diff --git a/genes2genes/VisualUtils.py b/genes2genes/VisualUtils.py
index 7e55a0e..904ddd3 100644
--- a/genes2genes/VisualUtils.py
+++ b/genes2genes/VisualUtils.py
@@ -404,7 +404,7 @@ def plot_heatmaps(mat_ref,mat_query,GENE_LIST, pathway_name, cluster=False, FIGS
     max_val = np.max([np.max(mat_ref),np.max(mat_query)]) 
     min_val = np.min([np.min(mat_ref),np.min(mat_query)]) 
     plt.subplot(1,2,1)
-    ax=sb.heatmap(df, vmax=max_val,vmin=min_val, cbar_kws = dict(use_gridspec=False,location="top")) 
+    ax=sb.heatmap(df, vmax=max_val,vmin=min_val, cbar_kws = dict(use_gridspec=False,location="top"), xticklabels=True, yticklabels=True) 
     plt.title('Reference')
     ax.yaxis.set_label_position("left")
     for tick in ax.get_yticklabels():
diff --git a/notebooks/Tutorial.ipynb b/notebooks/Tutorial.ipynb
index d7a1e86..347de76 100644
--- a/notebooks/Tutorial.ipynb
+++ b/notebooks/Tutorial.ipynb
@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "insured-murray",
+   "id": "noble-syntax",
    "metadata": {},
    "source": [
     "# Tutorial on single-cell trajectory alignment using Genes2Genes\n",
@@ -15,7 +15,7 @@
   {
    "cell_type": "code",
    "execution_count": 1,
-   "id": "gross-campus",
+   "id": "inappropriate-canada",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -36,7 +36,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "involved-egypt",
+   "id": "demanding-profit",
    "metadata": {},
    "source": [
     "### Load anndata reference and query objects\n",
@@ -49,18 +49,18 @@
   {
    "cell_type": "code",
    "execution_count": 2,
-   "id": "developed-breed",
+   "id": "automotive-context",
    "metadata": {},
    "outputs": [],
    "source": [
-    "input_dir = 'notebooks/data/'\n",
+    "input_dir = 'data/'\n",
     "adata_ref = anndata.read_h5ad(input_dir + 'adata_pam_local.h5ad') # Reference dataset\n",
     "adata_query = anndata.read_h5ad(input_dir +'adata_lps_local.h5ad') # Query dataset"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "favorite-pearl",
+   "id": "lightweight-scheduling",
    "metadata": {},
    "source": [
     "## 1. Preparing data for alignment "
@@ -68,7 +68,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "everyday-ratio",
+   "id": "mounted-syria",
    "metadata": {},
    "source": [
     "### Pseudotime range check\n",
@@ -78,7 +78,7 @@
   {
    "cell_type": "code",
    "execution_count": 3,
-   "id": "lightweight-management",
+   "id": "impressive-trustee",
    "metadata": {},
    "outputs": [
     {
@@ -102,7 +102,7 @@
   {
    "cell_type": "code",
    "execution_count": 4,
-   "id": "beneficial-major",
+   "id": "absolute-gothic",
    "metadata": {},
    "outputs": [
     {
@@ -125,7 +125,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "short-feature",
+   "id": "eligible-substance",
    "metadata": {},
    "source": [
     "### Determine the number of discrete pseudotime points to align\n",
@@ -136,7 +136,7 @@
   {
    "cell_type": "code",
    "execution_count": 5,
-   "id": "coral-detective",
+   "id": "blank-cause",
    "metadata": {},
    "outputs": [
     {
@@ -168,7 +168,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "curious-visitor",
+   "id": "turned-cliff",
    "metadata": {},
    "source": [
     "Accordingly, we go with `n_bins=14`"
@@ -177,7 +177,7 @@
   {
    "cell_type": "code",
    "execution_count": 6,
-   "id": "selective-payroll",
+   "id": "authorized-shanghai",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -186,7 +186,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "stopped-shore",
+   "id": "split-gibraltar",
    "metadata": {},
    "source": [
     "### Define which cell type annotations and color scheme to use for visualization purposes\n",
@@ -197,7 +197,7 @@
   {
    "cell_type": "code",
    "execution_count": 7,
-   "id": "sexual-narrow",
+   "id": "behavioral-greeting",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -213,7 +213,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "norman-hungarian",
+   "id": "terminal-cincinnati",
    "metadata": {},
    "source": [
     "Inspect the cell type compositions around each discrete pseudotime point (x-axis) to see if it reasonably represents the entire trajectory of interest. "
