Multigene Display Viewer

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Select pairwise distance metric Select the metric to compute the pairwise distance for genes, and if applicable, observations.

Enable subsampling

Select observation subsampling number Select a number of random observation samples from the total set to use. Saves on computation.

Create matrixplot, which aggregates mean expression of replicates based on the specified included groups.

Center the mean expression values around zero.

Choosing a diverging colorscale is recommended when enabling this option, and a sequential colorscale when disabling this option.

Perform hierarchical clustering of observation samples.

NOTE: Disables sorting by primary and secondary categories.

Perform hierarchical clustering of genes.

NOTE: Disables sorting by genes

Flip genes and observations axes.

Genes as columns, observations as rows.

Hide observation labels in axis

Hide gene labels in axis

Select comparison condition 1 Select the first query condition to compare to the reference condition.

Select comparison condition 2 Select the second query condition to compare to the reference condition.

Select reference condition Select the reference condition to compare to each of the query conditions. All conditions must come from the same category.

Adjust fold-change cutoff Choose the fold-change threshold that a query/ref comparison must exceed to be included. This value will be log2-transformed in plot.

Adjust FDR cutoff Choose the FDR (or qval) threshold a query/ref comparison must be under to be considered. Used in tandem with FDR cutoff.

Include genes where the query and ref expression is equal.

Include genes where the query and ref fold change ratio is 1 (log2FC = 0). This condition supercedes the fold-change threshold and adds these genes to that filtered set.

Adjust p-value threshold Choose a p-value where all data points above the line are considered significant. This value will be -log10-transformed in the plot.

Adjust log2 fold-change threshold

Lower Bounds

Upper Bounds

Choose bounds of log2 fold-change threshold. All data points outside of this range will be colored as up- or down-regulated.

Select query condition Select the query condition.

Select reference condition Select the reference condition. Condition must come from the same category as query condition.

Annotate nonsignificant genes.

Use adjusted p-values (q-values) instead of raw p-values.

Create stacked violin plot.

Each category group is in its own violin plot.

Add data points to violin plot.

Select differential expression test Select the differential expression testing algorithm to determine significance.

Adjust plot title If left blank, plot will have a default title or no title.

Select colorscale for plot Select the colorscale used in this plot. Leaving unselected will use a default colorscale particular to the plot type.

Reverse colorscale used in plot.

Cart name to create:

Fold-change:

Raw

Log2

Log10

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Multigene Display Viewer

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