fix conflict

rujinlong · Dec 26, 2022 · 6ba2c1a · 6ba2c1a
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diff --git a/app/rsconnect/shinyapps.io/rujinlong/DeepsmirUD.dcf b/app/rsconnect/shinyapps.io/rujinlong/DeepsmirUD.dcf
@@ -5,9 +5,16 @@ account: rujinlong
 server: shinyapps.io
 hostUrl: https://api.shinyapps.io/v1
 appId: 6295477
+<<<<<<< HEAD
 bundleId: 6673681
 url: https://rujinlong.shinyapps.io/DeepsmirUD/
 when: 1672056215.04623
 lastSyncTime: 1672056215.04629
+=======
+bundleId: 6674658
+url: https://rujinlong.shinyapps.io/DeepsmirUD/
+when: 1672091090.55488
+lastSyncTime: 1672091090.5549
+>>>>>>> dev
 asMultiple: FALSE
 asStatic: FALSE
diff --git a/app/www/nrFigure1.png b/app/www/nrFigure1.png
diff --git a/app/www/nrFigure10.png b/app/www/nrFigure10.png
diff --git a/app/www/nrFigure11.png b/app/www/nrFigure11.png
diff --git a/app/www/nrFigure12.png b/app/www/nrFigure12.png
diff --git a/app/www/nrFigure2.png b/app/www/nrFigure2.png
diff --git a/app/www/nrFigure3.png b/app/www/nrFigure3.png
diff --git a/app/www/nrFigure4.png b/app/www/nrFigure4.png
diff --git a/app/www/nrFigure5.png b/app/www/nrFigure5.png
diff --git a/app/www/nrFigure6.png b/app/www/nrFigure6.png
diff --git a/app/www/nrFigure7.png b/app/www/nrFigure7.png
diff --git a/app/www/nrFigure8.png b/app/www/nrFigure8.png
diff --git a/app/www/nrFigure9.png b/app/www/nrFigure9.png
diff --git a/app/www/tutorial1.Rmd b/app/www/tutorial1.Rmd
@@ -11,15 +11,15 @@ Through the "Novel regulatory effect" tab, users are directed to access the info
 
 ### Step 1. Database selection
 
-It provides a series of databases, which are made by using different p-values to filter data of the Psmir database. The databases are 0.05_op, 0.05_non_op, appv_0.01_op_up, appv_0.01_op_down, appv_0.01_non_op_up, appv_0.01_non_op_down, unappv_0.01_op_up, unappv_0.01_op_down, unappv_0.01_non_op_up, and unappv_0.01_non_op_down. appv is for FDA-approved. unappv is for FDA-unapproved. op is for overlapped, representing a miRNA or a small molecule in these small molecule-miRNA pairs are overlapped with miRNAs or small molecules in the DeepsmirUD training dataset. After the ‘0.05_non_op’ database is selected, tables and plots are loaded as in **Figure 1**.
+It provides a series of databases, which are made by using different p-values to filter data of the Psmir database. The databases are 0.05_op, 0.05_non_op, appv_0.01_op_up, appv_0.01_op_down, appv_0.01_non_op_up, appv_0.01_non_op_down, unappv_0.01_op_up, unappv_0.01_op_down, unappv_0.01_non_op_up, and unappv_0.01_non_op_down. appv is for FDA-approved. unappv is for FDA-unapproved. op is for overlapped, representing a miRNA or a small molecule in these small molecule-miRNA pairs are overlapped with miRNAs or small molecules in the DeepsmirUD training dataset. The loading page of the Psmir databases is shown in **Figure 1**. After the '0.05_non_op' database is selected, tables and plots are loaded as in **Figures 2-4**.
 
 <center>![Figure 1. Databases of predicted regulatory effects of the Psmir pairs](nrFigure1.png){width=95%}</center>
 
 </br>
 
 <center>![Figure 2. Novel regulatory effect data](nrFigure2.png){width=95%}</center>
 
-</br>
+**Figure 2** shows the tables and plots after page loading. The tables provide small molecule-miRNA pair information, their predicted probabilities of regulatory effects and labels of down- or up-regulation. For plots, we provide the matrix of correlation between models, histogram, distribution, and heatmap (**Figure 3** and **Figure 4**). The plots interactively change with data in the tables.
 
