@datagrok/peptides 1.14.1 → 1.15.1

package/dist/package.js.LICENSE.txt

@@ -0,0 +1,51 @@
+/**
+ * @license
+ *
+ * Copyright 2019 Google LLC. All Rights Reserved.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * ==============================================================================
+ */
+
+/**
+ * @license
+ * BSD 3-Clause License
+ *
+ * Copyright (c) 2017, Leland McInnes
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * * Redistributions of source code must retain the above copyright notice, this
+ *   list of conditions and the following disclaimer.
+ *
+ * * Redistributions in binary form must reproduce the above copyright notice,
+ *   this list of conditions and the following disclaimer in the documentation
+ *   and/or other materials provided with the distribution.
+ *
+ * * Neither the name of the copyright holder nor the names of its
+ *   contributors may be used to endorse or promote products derived from
+ *   this software without specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+ * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+ * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+ * SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+ * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+ * OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+ * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */

package/files/help/logo-summary-table.md

@@ -0,0 +1,23 @@
+# Logo Summary Table
+
+Logo Summary Table shows WebLogo, activity distribution and statistics for each of the clusters in data. Statistics include 
+mean difference, p-value, count and ratio.
+
+# Responsiveness
+
+Logo Summary Table reacts to filters applied to the data and shows only clusters of filtered rows. In this case WebLogo,
+activity distribution and statistics are calculated with respect to filtered rows.
+
+## Interactivity
+
+Logo Summary Tabl viewer selection follows default pattern as any other Datagrok viewer.
+
+|                  |                               |
+|------------------|-------------------------------|
+| Click            | Single selection of Cluster   |
+| Ctrl+Click       | Toggle Cluster selection state|
+| Shift+Click      | Add Cluster to selection      |
+| Ctrl+Shift+Click | Deselect Cluster              |
+
+Hovering over any cell will show tooltip with distribution and statistics of the monomer-position and highlight corresponding 
+points on other viewers.

package/files/help/monomer-position.md

@@ -0,0 +1,31 @@
+# Monomer-Position viewer
+
+Monomer-Position viewer is a matrix-like grid, where rows correspond to monomers and columns to positions. This viewer works in two modes: Mutation Cliffs and Invariant Map.
+
+## Mutation Cliffs mode
+
+Mutation Cliffs mode highlights the most signficant monomer-position pairs. The significance of the monomer-position is 
+color-coded with blue for negative mean difference of the sequences containing monomer-position vs. rest of the sequences,
+and red for positive mean difference. Color intensity is defined by p-value. The size of the circle represents the value of mean difference:
+smaller circles represent low mean difference values; large circles represent hight mean difference values. Some of the 
+cells contain number of unique sequences for given monomer-position, that form Mutation Cliff pairs.
+
+## Invariant Map mode
+
+Invariant Map mode shows number of sequences that contain monomer-position. Cells are color-coded based on the aggregation 
+function on some numeric column. By default average scaled activity values for given monomer-position is used. Column and
+aggregation function can be changed in viewer properties.
+
+## Interactivity
+
+Monomer-Position viewer selection follows default pattern as any other Datagrok viewer.
+
+|                  |                                        |
+|------------------|----------------------------------------|
+| Click            | Single selection of Monomer-Position   |
+| Ctrl+Click       | Toggle Monomer-Position selection state|
+| Shift+Click      | Add Monomer-Position to selection      |
+| Ctrl+Shift+Click | Deselect Monomer-Position              |
+
+Hovering over any cell will show tooltip with distribution and statistics of the monomer-position and highlight corresponding
+points on other viewers.

package/files/help/most-potent-residues.md

@@ -0,0 +1,17 @@
+# Most Potent Residues
+
+Most Potent Residues viewer for each position finds the most potent monomer and shows statistics for the monomer-position. Statistics include mean difference, p-value, count and ratio.
+
+## Interactivity
+
+Most Potent Residues viewer selection follows default pattern as any other Datagrok viewer.
+
+|                  |                                        |
+|------------------|----------------------------------------|
+| Click            | Single selection of Monomer-Position   |
+| Ctrl+Click       | Toggle Monomer-Position selection state|
+| Shift+Click      | Add Monomer-Position to selection      |
+| Ctrl+Shift+Click | Deselect Monomer-Position              |
+
+Hovering over any cell will show tooltip with distribution and statistics of the monomer-position and highlight corresponding 
+points on other viewers.

