl', target_col='target',pvalue_column='ttest pvalue', score_column='score'):
+        hit_dict = {
+            'gamma':{
+                'up_hit':'up_hit',
+                'down_hit':'essential_hit'
+            },
+            'tau':{
+                'up_hit':'up_hit', 
+                'down_hit':'down_hit'
+            },
+            'rho':{
+                'up_hit':'resistance_hit', 
+                'down_hit':'sensitivity_hit'
+            }
+        }
+        
+        keep_col = [target_col, score_column, pvalue_column]
+
+        scores = {score for score, col in self.phenotypes[run_name].columns}
+        sort_var = self.adata.var.sort_values(['targetType','target']).index.to_list()
+        
+        df_list = {}
+        for score in scores:
+            score_tag = score.split(':')[0]
+            # get label
+            df_label = ann_score_df(
+                self.phenotypes[run_name][score].loc[:,keep_col],
+                up_hit=hit_dict[score_tag]['up_hit'],
+                down_hit=hit_dict[score_tag]['down_hit'],
+                ctrl_label=ctrl_label,
+                threshold=threshold
+            )['label']
+            # get replicate phe
+            df_phe_reps = self.pdata[self.pdata.obs.score.eq(score_tag)].to_df().T
+            
+            # make table
+            df = pd.concat([self.phenotypes['compare_reps'][score], df_phe_reps, df_label],axis=1).loc[sort_var,:]
+            
+            df_list.update({score:df})
+        
+        out = pd.concat(df_list,axis=1)
+        
+        return out
+
 
 class GImaps(object):
     pass
\ No newline at end of file

From f1492922cf45c77c0bca721ab56fc8e5f849affc Mon Sep 17 00:00:00 2001
From: "Abolfazl (Abe)" <abea@arcinstitute.org>
Date: Wed, 22 May 2024 00:07:13 -0700
Subject: [PATCH 03/27] mend

---
 screenpro/assays.py | 26 +++++++++++++++++++++++---
 1 file changed, 23 insertions(+), 3 deletions(-)

diff --git a/screenpro/assays.py b/screenpro/assays.py
index cebc303..ebceeef 100644
--- a/screenpro/assays.py
+++ b/screenpro/assays.py
@@ -190,7 +190,7 @@ def calculateFlowBasedScreen(self, low_bin, high_bin, score_level, run_name=None
         # save phenotype name for reference
         self._add_phenotype_results(f'delta:{delta_name}')
 
-    def getPhenotypeScores(self, run_name, score_name, threshold=5, ctrl_label='negCtrl', target_col='target',pvalue_column='ttest pvalue', score_column='score'):
+    def getPhenotypeScores(self, score_name, run_name='auto', threshold=5, ctrl_label='negCtrl', target_col='target',pvalue_column='ttest pvalue', score_column='score'):
         """
         Get phenotype scores for a given score level
 
@@ -203,9 +203,19 @@ def getPhenotypeScores(self, run_name, score_name, threshold=5, ctrl_label='negC
             pvalue_column (str): column name for the p-value, default is 'ttest pvalue'
             score_column (str): column name for the score, default is 'score'
         """
+        if run_name == 'auto':
+            if len(list(self.phenotypes.keys())) == 1:
+                run_name = list(self.phenotypes.keys())[0]
+            else:
+                raise ValueError(
+                    'Multiple phenotype calculation runs found.'
+                    'Please specify run_name. Available runs: '
+                    '' + ', '.join(self.phenotypes.keys())
+                )
+        
         if score_name not in self.phenotype_names:
             raise ValueError(f"Phenotype '{score_name}' not found in self.phenotype_names")
-        
+
         keep_col = [target_col, score_column, pvalue_column]
 
         out = ann_score_df(
@@ -216,7 +226,7 @@ def getPhenotypeScores(self, run_name, score_name, threshold=5, ctrl_label='negC
 
         return out
 
-    def getAnnotatedTable(self, run_name, threshold=5, ctrl_label='negCtrl', target_col='target',pvalue_column='ttest pvalue', score_column='score'):
+    def getAnnotatedTable(self, run_name='auto', threshold=5, ctrl_label='negCtrl', target_col='target',pvalue_column='ttest pvalue', score_column='score'):
         hit_dict = {
             'gamma':{
                 'up_hit':'up_hit',
@@ -232,6 +242,16 @@ def getAnnotatedTable(self, run_name, threshold=5, ctrl_label='negCtrl', target_
             }
         }
         
+        if run_name == 'auto':
+            if len(list(self.phenotypes.keys())) == 1:
+                run_name = list(self.phenotypes.keys())[0]
+            else:
+                raise ValueError(
+                    'Multiple phenotype calculation runs found.'
+                    'Please specify run_name. Available runs: '
+                    '' + ', '.join(self.phenotypes.keys())
+                )
+
         keep_col = [target_col, score_column, pvalue_column]
 
         scores = {score for score, col in self.phenotypes[run_name].columns}

From 987f83e21c3d9ccf61df9028e6e966c81bf5e24c Mon Sep 17 00:00:00 2001
From: "Abolfazl (Abe)" <abea@arcinstitute.org>
Date: Wed, 22 May 2024 01:11:35 -0700
Subject: [PATCH 04/27] fix filter rule