 <center>![Figure 3. Correlation matrix, histogram, and probability distribution plots](nrFigure3.png){width=95%}</center>
 
@@ -33,43 +33,53 @@ It provides a series of databases, which are made by using different p-values to
 
 #### (1). by small molecules
 
-In a certain database, all small molecules are listed at dropdown ‘Filter by small molecule (compound)’ (**Figure 5**).
+In a certain database, all small molecules are listed at dropdown 'Filter by small molecule (compound)' (**Figure 5**). If you do not know which small molecules should be of your interest, you can follow what is shown in **Figure 5** for filtering small molecule-miRNA pairs. If you have an idea of which small molecule should be used, you can filter small molecule-miRNA pairs according to **Figure 6**.
+
+<center>![Figure 5. Select small molecule-miRNA pairs by applying a small molecule filter 'maprotiline' and 'sanguinarine'](nrFigure5.png){width=95%}</center>
+
+</br>
 
-<center>![Figure 5. Select small molecule-miRNA pairs by applying a small molecule filter ‘vorinostat’](nrFigure5.png){width=95%}</center>
+<center>![Figure 6. Select small molecule-miRNA pairs by typing in a small molecule 'vorinostat'.](nrFigure6.png){width=95%}</center>
 
 </br>
 
-If we drag the table scroll bar rightmost, it shows that miR-106b is upregulated by vorinostat and miR-1 is downregulated by vorinostat (**Figure 6**).
+If we drag the table scroll bar rightmost, it shows that miR-433 is upregulated by vorinostat and miR-448 is downregulated by vorinostat (**Figure 7**).
 
-<center>![Figure 6. Regulation types of vorinostat-miRNA pairs](nrFigure6.png){width=95%}</center>
+<center>![Figure 7. Regulation types of vorinostat-miRNA pairs.](nrFigure7.png){width=95%}</center>
 
 </br>
 
 #### (2). by miRNAs
 
-Similarly, we can select one of the miRNAs in the selected database to filter small molecule-miRNA pairs. There are 259 pairs left after a miR-7 filter is applied (**Figure 7** and **Figure 8**).
+Similarly, we can select one of the miRNAs in the selected database to filter small molecule-miRNA pairs. There are 206 pairs left after a miR-380 filter is applied (**Figure 8**). Similar to filtering pairs by small molecules, if you have an idea of which miRNA should be used in your case, you can type in a miRNA, for example, miR-433 (**Figure 9**).
 
-<center>![Figure 7. Select small molecule-miRNA pairs by applying a miRNA filter.](nrFigure7.png){width=95%}</center>
+<center>![Figure 8. Select small molecule-miRNA pairs by applying a small molecule filter 'miR-380'.](nrFigure8.png){width=95%}</center>
 
 </br>
 
-<center>![Figure 8. Regulation types of small molecule-miR-7 pairs.](nrFigure8.png){width=95%}</center>
+<center>![Figure 9. Select small molecule-miRNA pairs by typing in a miRNA 'miR-433'.](nrFigure9.png){width=95%}</center>
 
 </br>
 
+<center>![Figure 10. Figure 10. Regulation types of small molecule-miR-7 pairs.](nrFigure10.png){width=95%}</center>
+
+</br>
+
+If we drag the table scroll bar rightmost, we can see the predicted down-regulation and up-regulation types of small molecule-miR-448 pairs (**Figure 10**).
+
 #### (3). by multiple conditions
 
-Deepsmir-Web also allows users to screen the regulation pairs with multiple conditions (**Figure 9**).
+Deepsmir-Web also allows users to screen the regulation pairs with multiple conditions, for example, miR-433, FDA-approved, and P-value (**Figure 11**).
 
-<center>![Figure 9. Small molecule-miRNA pairs filtered by multiple conditions.](nrFigure9.png){width=95%}</center>
+<center>![Figure 11. Small molecule-miRNA pairs filtered by multiple conditions.](nrFigure11.png){width=95%}</center>
 
 </br>
 
 ## 2. Curated small molecule-miRNA pairs from Verse
 
-Similarly, for getting the regulatory effects of the Verse pairs users can apply as the same precedures as in Psmir.
+Similarly, for getting the regulatory effects of the Verse pairs users can apply as the same procedures as in Psmir (**Figure 12**).
 