package/files/icons/ribbon/logo-summary-viewer.svg

@@ -0,0 +1,8 @@
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+<path d="M28.9545 33H26.1L26.1182 31.3681H28.9545C29.7242 31.3681 30.3697 31.2271 30.8909 30.9451C31.4121 30.658 31.8061 30.2475 32.0727 29.7136C32.3394 29.1747 32.4727 28.53 32.4727 27.7795V27.2129C32.4727 26.6337 32.397 26.1225 32.2455 25.6793C32.0939 25.236 31.8697 24.8633 31.5727 24.5611C31.2818 24.2589 30.9212 24.0298 30.4909 23.8736C30.0606 23.7175 29.5667 23.6394 29.0091 23.6394H26.0455V22H29.0091C29.8939 22 30.7 22.1234 31.4273 22.3702C32.1606 22.617 32.7939 22.9721 33.3273 23.4354C33.8667 23.8938 34.2788 24.4428 34.5636 25.0824C34.8545 25.7221 35 26.4373 35 27.228V27.7795C35 28.5652 34.8545 29.2804 34.5636 29.9251C34.2788 30.5648 33.8667 31.1138 33.3273 31.5721C32.7939 32.0304 32.1576 32.383 31.4182 32.6298C30.6788 32.8766 29.8576 33 28.9545 33ZM27.5 22V33H25V22H27.5Z" fill="#40607F"/>
+</svg>

package/files/icons/ribbon/peptide-sar-vertical-viewer.svg

@@ -0,0 +1,10 @@
+<svg width="36" height="36" viewBox="0 0 36 36" fill="none" xmlns="http://www.w3.org/2000/svg">
+<path d="M30 7.5C30 6.94772 29.5523 6.5 29 6.5H15C14.4477 6.5 14 6.94772 14 7.5V7.5C14 8.05228 14.4477 8.5 15 8.5H29C29.5523 8.5 30 8.05228 30 7.5V7.5Z" fill="#B3BFCC"/>
+<path d="M30 14.5C30 13.9477 29.5523 13.5 29 13.5H15C14.4477 13.5 14 13.9477 14 14.5V14.5C14 15.0523 14.4477 15.5 15 15.5H29C29.5523 15.5 30 15.0523 30 14.5V14.5Z" fill="#B3BFCC"/>
+<path d="M30 21.5C30 20.9477 29.5523 20.5 29 20.5H15C14.4477 20.5 14 20.9477 14 21.5V21.5C14 22.0523 14.4477 22.5 15 22.5H29C29.5523 22.5 30 22.0523 30 21.5V21.5Z" fill="#B3BFCC"/>
+<path d="M30 28.5C30 27.9477 29.5523 27.5 29 27.5H15C14.4477 27.5 14 27.9477 14 28.5V28.5C14 29.0523 14.4477 29.5 15 29.5H29C29.5523 29.5 30 29.0523 30 28.5V28.5Z" fill="#B3BFCC"/>
+<circle cx="8" cy="7.5" r="3" fill="#40607F"/>
+<circle cx="8" cy="14.5" r="1.5" fill="#7990A5"/>
+<circle cx="8" cy="28.5" r="2" fill="#7990A5"/>
+<circle cx="8" cy="21.5" r="2" fill="#40607F"/>
+</svg>

package/files/icons/ribbon/peptide-sar-viewer.svg

@@ -0,0 +1,11 @@
+<svg width="36" height="36" viewBox="0 0 36 36" fill="none" xmlns="http://www.w3.org/2000/svg">
+<circle cx="9" cy="9.5" r="3" fill="#40607F"/>
+<circle cx="18" cy="9.5" r="2" fill="#7990A5"/>
+<circle cx="9" cy="18" r="2" fill="#7990A5"/>
+<circle cx="9" cy="27" r="2" fill="#7990A5"/>
+<circle cx="18" cy="18" r="1.5" fill="#7990A5"/>
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+<circle cx="28" cy="9.5" r="3" fill="#40607F"/>
+<circle cx="18" cy="27" r="3" fill="#40607F"/>
+</svg>

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@datagrok/peptides",
   "friendlyName": "Peptides",
-  "version": "1.14.1",
+  "version": "1.15.1",
   "author": {
     "name": "Volodymyr Dyma",
     "email": "vdyma@datagrok.ai"
@@ -13,10 +13,10 @@
     "directory": "packages/Peptides"
   },
   "dependencies": {
-    "@datagrok-libraries/bio": "^5.38.2",
-    "@datagrok-libraries/ml": "^6.3.40",
-    "@datagrok-libraries/statistics": "^1.2.7",
-    "@datagrok-libraries/utils": "^4.1.13",
+    "@datagrok-libraries/bio": "^5.38.13",
+    "@datagrok-libraries/ml": "^6.3.49",
+    "@datagrok-libraries/statistics": "^1.2.8",
+    "@datagrok-libraries/utils": "^4.1.18",
     "@datagrok-libraries/tutorials": "^1.3.7",
     "cash-dom": "^8.1.5",
     "datagrok-api": "^1.16.4",