---
 screenpro/utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/screenpro/utils.py b/screenpro/utils.py
index 681652f..18fa169 100644
--- a/screenpro/utils.py
+++ b/screenpro/utils.py
@@ -35,7 +35,7 @@ def find_low_counts(adata, filter_type='either', minimum_reads=50):
     """
     count_bin = adata.X >= minimum_reads
     if filter_type == 'either':
-        out = adata[:, count_bin.any(axis=0)].copy()
+        out = adata[:, ~(~count_bin.all(axis=0))].copy()
     elif filter_type == 'all':
         out = adata[:, count_bin.all(axis=0)].copy()
 

From cd9d99ad895291b2b3c193b8a269107b1b100342 Mon Sep 17 00:00:00 2001
From: "Abolfazl (Abe)" <abea@arcinstitute.org>
Date: Wed, 22 May 2024 02:48:51 -0700
Subject: [PATCH 05/27] add `sum` option for count filter

---
 screenpro/utils.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/screenpro/utils.py b/screenpro/utils.py
index 18fa169..c02214c 100644
--- a/screenpro/utils.py
+++ b/screenpro/utils.py
@@ -38,7 +38,9 @@ def find_low_counts(adata, filter_type='either', minimum_reads=50):
         out = adata[:, ~(~count_bin.all(axis=0))].copy()
     elif filter_type == 'all':
         out = adata[:, count_bin.all(axis=0)].copy()
-
+    elif filter_type == 'sum':
+        out = adata[:, adata.to_df().sum(axis=0) >= minimum_reads].copy()
+    
     # print the number of removed variables
     n_removed = adata.shape[1] - out.shape[1]
     print(

From 60654cf50c62f4fd510c3599303c753cc7d12e96 Mon Sep 17 00:00:00 2001
From: "Abolfazl (Abe)" <abea@arcinstitute.org>
Date: Wed, 22 May 2024 02:51:38 -0700
Subject: [PATCH 06/27] mend

---
 screenpro/utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/screenpro/utils.py b/screenpro/utils.py
index c02214c..e792b00 100644
--- a/screenpro/utils.py
+++ b/screenpro/utils.py
@@ -44,7 +44,7 @@ def find_low_counts(adata, filter_type='either', minimum_reads=50):
     # print the number of removed variables
     n_removed = adata.shape[1] - out.shape[1]
     print(
-        f"{n_removed} variables with less than {minimum_reads} reads in {filter_type} replicates / experiment"
+        f"{n_removed} variables with less than {minimum_reads} reads are removed. (filter_type:{filter_type})"
     )
 
     adata.var['low_count'] = ~adata.var.index.isin(out.var.index.to_list())

From e12e4e687234461833d75429777f779d92d222ba Mon Sep 17 00:00:00 2001
From: "Abolfazl (Abe)" <abea@arcinstitute.org>
Date: Wed, 22 May 2024 02:59:13 -0700
Subject: [PATCH 07/27] mend

---
 screenpro/utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/screenpro/utils.py b/screenpro/utils.py
index e792b00..736ea0c 100644
--- a/screenpro/utils.py
+++ b/screenpro/utils.py
@@ -44,7 +44,7 @@ def find_low_counts(adata, filter_type='either', minimum_reads=50):
     # print the number of removed variables
     n_removed = adata.shape[1] - out.shape[1]
     print(
-        f"{n_removed} variables with less than {minimum_reads} reads are removed. (filter_type:{filter_type})"
+        f"{n_removed} variables with less than {minimum_reads} reads (filter_type:{filter_type})"
     )
 
     adata.var['low_count'] = ~adata.var.index.isin(out.var.index.to_list())

From 26a2383a9ffd0a9fb0dc3efab53b6dfd4d107d63 Mon Sep 17 00:00:00 2001
From: "Abolfazl (Abe)" <abea@arcinstitute.org>
Date: Wed, 22 May 2024 03:04:44 -0700
Subject: [PATCH 08/27] mend

---
 screenpro/utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/screenpro/utils.py b/screenpro/utils.py
index 736ea0c..2e8218f 100644
--- a/screenpro/utils.py
+++ b/screenpro/utils.py
@@ -44,7 +44,7 @@ def find_low_counts(adata, filter_type='either', minimum_reads=50):
     # print the number of removed variables
     n_removed = adata.shape[1] - out.shape[1]
     print(
-        f"{n_removed} variables with less than {minimum_reads} reads (filter_type:{filter_type})"
+        f"{n_removed} variables with less than {minimum_reads} reads (filter_type: '{filter_type}')"
     )
 
     adata.var['low_count'] = ~adata.var.index.isin(out.var.index.to_list())

From 70bd9e933bfb15724ebdf6ba9ff5cc2459887480 Mon Sep 17 00:00:00 2001
From: "Abolfazl (Abe)" <abea@arcinstitute.org>
Date: Wed, 22 May 2024 20:05:23 -0700
Subject: [PATCH 09/27] fix value filter

---
 screenpro/plotting.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/screenpro/plotting.py b/screenpro/plotting.py
index df33575..da7ed43 100644
--- a/screenpro/plotting.py
+++ b/screenpro/plotting.py
@@ -88,9 +88,9 @@ def plot_volcano(ax, df_in, threshold, up_hit='resistance_hit', down_hit='sensit
                alpha=0.9, s=dot_size, c='#fcae91', label=up_hit)
     ax.scatter(df.loc[df['label'] == down_hit, 'score'], df.loc[df['label'] == down_hit, '-log10(pvalue)'],
                alpha=0.9, s=dot_size, c='#bdd7e7', label=down_hit)
-    ax.scatter(df.loc[df['label'] == 'non-targeting', 'score'],
-               df.loc[df['label'] == 'non-targeting', '-log10(pvalue)'],
-               alpha=0.1, s=dot_size, c='gray', label='non-targeting')
+    ax.scatter(df.loc[df['label'] == ctrl_label, 'score'],
+               df.loc[df['label'] == ctrl_label, '-log10(pvalue)'],
+               alpha=0.1, s=dot_size, c='gray', label=ctrl_label)
 