-<center>![Figure 10. Regulatory effects of small molecule pairs curated from Verse.](nrFigure10.png){width=95%}</center>
+<center>![Figure 12. Regulatory effects of small molecule pairs curated from Verse.](nrFigure12.png){width=95%}</center>
 
 </br>
 

diff --git a/app/www/tutorial1.md b/app/www/tutorial1.md
@@ -17,8 +17,9 @@ unappv_0.01_op_down, unappv_0.01_non_op_up, and unappv_0.01_non_op_down.
 appv is for FDA-approved. unappv is for FDA-unapproved. op is for
 overlapped, representing a miRNA or a small molecule in these small
 molecule-miRNA pairs are overlapped with miRNAs or small molecules in
-the DeepsmirUD training dataset. After the ‘0.05_non_op’ database is
-selected, tables and plots are loaded as in **Figure 1**.
+the DeepsmirUD training dataset. The loading page of the Psmir databases
+is shown in **Figure 1**. After the ‘0.05_non_op’ database is selected,
+tables and plots are loaded as in **Figures 2-4**.
 
 <center>
 
@@ -29,7 +30,6 @@ alt="Figure 1. Databases of predicted regulatory effects of the Psmir pairs" />
 regulatory effects of the Psmir pairs</figcaption>
 </figure>
 
-</center>
 </center>
 
 </br>
@@ -45,7 +45,12 @@ data</figcaption>
 
 </center>
 
-</br>
+**Figure 2** shows the tables and plots after page loading. The tables
+provide small molecule-miRNA pair information, their predicted
+probabilities of regulatory effects and labels of down- or
+up-regulation. For plots, we provide the matrix of correlation between
+models, histogram, distribution, and heatmap (**Figure 3** and **Figure
+4**). The plots interactively change with data in the tables.
 
 <center>
 
@@ -77,32 +82,50 @@ alt="Figure 4. Heatmap plot" />
 #### (1). by small molecules
 
 In a certain database, all small molecules are listed at dropdown
-‘Filter by small molecule (compound)’ (**Figure 5**).
+‘Filter by small molecule (compound)’ (**Figure 5**). If you do not know
+which small molecules should be of your interest, you can follow what is
+shown in **Figure 5** for filtering small molecule-miRNA pairs. If you
+have an idea of which small molecule should be used, you can filter
+small molecule-miRNA pairs according to **Figure 6**.
 
 <center>
 
 <figure>
 <img src="nrFigure5.png" style="width:95.0%"
-alt="Figure 5. Select small molecule-miRNA pairs by applying a small molecule filter ‘vorinostat’" />
+alt="Figure 5. Select small molecule-miRNA pairs by applying a small molecule filter ‘maprotiline’ and ‘sanguinarine’" />
 <figcaption aria-hidden="true">Figure 5. Select small molecule-miRNA
-pairs by applying a small molecule filter ‘vorinostat’</figcaption>
+pairs by applying a small molecule filter ‘maprotiline’ and
+‘sanguinarine’</figcaption>
 </figure>
 
 </center>
 
 </br>
 
-If we drag the table scroll bar rightmost, it shows that miR-106b is
-upregulated by vorinostat and miR-1 is downregulated by vorinostat
-(**Figure 6**).
-
 <center>
 
 <figure>
 <img src="nrFigure6.png" style="width:95.0%"
-alt="Figure 6. Regulation types of vorinostat-miRNA pairs" />
-<figcaption aria-hidden="true">Figure 6. Regulation types of
-vorinostat-miRNA pairs</figcaption>
+alt="Figure 6. Select small molecule-miRNA pairs by typing in a small molecule ‘vorinostat’." />
+<figcaption aria-hidden="true">Figure 6. Select small molecule-miRNA
+pairs by typing in a small molecule ‘vorinostat’.</figcaption>
+</figure>
+
+</center>
+
+</br>
+
+If we drag the table scroll bar rightmost, it shows that miR-433 is
+upregulated by vorinostat and miR-448 is downregulated by vorinostat
+(**Figure 7**).
+
+<center>
+
+<figure>
+<img src="nrFigure7.png" style="width:95.0%"
+alt="Figure 7. Regulation types of vorinostat-miRNA pairs." />
+<figcaption aria-hidden="true">Figure 7. Regulation types of
+vorinostat-miRNA pairs.</figcaption>
 </figure>
 
 </center>
@@ -112,16 +135,18 @@ vorinostat-miRNA pairs</figcaption>
 #### (2). by miRNAs
 
 Similarly, we can select one of the miRNAs in the selected database to
-filter small molecule-miRNA pairs. There are 259 pairs left after a
-miR-7 filter is applied (**Figure 7** and **Figure 8**).
+filter small molecule-miRNA pairs. There are 206 pairs left after a
+miR-380 filter is applied (**Figure 8**). Similar to filtering pairs by
+small molecules, if you have an idea of which miRNA should be used in
+your case, you can type in a miRNA, for example, miR-433 (**Figure 9**).
 
