bio_fc_heatmap | R Documentation |
This function exports a complex heatmap looking at the expression of different modules which can be customised
bio_fc_heatmap( exp, var, prefix = "", stars = FALSE, overlay = TRUE, logp = FALSE )
exp |
Expression Data |
var |
Vector classing samples by variables |
prefix |
Prefix to Heatmap titles |
stars |
whether pvales should be written as numeric or start (default=FALSE) |
overlay |
pvalues on fold change Heatmap or besidde (default = TRUE) |
logp |
Whether or not to log the pvalues |
... |
Other parameters to pass to Complex Heatmap |
A list containing the mean expression for each group, the fold change between groups, the pvalues comparing the expression from different groups, a heatmap with mean expression, a heatmap containing the fold change and p-values.
m.var = metadata.final[metadata.final$Pathotype %in% c("Fibroid", "Lymphoid"), ] exp = t(rldMatrix[, match(m.var$SampleID..QMUL.or.Genentech., colnames(rldMatrix))]) var = droplevels(m.var$Pathotype) fc = bio_fold.change(exp, var) p = bio_p.vals(exp, var)
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