     # Set x-axis and y-axis labels
     ax.set_xlabel('phenotype score')

From 080734088cc5cdd103cce18b80e4a515af8fc561 Mon Sep 17 00:00:00 2001
From: "Abolfazl (Abe)" <abea@arcinstitute.org>
Date: Thu, 23 May 2024 01:13:44 -0700
Subject: [PATCH 10/27] update hit labels

---
 screenpro/assays.py | 33 ++++++++++++++++++++++++++-------
 1 file changed, 26 insertions(+), 7 deletions(-)

diff --git a/screenpro/assays.py b/screenpro/assays.py
index ebceeef..5dd8ed0 100644
--- a/screenpro/assays.py
+++ b/screenpro/assays.py
@@ -203,6 +203,21 @@ def getPhenotypeScores(self, score_name, run_name='auto', threshold=5, ctrl_labe
             pvalue_column (str): column name for the p-value, default is 'ttest pvalue'
             score_column (str): column name for the score, default is 'score'
         """
+        hit_dict = {
+            'gamma':{
+                'up_hit':'up_hit',
+                'down_hit':'essential_hit'
+            },
+            'tau':{
+                'up_hit':'up_hit', 
+                'down_hit':'down_hit'
+            },
+            'rho':{
+                'up_hit':'resistance_hit', 
+                'down_hit':'sensitivity_hit'
+            }
+        }
+
         if run_name == 'auto':
             if len(list(self.phenotypes.keys())) == 1:
                 run_name = list(self.phenotypes.keys())[0]
@@ -217,10 +232,12 @@ def getPhenotypeScores(self, score_name, run_name='auto', threshold=5, ctrl_labe
             raise ValueError(f"Phenotype '{score_name}' not found in self.phenotype_names")
 
         keep_col = [target_col, score_column, pvalue_column]
-
+        score_tag = score_name.split(':')[0]
         out = ann_score_df(
             self.phenotypes[run_name][score_name].loc[:,keep_col],
             ctrl_label=ctrl_label, 
+            up_hit=hit_dict[score_tag]['up_hit'],
+            down_hit=hit_dict[score_tag]['down_hit'],
             threshold=threshold
         )
 
@@ -254,15 +271,15 @@ def getAnnotatedTable(self, run_name='auto', threshold=5, ctrl_label='negCtrl',
 
         keep_col = [target_col, score_column, pvalue_column]
 
-        scores = {score for score, col in self.phenotypes[run_name].columns}
+        score_names = {s for s, col in self.phenotypes[run_name].columns}
         sort_var = self.adata.var.sort_values(['targetType','target']).index.to_list()
         
         df_list = {}
-        for score in scores:
-            score_tag = score.split(':')[0]
+        for score_name in score_names:
+            score_tag = score_name.split(':')[0]
             # get label
             df_label = ann_score_df(
-                self.phenotypes[run_name][score].loc[:,keep_col],
+                self.phenotypes[run_name][score_name].loc[:,keep_col],
                 up_hit=hit_dict[score_tag]['up_hit'],
                 down_hit=hit_dict[score_tag]['down_hit'],
                 ctrl_label=ctrl_label,
@@ -272,9 +289,11 @@ def getAnnotatedTable(self, run_name='auto', threshold=5, ctrl_label='negCtrl',
             df_phe_reps = self.pdata[self.pdata.obs.score.eq(score_tag)].to_df().T
             
             # make table
-            df = pd.concat([self.phenotypes['compare_reps'][score], df_phe_reps, df_label],axis=1).loc[sort_var,:]
+            df = pd.concat([
+                self.phenotypes['compare_reps'][score_name], df_phe_reps, df_label
+            ],axis=1).loc[sort_var,:]
             
-            df_list.update({score:df})
+            df_list.update({score_name:df})
         
         out = pd.concat(df_list,axis=1)
         

From c586b7bca22c7017583e4475603c0f7ba4144d64 Mon Sep 17 00:00:00 2001
From: "Abolfazl (Abe)" <abea@arcinstitute.org>
Date: Thu, 23 May 2024 13:36:05 -0700
Subject: [PATCH 11/27] add codes for interactive plots

---
 screenpro/dashboard.py | 256 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 256 insertions(+)
 create mode 100644 screenpro/dashboard.py