 <center>
 
 <figure>
-<img src="nrFigure7.png" style="width:95.0%"
-alt="Figure 7. Select small molecule-miRNA pairs by applying a miRNA filter." />
-<figcaption aria-hidden="true">Figure 7. Select small molecule-miRNA
-pairs by applying a miRNA filter.</figcaption>
+<img src="nrFigure8.png" style="width:95.0%"
+alt="Figure 8. Select small molecule-miRNA pairs by applying a small molecule filter ‘miR-380’." />
+<figcaption aria-hidden="true">Figure 8. Select small molecule-miRNA
+pairs by applying a small molecule filter ‘miR-380’.</figcaption>
 </figure>
 
 </center>
@@ -131,27 +156,45 @@ pairs by applying a miRNA filter.</figcaption>
 <center>
 
 <figure>
-<img src="nrFigure8.png" style="width:95.0%"
-alt="Figure 8. Regulation types of small molecule-miR-7 pairs." />
-<figcaption aria-hidden="true">Figure 8. Regulation types of small
-molecule-miR-7 pairs.</figcaption>
+<img src="nrFigure9.png" style="width:95.0%"
+alt="Figure 9. Select small molecule-miRNA pairs by typing in a miRNA ‘miR-433’." />
+<figcaption aria-hidden="true">Figure 9. Select small molecule-miRNA
+pairs by typing in a miRNA ‘miR-433’.</figcaption>
 </figure>
 
 </center>
 
 </br>
 
+<center>
+
+<figure>
+<img src="nrFigure10.png" style="width:95.0%"
+alt="Figure 10. Figure 10. Regulation types of small molecule-miR-7 pairs." />
+<figcaption aria-hidden="true">Figure 10. Figure 10. Regulation types of
+small molecule-miR-7 pairs.</figcaption>
+</figure>
+
+</center>
+
+</br>
+
+If we drag the table scroll bar rightmost, we can see the predicted
+down-regulation and up-regulation types of small molecule-miR-448 pairs
+(**Figure 10**).
+
 #### (3). by multiple conditions
 
 Deepsmir-Web also allows users to screen the regulation pairs with
-multiple conditions (**Figure 9**).
+multiple conditions, for example, miR-433, FDA-approved, and P-value
+(**Figure 11**).
 
 <center>
 
 <figure>
-<img src="nrFigure9.png" style="width:95.0%"
-alt="Figure 9. Small molecule-miRNA pairs filtered by multiple conditions." />
-<figcaption aria-hidden="true">Figure 9. Small molecule-miRNA pairs
+<img src="nrFigure11.png" style="width:95.0%"
+alt="Figure 11. Small molecule-miRNA pairs filtered by multiple conditions." />
+<figcaption aria-hidden="true">Figure 11. Small molecule-miRNA pairs
 filtered by multiple conditions.</figcaption>
 </figure>
 
@@ -162,14 +205,14 @@ filtered by multiple conditions.</figcaption>
 ## 2. Curated small molecule-miRNA pairs from Verse
 
 Similarly, for getting the regulatory effects of the Verse pairs users
-can apply as the same precedures as in Psmir.
+can apply as the same procedures as in Psmir (**Figure 12**).
 
 <center>
 
 <figure>
-<img src="nrFigure10.png" style="width:95.0%"
-alt="Figure 10. Regulatory effects of small molecule pairs curated from Verse." />
-<figcaption aria-hidden="true">Figure 10. Regulatory effects of small
+<img src="nrFigure12.png" style="width:95.0%"
+alt="Figure 12. Regulatory effects of small molecule pairs curated from Verse." />
+<figcaption aria-hidden="true">Figure 12. Regulatory effects of small
 molecule pairs curated from Verse.</figcaption>
 </figure>