plotTopZallPath | R Documentation |
plotTopZ
. However in this case all the pathways contributing to each LV are show seperatly. Useful for seeing pathway usage for a single LV or understading the differences between two closely related LVsvisualize the top genes contributing to the LVs similarily to plotTopZ
. However in this case all the pathways contributing to each LV are show seperatly. Useful for seeing pathway usage for a single LV or understading the differences between two closely related LVs
plotTopZallPath(
plierRes,
data,
priorMat,
top = 10,
index = NULL,
regress = F,
fdr.cutoff = 0.2,
...
)
plierRes |
the result returned by PLIER |
data |
the data to be displayed in a heatmap, typically the z-scored input data (or some subset thereof) |
priorMat |
the same gene by geneset binary matrix that was used to run PLIER |
top |
the top number of genes to use |
index |
the subset of LVs to display |
regress |
remove the effect of all other LVs before plotting top genes, will take longer but can be useful to see distinct patterns in highly correlated genes. |
fdr.cutoff |
Significance cutoff for a pathway to be plotted |
... |
Additional arguments to be passed to pheatmap, such as a column annotation data.frame |
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