edits to prediction results page (jobresults.html)

[billspat]

• Validation section

The numbers of genes in the first two sentences are missing. “The number of genes in the input file was . The number of those genes that were uniquely mapped to an Entrez ID and were also in the network is .” - I

Because these are input genes, the table below should show ALL the input genes and not just the top 500. And, so, we don’t need another link to download the whole gene table; users should be able to just use the buttons just above the table.

• Validation section, Change the text as follows:

There were X genes in the input. Out of these, X genes were uniquely mapped to an Entrez ID and present in the chosen network.

Use the buttons on the top-right of the table to download the table of genes shown below.

• Network Graph tab

  • in the Directions with three bullet points. First bullet point says “Clicking a node will display additional information about the gene on the right side” but this information actually shows up on the left side.

  • change the text

Change text above visualization as follows:

The visualization below shows the network of the top 50 genes based on predicted probability.

Directions: Click a node to display additional information about the gene on the left panel. Drag a node to make it sticky (it will no longer move by itself). Double click a sticky node to allow it to move freely again. Use the slider to select more or less genes (nodes) to show based on gene probability.

The current view of the graph can be exported as a PNG or SVG file. The entire list of edges can be downloaded as a tab-separated file.

• Parameters/summary table above the tabs

  • Make the main header and overall paddings consistent with all the other pages.

• Download all results button at the top-right

  • Change button text to “Download all results as zip file”.

  • Remove the “?” icon. The button’s quite self explanatory.

  • Right-align the button exactly with the box/table below.

  • Tab design and text

  • Make the tab selection more obvious by making the line (that wraps above the selected tab and below the other tabs) a little thicker.

  • Change “Similarities to Disease” to “Similarities to Diseases”.

  • Change “Validation Data” to “Input Genes”

• DataTables design under all tabs The tables contain a lot of empty space. So, they need not span the entire width of the page. Reduce the width to 75% current width, center-align with the page, and adjust the widths of specific columns based on content.

  • comment: this is only a problem when the screen is wide. can we also have the tables take up the full width when the page is narrow? e.g. putting the tables in a row/column and have the column use breakpoints? *

• Gene Prediction table

  • make “Rank” the first column on the left == Move Rank to column 1 and keep the width to the minimum.
  • Make the widths of columns ‘Entrez’, ‘Symbol’, ‘Probability’, ‘Known/Novel’, and ‘Class-Label’ the same and snug. -0 Make the ‘Name’ column use the remaining width.

• Similarities to BPs/Diseases table: make “Rank” the first column on the left.

  • Gene Predictions tab help: Change and layout the text as follows:

The table below shows the top 500 genes with the highest prediction probability.

• Probability: Indicates the gene’s network-based similarity to the input genes.
• Rank: Rank of the gene when sorted by prediction probability (up to several decimals).
• Class-Labels: ‘P’ – gene was considered in positive class during training, ‘N’ – gene was considered in negative class during training, and ‘U’ – gene was not considered at all during training.
• Known/Novel: Indicates whether the gene was part of the input gene list (therefore ‘Known’) or not (therefore ‘Novel’).

Use the buttons on the top-right of the table to download the top predictions. Download the prediction probability of all the genes in the network as a tab-separated file at this link.

• Similarities to Biological Processes, Change the text as follows:

The table below shows network-based ML models trained on sets of genes associated with Gene Ontology Biological Process terms ranked by their similarity to the custom ML model trained on the input genes. See the Help page for more information.

Use the buttons on the top-right of the table to download the table of terms shown below. Download the similarity to all Biological Processes as a tab-separated file at this link.

• Similarities to Disease, Change the text as follows:

The table below shows network-based ML models trained on sets of genes associated with diseases in the DisGeNet database ranked by their similarity to the custom ML model trained on the input genes. See the Help page for more information.

Use the buttons on the top-right of the table to download the table of terms shown below. Download the similarity to all Diseases as a tab-separated file at this link.

[billspat]

moving changes to order of data tables into a new issue since it's a different part of the code.

[billspat]

I made all text changes and to have the tabs look more prominent than the very thin border, I used "pills' or buttons that were blue text to indicate they are links. In addition I changed the download links to green to match the download zip link, but outlined so they didn't dominate the page. closing.