diff --git a/screenpro/dashboard.py b/screenpro/dashboard.py
new file mode 100644
index 0000000..f71cb5d
--- /dev/null
+++ b/screenpro/dashboard.py
@@ -0,0 +1,256 @@
+## Copyright (c) 2022-2024 ScreenPro2 Development Team.
+## All rights reserved.
+## Gilbart Lab, UCSF / Arc Institute.
+## Multi-Omics Tech Center, Arc Insititue.
+
+import pandas as pd
+import bokeh
+
+
+class DrugScreenDashboard:
+    
+    def __init__(self, screen, treated, untreated, t0='T0', threshold=3, ctrl_label='negative_control',run_name='auto'):
+        self.threshold = threshold
+        self.ctrl_label = ctrl_label
+        self.run_name = run_name
+        self.gamma_score_name = f'gamma:{untreated}_vs_{T0}'
+        self.rho_score_name = f'rho:{treated}_vs_{untreated}'
+        self.plots = {}
+
+    def _prep_data(self):
+
+        gamma = screen.getPhenotypeScores(
+            run_name=self.run_name,
+            score_name=self.gamma_score_name,
+            ctrl_label=self.ctrl_label,
+            threshold=self.threshold,
+        )
+
+        rho = screen.getPhenotypeScores(
+            run_name=self.run_name,
+            score_name=self.rho_score_name,
+            ctrl_label=self.ctrl_label,
+            threshold=self.threshold
+        )
+
+        df = pd.DataFrame({
+            'target': rho['target'],
+            'rho_score': rho['score'],
+            'rho_pvalue': rho['pvalue'],
+            'rho_label': rho['label'],
+            '-log10(rho_pvalue)': np.log10(rho['pvalue']) * -1,
+            'gamma_score': gamma.loc[rho.index,'score'],
+            'gamma_pvalue': gamma.loc[rho.index,'pvalue'],
+            'gamma_label': gamma.loc[rho.index,'label'],
+            '-log10(gamma_pvalue)': np.log10(gamma.loc[rho.index,'pvalue']) * -1,
+        })
+
+        return df
+    
+    def _plot_scatter(
+            self,
+            x_source,y_source,
+            xaxis_label,yaxis_label,
+            up_hit, down_hit,
+            hit_label_col,
+            x_min, x_max, y_min, y_max,
+            title='',
+            dot_size=1,
+            width=500, height=400,
+            toolbar_location='below',
+        ):
+
+        df = self._prep_data()
+
+        # if filter_labels is not None:
+        #     df = df[df['label'].isin(filter_labels)]
+
+        TOOLS = "box_select,box_zoom,lasso_select,reset,save,wheel_zoom,pan,copy,undo,redo,reset,examine,fullscreen"
+
+        # create a new plot with a specific size
+        TOOLTIPS = [
+            ("name", "@target"),
+            ("rho score", "@rho_score"),
+            ("rho p-value", "@rho_pvalue"),
+            ("rho label", "@rho_label"),
+            ("gamma score", "@gamma_score"),
+            ("gamma p-value", "@gamma_pvalue"),
+            ("gamma label", "@gamma_label"),        
+        ]
+        p = bokeh.plotting.figure(
+            sizing_mode="stretch_width",
+            tools=TOOLS,
+            tooltips=TOOLTIPS,
+            toolbar_location=toolbar_location,
+            title=title,
+            max_width=width, height=height, 
+        )
+        p.toolbar.autohide = True
+
+        source = bokeh.models.ColumnDataSource(
+            df.loc[df[hit_label_col] == 'target_non_hit',:]
+        )
+        p.scatter(
+            x=x_source, y=y_source,
+            source=source,
+            alpha=0.2,
+            size=dot_size * 1.2, 
+            color='gray', 
+            legend_label='target_non_hit',
+            name='circles'
+        )
+
+        # size_mapper=bokeh.models.LinearInterpolator(
+        #     x=[df['1/gamma_score'].min(),df['1/gamma_score'].max()],
+        #     y=[1,100]
+        # )
+
+        source = bokeh.models.ColumnDataSource(
+            df.loc[df[hit_label_col] == up_hit,:]
+        )
+        p.scatter(
+            x=x_source, y=y_source,
+            source=source,
+            alpha=0.8,
+            size=dot_size * 1.2, 
+            # size={'field':'1/gamma_score','transform':size_mapper},
+            color='#fcae91',
+            legend_label=up_hit,
+            name='circles'
+        )
+        
+        source = bokeh.models.ColumnDataSource(
+            df.loc[df[hit_label_col] == down_hit,:]
+        )
+        p.scatter(
+            x=x_source, y=y_source,
+            source=source,
+            alpha=0.8,
+            # size={'field':'1/gamma_score','transform':size_mapper},
+            size=dot_size * 1.2, 
+            color='#bdd7e7',
+            legend_label=down_hit,
+            name='circles'
+        )
+        
+        source = bokeh.models.ColumnDataSource(
+            df.loc[df[hit_label_col] == self.ctrl_label,:]
+        )
+        p.scatter(
+            x=x_source, y=y_source,
+            source=source,
+            alpha=0.2,
+            size=dot_size*0.8, 
+            color='silver',
+            legend_label=self.ctrl_label,
+            name='circles'
+        )
+        
+        # Set x-axis and y-axis labels
+        p.xaxis.axis_label = xaxis_label
+        p.xaxis.axis_label_text_font_style = 'normal'
+        p.yaxis.axis_label = yaxis_label
+        p.yaxis.axis_label_text_font_style = 'normal'
+
+        # Set x-axis limits
+        p.x_range.start = x_min
+        p.x_range.end = x_max
+
+        # Set y-axis limits
+        p.y_range.start = y_min
+        p.y_range.end = y_max
+
+        # Add legend
+        p.legend.location = "top_left"
+
+        p.title.text = title
+        p.title.align = 'center'
+        p.title.text_font_size = '12pt'
+        p.title.text_font_style = 'bold'
+
+        return p
+
+    def _get_html(self, p):
+        html = bokeh.embed.file_html(p, bokeh.resources.CDN, "")
+        return html
+    
+    def RhoVolcanoPlot(
+        self,
+        x_source='rho_score', y_source='-log10(rho_pvalue)',
+        xaxis_label='phenotype score',
+        yaxis_label='-log10(p-value)',
+        up_hit='resistance_hit', down_hit='sensitivity_hit',
+        hit_label_col='rho_label',
+        x_min=-2.5, x_max=2.5, y_min=0, y_max=5.5,
+        return_html=True,
+        **kwargs
+        ):
+        p = self._plot_scatter(
+            x_source, y_source,
+            xaxis_label, yaxis_label,
+            up_hit, down_hit,
+            hit_label_col,
+            x_min, x_max, y_min, y_max,
+            **kwargs
+        )
+
+        if return_html:
+            return self._get_html(p)
+                    
+        self.plots.update(
+            {'RhoVolcanoPlot': p}
+        )
+
+    def GammaVolcanoPlot(
+        self,
+        x_source='gamma_score', y_source='-log10(gamma_pvalue)',
+        xaxis_label='phenotype score',
+        yaxis_label='-log10(p-value)',
+        up_hit='up_hit', down_hit='essential_hit',
+        hit_label_col='gamma_label',
+        x_min=-2.5, x_max=2.5, y_min=0, y_max=5.5,
+        return_html=True,
+        **kwargs
+        ):
+        p = self._plot_scatter(
+            x_source, y_source,
+            xaxis_label, yaxis_label,
+            up_hit, down_hit,
+            hit_label_col,
+            x_min, x_max, y_min, y_max,
+            **kwargs
+        )
+
+        if return_html:
+            return self._get_html(p)
+        
+        self.plots.update(
+            {'GammaVolcanoPlot': p}
+        )
+    
+    def RhoGammaScatter(
+        self,
+        x_source='rho_score', y_source='gamma_score',
+        xaxis_label='rho score',
+        yaxis_label='gamma score',
+        up_hit='resistance_hit', down_hit='sensitivity_hit',
+        hit_label_col='rho_label',
+        return_html=True,
+        x_min=-2.5, x_max=2.5, y_min=-2.5, y_max=2.5,
+        **kwargs
+        ):
+        p = self._plot_scatter(
+            x_source, y_source,
+            xaxis_label, yaxis_label,
+            up_hit, down_hit,
+            hit_label_col,
+            x_min, x_max, y_min, y_max,
+            **kwargs
+        )
+
+        if return_html:
+            return self._get_html(p)
+        
+        self.plots.update(
+            {'GammaRhoScatter': p}
+        )

