From 2bfdaa97c6df7590a796f5bed41fac2c712b52b3 Mon Sep 17 00:00:00 2001
From: anishmss <anish.ms.shrestha@gmail.com>
Date: Mon, 4 Sep 2023 15:22:39 +0800
Subject: [PATCH] Add links to wiki in page description

---
 pages/analysis/browse_loci.py |  2 +-
 pages/analysis/co_expr.py     | 20 ++++++++++++++++++--
 pages/analysis/lift_over.py   | 16 ++++++++++++++--
 pages/analysis/text_mining.py | 20 +++++++++++++++++---
 pages/analysis/tf_enrich.py   | 16 +++++++++++++---
 5 files changed, 63 insertions(+), 11 deletions(-)

diff --git a/pages/analysis/browse_loci.py b/pages/analysis/browse_loci.py
index fbd1963f..b19a4608 100644
--- a/pages/analysis/browse_loci.py
+++ b/pages/analysis/browse_loci.py
@@ -11,7 +11,7 @@
     hidden=True,
     children=[
         html.Div([
-            html.P('WRITE ME')
+            html.P('In this page, you can genome-browse your input intervals.')
         ], className='analysis-intro p-3'),
 
         html.Br(),
diff --git a/pages/analysis/co_expr.py b/pages/analysis/co_expr.py
index 7b3f41aa..9d9c1a95 100644
--- a/pages/analysis/co_expr.py
+++ b/pages/analysis/co_expr.py
@@ -121,8 +121,24 @@
     children=[
 
         html.Div([
-            html.P('In this page, you can search for modules (a.k.a. communities, clusters) in rice co-expression networks, which are significantly enriched in the genes implicated by your GWAS. '
-                   'Likely functions of the modules are inferred by enrichment analysis against several ontologies and pathway databases.')
+            html.P(
+                [
+                   'In this page, you can search for modules (a.k.a. communities, clusters) in rice co-expression networks, '
+                   'which are significantly enriched in the genes implicated by your GWAS. '
+                   'Likely functions of the modules are inferred by enrichment analysis against several ontologies and pathway databases. Click ',
+                   dcc.Link(
+                    ['here ', html.I(
+                        id='demo-link',
+                        className='fa-solid fa-up-right-from-square fa-2xs'
+                    )],
+                    href='https://github.com/bioinfodlsu/rice-pilaf/wiki/2.3-Co%E2%80%90expression-Network-Analysis',
+                    target='_blank',
+                    className='top-navbar-item'
+                ),
+                ' for user guide.'
+
+                ]
+            )
         ], className='analysis-intro p-3'),
 
         html.Br(),
diff --git a/pages/analysis/lift_over.py b/pages/analysis/lift_over.py
index 7352d528..cb1618fe 100644
--- a/pages/analysis/lift_over.py
+++ b/pages/analysis/lift_over.py
@@ -13,8 +13,20 @@
     children=[
         html.Div([
             html.P(
-                'In this page, you can obtain the list of genes overlapping your input intervals. '
-                'Optionally, you can choose genomes to lift-over your Nipponbare coordinates to.'),
+               ['In this page, you can obtain the list of genes overlapping your input intervals. '
+                'Optionally, you can choose genomes to lift-over your Nipponbare coordinates to. Click ',
+                 dcc.Link(
+                    ['here ', html.I(
+                        id='demo-link',
+                        className='fa-solid fa-up-right-from-square fa-2xs'
+                    )],
+                    href='https://github.com/bioinfodlsu/rice-pilaf/wiki/2.1-Gene-List-and-Lift%E2%80%90over',
+                    target='_blank',
+                    className='top-navbar-item'
+                ),
+                ' for user guide.'
+               ]
+            )
         ], className='analysis-intro p-3'),
 
         html.Br(),
diff --git a/pages/analysis/text_mining.py b/pages/analysis/text_mining.py
index 9ac170ad..649ea5d5 100644
--- a/pages/analysis/text_mining.py
+++ b/pages/analysis/text_mining.py
@@ -12,9 +12,23 @@
     children=[
 
         html.Div([
-            html.P('In this page, you can retrieve gene names associated with traits, diseases, chemicals, etc. from a database constructed from text-mined PubMed abstracts. '
-                   # 'Conversely, you can retrieve literature that associates your gene of interest to some phenotype.'
-                   ),
+            html.P(
+                [
+                   'In this page, you can retrieve gene names associated with traits, diseases, chemicals, etc. '
+                   'from a database constructed from text-mined PubMed abstracts. Click ',
+                    dcc.Link(
+                    ['here ', html.I(
+                        id='demo-link',
+                        className='fa-solid fa-up-right-from-square fa-2xs'
+                    )],
+                    href='https://github.com/bioinfodlsu/rice-pilaf/wiki/2.2-Gene-retrieval-by-text-mining',
+                    target='_blank',
+                    className='top-navbar-item'
+                    ),
+                    ' for user guide.'
+                ]
+
+            ),
         ], className='analysis-intro p-3'),
 
         html.Br(),
diff --git a/pages/analysis/tf_enrich.py b/pages/analysis/tf_enrich.py
index f5fd21d7..32eff8ba 100644
--- a/pages/analysis/tf_enrich.py
+++ b/pages/analysis/tf_enrich.py
@@ -12,9 +12,19 @@
     children=[
         html.Div([
             html.P(
-                'Perhaps your intervals contain variants that influence regulatory elements, for example by affecting binding affinity.'),
-            html.P(
-                'In this page, you can search for transcription factors whose binding sites overlap significantly with your intervals.')
+                ['In this page, you can search for transcription factors whose binding sites overlap significantly with your intervals,'
+                'the idea being that your intervals might contain variants that affect the binding affinity of transcription factors. Click ',
+                dcc.Link(
+                    ['here ', html.I(
+                        id='demo-link',
+                        className='fa-solid fa-up-right-from-square fa-2xs'
+                    )],
+                    href='https://github.com/bioinfodlsu/rice-pilaf/wiki/2.4-Regulatory-Feature-Enrichment',
+                    target='_blank',
+                    className='top-navbar-item'
+                ),
+                ' for user guide.']
+            )
         ], className='analysis-intro p-3'),
 
         html.Br(),