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InteractiveFeatureExploration

Workflow

Interactive visualization of phenotypic features in zebrafish
PCAscreeningzebrafishjavascript viewsvisualizationfeatures
Interactive feature exploration dashboard- Install any missing KNIME extensions- Download the excel table FeatureTable.xlsx from the open science framework (or from Biorxiv supplementary data)https://doi.org/10.17605/OSF.IO/WPN2Mor from the KNIME Hub (workflow only) : https://kni.me/w/O3Q36l_xNLQ85IRg- In the excel reader node, load the excel file ExplorationToolData.xls- Execute the workflow by right-clicking on the rightmost node (Interactive Dashboard) and select "Execute and Open Views" This will automatically display the interactive dashboard after a few seconds.Associated publicationIn vivo high-content screening in zebrafish for developmental nephrotoxicity of approved drugsJH Westhoff, PJ Steenbergen, LSV Thomas, J Heigwer, T Bruckner, L Cooper, B Tönshoff, GF Hoffmann, J GehrigFrontiers in cell and developmental biology doi: https://doi.org/10.3389/fcell.2020.00583Youtube Tutorial : How to use the workflowhttps://youtu.be/A4Eqe1Aju4AAdapt to own dataMake sure your data is normalised (0-1 or Z-score normalisation) so that they cover similar value ranges.Otherwise if one feature is in the 100 range while another in the 0.1 range, the PCA will be much more influenced by the feature in the 100range (especially in terms of variations e.g. variation in range 10-50 compared to maybe 0,1-1 Read feature tableUse a column as color(default normal ratio)Right clickExecute and Open viewremove RowId Excel Reader (XLS) Color Manager InteractiveDashboard Column Filter Interactive feature exploration dashboard- Install any missing KNIME extensions- Download the excel table FeatureTable.xlsx from the open science framework (or from Biorxiv supplementary data)https://doi.org/10.17605/OSF.IO/WPN2Mor from the KNIME Hub (workflow only) : https://kni.me/w/O3Q36l_xNLQ85IRg- In the excel reader node, load the excel file ExplorationToolData.xls- Execute the workflow by right-clicking on the rightmost node (Interactive Dashboard) and select "Execute and Open Views" This will automatically display the interactive dashboard after a few seconds.Associated publicationIn vivo high-content screening in zebrafish for developmental nephrotoxicity of approved drugsJH Westhoff, PJ Steenbergen, LSV Thomas, J Heigwer, T Bruckner, L Cooper, B Tönshoff, GF Hoffmann, J GehrigFrontiers in cell and developmental biology doi: https://doi.org/10.3389/fcell.2020.00583Youtube Tutorial : How to use the workflowhttps://youtu.be/A4Eqe1Aju4AAdapt to own dataMake sure your data is normalised (0-1 or Z-score normalisation) so that they cover similar value ranges.Otherwise if one feature is in the 100 range while another in the 0.1 range, the PCA will be much more influenced by the feature in the 100range (especially in terms of variations e.g. variation in range 10-50 compared to maybe 0,1-1 Read feature tableUse a column as color(default normal ratio)Right clickExecute and Open viewremove RowIdExcel Reader (XLS) Color Manager InteractiveDashboard Column Filter

Download

Get this workflow from the following link: Download

Nodes

InteractiveFeatureExploration consists of the following 29 nodes(s):

Plugins

InteractiveFeatureExploration contains nodes provided by the following 7 plugin(s):