From 9523b838faa0ecdefde34009cf8bf44c1f578143 Mon Sep 17 00:00:00 2001
From: "Abolfazl (Abe)" <abea@arcinstitute.org>
Date: Thu, 23 May 2024 13:36:17 -0700
Subject: [PATCH 12/27] add bokeh

---
 docs/source/conf.py | 1 +
 environment.yml     | 1 +
 2 files changed, 2 insertions(+)

diff --git a/docs/source/conf.py b/docs/source/conf.py
index 7cb5d44..70bdce6 100755
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -43,6 +43,7 @@
     "polars",
     "biobear",
     "numba",
+    "bokeh",
     "pydeseq2",
     "watermark"
 ]
diff --git a/environment.yml b/environment.yml
index 4ee05be..5ac5774 100644
--- a/environment.yml
+++ b/environment.yml
@@ -15,6 +15,7 @@ dependencies:
   - matplotlib<3.7
   - seaborn
   - pyarrow
+  - bokeh
   - ipykernel
   - mscorefonts
   - rust>=1.72

From bb836b66cecece9e73703713436a694f805a9ecc Mon Sep 17 00:00:00 2001
From: "Abolfazl (Abe)" <abea@arcinstitute.org>
Date: Thu, 23 May 2024 13:46:10 -0700
Subject: [PATCH 13/27] add `DataDashboard` class

---
 screenpro/dashboard.py | 50 +++++++++++++++++++++++++-----------------
 1 file changed, 30 insertions(+), 20 deletions(-)

diff --git a/screenpro/dashboard.py b/screenpro/dashboard.py
index f71cb5d..6ea1199 100644
--- a/screenpro/dashboard.py
+++ b/screenpro/dashboard.py
@@ -7,7 +7,33 @@
 import bokeh
 
 
-class DrugScreenDashboard:
+class DataDashboard:
+
+    def __init__(self):
+        pass
+
+    def _new_plot(self,TOOLTIPS,width,height,toolbar_location):
+        
+        TOOLS = "box_select,box_zoom,lasso_select,reset,save,wheel_zoom,pan,copy,undo,redo,reset,examine,fullscreen"
+
+        # create a new plot with a specific size
+        p = bokeh.plotting.figure(
+            sizing_mode="stretch_width",
+            tools=TOOLS,
+            tooltips=TOOLTIPS,
+            toolbar_location=toolbar_location,
+            title=title,
+            max_width=width, height=height, 
+        )
+        p.toolbar.autohide = True
+        return p
+    
+    def _get_html(self, p):
+        html = bokeh.embed.file_html(p, bokeh.resources.CDN, "")
+        return html
+
+
+class DrugScreenDashboard(DataDashboard):
     
     def __init__(self, screen, treated, untreated, t0='T0', threshold=3, ctrl_label='negative_control',run_name='auto'):
         self.threshold = threshold
@@ -16,6 +42,7 @@ def __init__(self, screen, treated, untreated, t0='T0', threshold=3, ctrl_label=
         self.gamma_score_name = f'gamma:{untreated}_vs_{T0}'
         self.rho_score_name = f'rho:{treated}_vs_{untreated}'
         self.plots = {}
+        super().__init__(self)
 
     def _prep_data(self):
 
