pairs plots

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Mathew Baldwin

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Jun 12, 2020, 5:14:24 PM6/12/20

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Hi All,

Was hoping you might be able to help. Under the 'compare signatures' tab some very nice pairs plots are shown for different comparisons.

These are the log2FC of a gene in comparison A vs the log2FC of a gene in comparison B.

How is the list of genes filtered prior to entry into the dot plot? (e.g. Top 1000 rows with greatest Log2FC variance across comparisons vs all genes vs something else)

I have tried replicating the dot plots with the same data but get very different correlations.

thanks,

Mat

Ivo Kwee

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Jun 17, 2020, 6:22:32 AM6/17/20

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Hi Mathew.

The splom plot (scatterplot matrix) actually shows all the genes. The relevant code is in IntersectionModule.R in the function cmp_scatterPlotMatrix.PLOT(). Previously, genes were filtered according to the mean-squared but now all genes are shown because plotly handles it nicely. You can see that ntop=99999 so effectively the filter is doing nothing. However for many datasets, genes may have already been prefiltered from the start. For example, the arginine example data is already prefiltered to 5000 (most varying) genes using the SD.

Can you tell us how you replicated the plots and which data set you used? Are your logFC the same as ours?