@@ -222,7 +222,7 @@
   {
    "cell_type": "code",
    "execution_count": 8,
-   "id": "taken-opposition",
+   "id": "recreational-aerospace",
    "metadata": {},
    "outputs": [
     {
@@ -253,7 +253,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "failing-botswana",
+   "id": "imported-lawsuit",
    "metadata": {},
    "source": [
     "## 2. G2G trajectory alignment"
@@ -262,7 +262,7 @@
   {
    "cell_type": "code",
    "execution_count": 9,
-   "id": "important-survivor",
+   "id": "little-fisher",
    "metadata": {},
    "outputs": [
     {
@@ -281,7 +281,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "experienced-serbia",
+   "id": "stainless-pacific",
    "metadata": {},
    "source": [
     "### Aligning all genes"
@@ -290,7 +290,7 @@
   {
    "cell_type": "code",
    "execution_count": 15,
-   "id": "alpine-italian",
+   "id": "quantitative-float",
    "metadata": {},
    "outputs": [
     {
@@ -337,7 +337,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "suited-commander",
+   "id": "rolled-pantyhose",
    "metadata": {},
    "source": [
     "To access gene-level alignments, use the dictionary: `aligner.results_map` which carries all gene alignment objects. <br>\n",
@@ -347,7 +347,7 @@
   {
    "cell_type": "code",
    "execution_count": 11,
-   "id": "occupational-remains",
+   "id": "norman-verse",
    "metadata": {},
    "outputs": [
     {
@@ -391,7 +391,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "alert-silence",
+   "id": "tracked-pathology",
    "metadata": {},
    "source": [
     "Visualise alignment in terms of both the cell-type compositions, as well as actual and interpolated gene expression. <br>\n",
@@ -403,7 +403,7 @@
   {
    "cell_type": "code",
    "execution_count": 12,
-   "id": "radio-mirror",
+   "id": "double-moses",
    "metadata": {},
    "outputs": [
     {
@@ -445,7 +445,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "entitled-brass",
+   "id": "optimum-logan",
    "metadata": {},
    "source": [
     "### Aggregate (average) cell-level alignment across all aligned genes\n",
@@ -456,7 +456,7 @@
   {
    "cell_type": "code",
    "execution_count": 13,
-   "id": "spanish-bowling",
+   "id": "circular-missouri",
    "metadata": {},
    "outputs": [
     {
@@ -486,7 +486,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "powered-wyoming",
+   "id": "biblical-shelter",
    "metadata": {},
    "source": [
     "## 3. Analysing gene-level alignments\n",
@@ -497,7 +497,7 @@
   {
    "cell_type": "code",
    "execution_count": 14,
-   "id": "chubby-stomach",
+   "id": "atmospheric-massage",
    "metadata": {},
    "outputs": [
     {
@@ -695,7 +695,7 @@
   {
    "cell_type": "code",
    "execution_count": 16,
-   "id": "controversial-calgary",
+   "id": "naughty-criminal",
    "metadata": {},
    "outputs": [
     {
@@ -715,7 +715,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "under-sponsorship",
+   "id": "addressed-indication",
    "metadata": {},
    "source": [
     "A ranked list of genes based on their first match occurrence "
@@ -724,7 +724,7 @@
   {
    "cell_type": "code",
    "execution_count": 17,
-   "id": "cleared-jimmy",
+   "id": "interior-hearing",
    "metadata": {},
    "outputs": [
     {
@@ -832,7 +832,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "retired-legislation",
+   "id": "talented-canadian",
    "metadata": {},
    "source": [
     "## Gene-set overrepresentation analysis on the top dissimilar genes \n",
@@ -843,7 +843,7 @@
   {
    "cell_type": "code",
    "execution_count": 18,
-   "id": "bound-sheep",
+   "id": "dangerous-documentary",
    "metadata": {},
    "outputs": [
     {
@@ -1006,7 +1006,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "helpful-remove",
+   "id": "alert-shannon",
    "metadata": {},
    "source": [
     "## Clustering alignments \n",
@@ -1017,7 +1017,7 @@
   {
    "cell_type": "code",
    "execution_count": 19,
-   "id": "grand-pakistan",
+   "id": "actual-midnight",
    "metadata": {},
    "outputs": [
     {
@@ -1061,7 +1061,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "metallic-duncan",