@@ -62,12 +89,6 @@ def _plot_scatter(
 
         df = self._prep_data()
 
-        # if filter_labels is not None:
-        #     df = df[df['label'].isin(filter_labels)]
-
-        TOOLS = "box_select,box_zoom,lasso_select,reset,save,wheel_zoom,pan,copy,undo,redo,reset,examine,fullscreen"
-
-        # create a new plot with a specific size
         TOOLTIPS = [
             ("name", "@target"),
             ("rho score", "@rho_score"),
@@ -77,15 +98,8 @@ def _plot_scatter(
             ("gamma p-value", "@gamma_pvalue"),
             ("gamma label", "@gamma_label"),        
         ]
-        p = bokeh.plotting.figure(
-            sizing_mode="stretch_width",
-            tools=TOOLS,
-            tooltips=TOOLTIPS,
-            toolbar_location=toolbar_location,
-            title=title,
-            max_width=width, height=height, 
-        )
-        p.toolbar.autohide = True
+
+        p = self._new_plot(TOOLTIPS,width,height,toolbar_location)
 
         source = bokeh.models.ColumnDataSource(
             df.loc[df[hit_label_col] == 'target_non_hit',:]
@@ -169,10 +183,6 @@ def _plot_scatter(
         p.title.text_font_style = 'bold'
 
         return p
-
-    def _get_html(self, p):
-        html = bokeh.embed.file_html(p, bokeh.resources.CDN, "")
-        return html
     
     def RhoVolcanoPlot(
         self,

From 987277b0ae9d7d5b6ed8a69fd380f530d126fe84 Mon Sep 17 00:00:00 2001
From: "Abolfazl (Abe)" <abea@arcinstitute.org>
Date: Thu, 23 May 2024 13:46:24 -0700
Subject: [PATCH 14/27] import dashboard module

---
 screenpro/__init__.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/screenpro/__init__.py b/screenpro/__init__.py
index 69ca0c5..63c4240 100644
--- a/screenpro/__init__.py
+++ b/screenpro/__init__.py
@@ -1,11 +1,14 @@
 from . import plotting as pl
 from . import phenoscore as ps
+
 from . import utils
 from . import ngs
 from . import load
+from . import dashboard
+
 from .ngs import Counter
 from .assays import PooledScreens, GImaps
 
 __version__ = "0.3.2"
 __author__ = "Abe Arab"
-__email__ = 'abea@arcinstitute.org' # "abarbiology@gmail.com"
\ No newline at end of file
+__email__ = 'abea@arcinstitute.org' # "abarbiology@gmail.com"

From 70ac8099340fe3d6607b753dfe85a0ada4d6d9b9 Mon Sep 17 00:00:00 2001
From: "Abolfazl (Abe)" <abea@arcinstitute.org>
Date: Thu, 23 May 2024 13:48:51 -0700
Subject: [PATCH 15/27] mend

---
 screenpro/dashboard.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/screenpro/dashboard.py b/screenpro/dashboard.py
index 6ea1199..6d387f5 100644
--- a/screenpro/dashboard.py
+++ b/screenpro/dashboard.py
@@ -5,6 +5,7 @@
 
 import pandas as pd
 import bokeh
+import bokeh.plotting
 
 
 class DataDashboard:

From b0eb44ad543d53ec742bfe0ef8b5bdabae13a251 Mon Sep 17 00:00:00 2001
From: "Abolfazl (Abe)" <abea@arcinstitute.org>
Date: Thu, 23 May 2024 13:50:12 -0700
Subject: [PATCH 16/27] mend

---
 screenpro/dashboard.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/screenpro/dashboard.py b/screenpro/dashboard.py
index 6d387f5..759b5ce 100644
--- a/screenpro/dashboard.py
+++ b/screenpro/dashboard.py
@@ -40,7 +40,7 @@ def __init__(self, screen, treated, untreated, t0='T0', threshold=3, ctrl_label=
         self.threshold = threshold
         self.ctrl_label = ctrl_label
         self.run_name = run_name
-        self.gamma_score_name = f'gamma:{untreated}_vs_{T0}'
+        self.gamma_score_name = f'gamma:{untreated}_vs_{t0}'
         self.rho_score_name = f'rho:{treated}_vs_{untreated}'
         self.plots = {}
         super().__init__(self)

From fde96e08c9e9becb5c961313c9a9ddcfbfbed862 Mon Sep 17 00:00:00 2001
From: "Abolfazl (Abe)" <abea@arcinstitute.org>
Date: Thu, 23 May 2024 13:51:58 -0700
Subject: [PATCH 17/27] mend

---
 screenpro/dashboard.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/screenpro/dashboard.py b/screenpro/dashboard.py
index 759b5ce..dd91824 100644
--- a/screenpro/dashboard.py
+++ b/screenpro/dashboard.py
@@ -43,7 +43,7 @@ def __init__(self, screen, treated, untreated, t0='T0', threshold=3, ctrl_label=
         self.gamma_score_name = f'gamma:{untreated}_vs_{t0}'
         self.rho_score_name = f'rho:{treated}_vs_{untreated}'
         self.plots = {}
-        super().__init__(self)
+        super().__init__()
 
     def _prep_data(self):
 

From ef35c51b4abf6ada35945b5a5813989dfb7432bd Mon Sep 17 00:00:00 2001
From: "Abolfazl (Abe)" <abea@arcinstitute.org>
Date: Thu, 23 May 2024 13:54:46 -0700
Subject: [PATCH 18/27] mend