+   "id": "civilian-leather",
    "metadata": {},
    "source": [
     "Run clustering with the chosen distance threshold. In this case we select 0.37"
@@ -1070,7 +1070,7 @@
   {
    "cell_type": "code",
    "execution_count": 20,
-   "id": "equal-above",
+   "id": "possible-portland",
    "metadata": {},
    "outputs": [
     {
@@ -1090,7 +1090,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "forty-psychology",
+   "id": "informed-avatar",
    "metadata": {},
    "source": [
     "Visualise gene alignment grouped together in each cluster <br>\n",
@@ -1100,7 +1100,7 @@
   {
    "cell_type": "code",
    "execution_count": 21,
-   "id": "alert-story",
+   "id": "super-configuration",
    "metadata": {},
    "outputs": [
     {
@@ -1127,7 +1127,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "fancy-meter",
+   "id": "impossible-cigarette",
    "metadata": {},
    "source": [
     "Visualise the distance matrix used in the clustering "
@@ -1136,7 +1136,7 @@
   {
    "cell_type": "code",
    "execution_count": 22,
-   "id": "suspected-ordering",
+   "id": "professional-questionnaire",
    "metadata": {},
    "outputs": [
     {
@@ -1156,7 +1156,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "welcome-darwin",
+   "id": "discrete-magnet",
    "metadata": {},
    "source": [
     "Print the aggregate (average) cell-level alignments for each cluster"
@@ -1165,7 +1165,7 @@
   {
    "cell_type": "code",
    "execution_count": 23,
-   "id": "swiss-marketplace",
+   "id": "catholic-intake",
    "metadata": {},
    "outputs": [
     {
@@ -1189,7 +1189,7 @@
   {
    "cell_type": "code",
    "execution_count": 24,
-   "id": "continent-ancient",
+   "id": "developing-letters",
    "metadata": {},
    "outputs": [
     {
@@ -1230,7 +1230,7 @@
   {
    "cell_type": "code",
    "execution_count": 25,
-   "id": "neural-wales",
+   "id": "peripheral-oregon",
    "metadata": {},
    "outputs": [
     {
@@ -1251,7 +1251,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "confirmed-nepal",
+   "id": "bridal-insulin",
    "metadata": {},
    "source": [
     "### Average alignment of any given subset of genes \n",
@@ -1261,7 +1261,7 @@
   {
    "cell_type": "code",
    "execution_count": 26,
-   "id": "operational-wayne",
+   "id": "wound-calculation",
    "metadata": {},
    "outputs": [
     {
@@ -1289,7 +1289,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "alone-maryland",
+   "id": "nonprofit-pricing",
    "metadata": {},
    "source": [
     "###  Exploring alignment and trends of a given gene set"
@@ -1297,7 +1297,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "welcome-wilderness",
+   "id": "designed-location",
    "metadata": {},
    "source": [
     "Following call extracts a specified pathway gene set from msigdb database. It requires downloading the database from https://www.gsea-msigdb.org/gsea/downloads.jsp and specifying path to the msigdb folder and its version. "
@@ -1306,7 +1306,7 @@
   {
    "cell_type": "code",
    "execution_count": 27,
-   "id": "surprised-bryan",
+   "id": "surrounded-receptor",
    "metadata": {},
    "outputs": [
     {
@@ -1321,7 +1321,7 @@
     }
    ],
    "source": [
-    "IGS = PathwayAnalyser.InterestingGeneSets(MSIGDB_PATH='../../OrgAlign/msigdb', version='7.5.1') # need to create db folder and pass args\n",
+    "IGS = PathwayAnalyser.InterestingGeneSets(MSIGDB_PATH='<directory_path_to_specify>/msigdb', version='7.5.1') # need to create db folder and pass args\n",
     "IGS.add_new_set_from_msigdb('hallmark', 'HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION', aligner.gene_list, 'EMT')   \n",
     "IGS.SETS['EMT']"
    ]
@@ -1329,7 +1329,7 @@
   {
    "cell_type": "code",
    "execution_count": 28,
-   "id": "aboriginal-dakota",
+   "id": "fatty-playlist",
    "metadata": {},
    "outputs": [
     {
@@ -1371,7 +1371,7 @@
   {
    "cell_type": "code",
    "execution_count": 29,
-   "id": "single-medium",
+   "id": "motivated-thunder",
    "metadata": {},
    "outputs": [
     {
@@ -1413,7 +1413,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "secret-terminology",
+   "id": "living-nudist",
    "metadata": {},
    "outputs": [],
    "source": []