---
 screenpro/dashboard.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/screenpro/dashboard.py b/screenpro/dashboard.py
index dd91824..1189655 100644
--- a/screenpro/dashboard.py
+++ b/screenpro/dashboard.py
@@ -47,7 +47,7 @@ def __init__(self, screen, treated, untreated, t0='T0', threshold=3, ctrl_label=
 
     def _prep_data(self):
 
-        gamma = screen.getPhenotypeScores(
+        gamma = self.screen.getPhenotypeScores(
             run_name=self.run_name,
             score_name=self.gamma_score_name,
             ctrl_label=self.ctrl_label,

From 8a229f61eb314dfcf84fde54bbe3fa590363f47b Mon Sep 17 00:00:00 2001
From: "Abolfazl (Abe)" <abea@arcinstitute.org>
Date: Thu, 23 May 2024 13:56:35 -0700
Subject: [PATCH 19/27] mend

---
 screenpro/dashboard.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/screenpro/dashboard.py b/screenpro/dashboard.py
index 1189655..bb21f4d 100644
--- a/screenpro/dashboard.py
+++ b/screenpro/dashboard.py
@@ -37,6 +37,7 @@ def _get_html(self, p):
 class DrugScreenDashboard(DataDashboard):
     
     def __init__(self, screen, treated, untreated, t0='T0', threshold=3, ctrl_label='negative_control',run_name='auto'):
+        self.screen = screen
         self.threshold = threshold
         self.ctrl_label = ctrl_label
         self.run_name = run_name

From 84144110e6c9fc5e4de64ff2f5494115474a0682 Mon Sep 17 00:00:00 2001
From: "Abolfazl (Abe)" <abea@arcinstitute.org>
Date: Thu, 23 May 2024 13:58:23 -0700
Subject: [PATCH 20/27] mend

---
 screenpro/dashboard.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/screenpro/dashboard.py b/screenpro/dashboard.py
index bb21f4d..7cfaf01 100644
--- a/screenpro/dashboard.py
+++ b/screenpro/dashboard.py
@@ -46,9 +46,9 @@ def __init__(self, screen, treated, untreated, t0='T0', threshold=3, ctrl_label=
         self.plots = {}
         super().__init__()
 
-    def _prep_data(self):
+    def _prep_data(self,screen):
 
-        gamma = self.screen.getPhenotypeScores(
+        gamma = screen.getPhenotypeScores(
             run_name=self.run_name,
             score_name=self.gamma_score_name,
             ctrl_label=self.ctrl_label,
@@ -89,7 +89,7 @@ def _plot_scatter(
             toolbar_location='below',
         ):
 
-        df = self._prep_data()
+        df = self._prep_data(self.screen)
 
         TOOLTIPS = [
             ("name", "@target"),

From 2883fd14b90176ad7cfca5fef3e1d5d6385c8ae0 Mon Sep 17 00:00:00 2001
From: "Abolfazl (Abe)" <abea@arcinstitute.org>
Date: Thu, 23 May 2024 13:59:05 -0700
Subject: [PATCH 21/27] mend

---
 screenpro/dashboard.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/screenpro/dashboard.py b/screenpro/dashboard.py
index 7cfaf01..cd1efba 100644
--- a/screenpro/dashboard.py
+++ b/screenpro/dashboard.py
@@ -3,6 +3,7 @@
 ## Gilbart Lab, UCSF / Arc Institute.
 ## Multi-Omics Tech Center, Arc Insititue.
 
+improt numpy as np
 import pandas as pd
 import bokeh
 import bokeh.plotting

From 894ca8ca1b35767b51006d154508f36a1255a4e9 Mon Sep 17 00:00:00 2001
From: "Abolfazl (Abe)" <abea@arcinstitute.org>
Date: Thu, 23 May 2024 14:00:26 -0700
Subject: [PATCH 22/27] fix typo

---
 screenpro/dashboard.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/screenpro/dashboard.py b/screenpro/dashboard.py
index cd1efba..f9efd9b 100644
--- a/screenpro/dashboard.py
+++ b/screenpro/dashboard.py
@@ -3,7 +3,7 @@
 ## Gilbart Lab, UCSF / Arc Institute.
 ## Multi-Omics Tech Center, Arc Insititue.
 
-improt numpy as np
+import numpy as np
 import pandas as pd
 import bokeh
 import bokeh.plotting

From 96fdf002e27f0271bd8dfe8a5311b7db506bb5f6 Mon Sep 17 00:00:00 2001
From: "Abolfazl (Abe)" <abea@arcinstitute.org>
Date: Thu, 23 May 2024 14:03:13 -0700
Subject: [PATCH 23/27] mend

---
 screenpro/dashboard.py | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/screenpro/dashboard.py b/screenpro/dashboard.py
index f9efd9b..1f5826b 100644
--- a/screenpro/dashboard.py
+++ b/screenpro/dashboard.py
@@ -14,7 +14,7 @@ class DataDashboard:
     def __init__(self):
         pass
 
-    def _new_plot(self,TOOLTIPS,width,height,toolbar_location):
+    def _new_plot(self,title,tooltips,width,height,toolbar_location):
         
         TOOLS = "box_select,box_zoom,lasso_select,reset,save,wheel_zoom,pan,copy,undo,redo,reset,examine,fullscreen"
 
@@ -22,7 +22,7 @@ def _new_plot(self,TOOLTIPS,width,height,toolbar_location):
         p = bokeh.plotting.figure(
             sizing_mode="stretch_width",
             tools=TOOLS,
-            tooltips=TOOLTIPS,
+            tooltips=tooltips,
             toolbar_location=toolbar_location,
             title=title,
             max_width=width, height=height, 
@@ -102,7 +102,13 @@ def _plot_scatter(
             ("gamma label", "@gamma_label"),        
         ]
 
-        p = self._new_plot(TOOLTIPS,width,height,toolbar_location)
+        p = self._new_plot(
+            title=title,
+            tooltips=TOOLTIPS,
+            width=width,
+            height=height,
+            toolbar_location=toolbar_location
+        )
 
         source = bokeh.models.ColumnDataSource(
             df.loc[df[hit_label_col] == 'target_non_hit',:]

From 5cea9b67536109f8ec1bbbf25a699c4873ef3058 Mon Sep 17 00:00:00 2001
From: "Abolfazl (Abe)" <abea@arcinstitute.org>
Date: Thu, 23 May 2024 14:09:14 -0700
Subject: [PATCH 24/27] improve axis limits

---
 screenpro/dashboard.py | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/screenpro/dashboard.py b/screenpro/dashboard.py
index 1f5826b..bbc8878 100644
--- a/screenpro/dashboard.py
+++ b/screenpro/dashboard.py
@@ -92,6 +92,11 @@ def _plot_scatter(
 
         df = self._prep_data(self.screen)
 
+        if y_max == 'auto': y_max = df[y_source].max() * 1.2
+        if x_max == 'auto': x_max = df[x_source].max() * 1.2
+        if y_min == 'auto': y_min = df[y_source].min() * 1.2
+        if x_min == 'auto': x_min = df[x_source].min() * 1.2
+
         TOOLTIPS = [
             ("name", "@target"),
             ("rho score", "@rho_score"),
@@ -200,7 +205,7 @@ def RhoVolcanoPlot(
         yaxis_label='-log10(p-value)',
         up_hit='resistance_hit', down_hit='sensitivity_hit',
         hit_label_col='rho_label',
-        x_min=-2.5, x_max=2.5, y_min=0, y_max=5.5,
+        x_min=-2.5, x_max=2.5, y_min=0, y_max='auto',
         return_html=True,
         **kwargs
         ):
@@ -227,7 +232,7 @@ def GammaVolcanoPlot(
         yaxis_label='-log10(p-value)',
         up_hit='up_hit', down_hit='essential_hit',
         hit_label_col='gamma_label',
-        x_min=-2.5, x_max=2.5, y_min=0, y_max=5.5,
+        x_min=-2.5, x_max=2.5, y_min=0, y_max='auto',
         return_html=True,
         **kwargs
         ):

From b5bc4e61979177d71aca00c7b4e20a7f0984e264 Mon Sep 17 00:00:00 2001
From: "Abolfazl (Abe)" <abea@arcinstitute.org>
Date: Thu, 23 May 2024 14:11:31 -0700
Subject: [PATCH 25/27] add `legend_loc`

---
 screenpro/dashboard.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/screenpro/dashboard.py b/screenpro/dashboard.py
index bbc8878..066d787 100644
--- a/screenpro/dashboard.py
+++ b/screenpro/dashboard.py
@@ -88,6 +88,7 @@ def _plot_scatter(
             dot_size=1,
             width=500, height=400,
             toolbar_location='below',
+            legend_loc="top_left"
         ):
 
         df = self._prep_data(self.screen)
@@ -189,7 +190,7 @@ def _plot_scatter(
         p.y_range.end = y_max
 
         # Add legend
-        p.legend.location = "top_left"
+        p.legend.location = legend_loc
 
         p.title.text = title
         p.title.align = 'center'

From d7b175ae6dd2ac267fb2b8031f1e637506206201 Mon Sep 17 00:00:00 2001
From: "Abolfazl (Abe)" <abea@arcinstitute.org>
Date: Thu, 23 May 2024 14:13:52 -0700
Subject: [PATCH 26/27] mend

---
 screenpro/dashboard.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/screenpro/dashboard.py b/screenpro/dashboard.py
index 066d787..d709e37 100644
--- a/screenpro/dashboard.py
+++ b/screenpro/dashboard.py
@@ -190,7 +190,10 @@ def _plot_scatter(
         p.y_range.end = y_max
 
         # Add legend
-        p.legend.location = legend_loc
+        if legend_loc == False or legend_loc == None:
+            p.legend.visible = False
+        else:
+            p.legend.location = legend_loc
 
         p.title.text = title
         p.title.align = 'center'

From d2377f6b9fa2db53ebbe4c7860a5ff10d6888764 Mon Sep 17 00:00:00 2001
From: "Abolfazl (Abe)" <abea@arcinstitute.org>
Date: Thu, 23 May 2024 15:06:05 -0700
Subject: [PATCH 27/27] bump version 0.3.3

---
 screenpro/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/screenpro/__init__.py b/screenpro/__init__.py
index 63c4240..4e4dabe 100644
--- a/screenpro/__init__.py
+++ b/screenpro/__init__.py
@@ -9,6 +9,6 @@
 from .ngs import Counter
 from .assays import PooledScreens, GImaps
 
-__version__ = "0.3.2"
+__version__ = "0.3.3"
 __author__ = "Abe Arab"
 __email__ = 'abea@arcinstitute.org' # "abarbiology@gmail.com"