## ---- echo = FALSE, message = FALSE--------------------------------------
library(knitr)
knitr::opts_chunk$set(
# cache = TRUE,
dpi = 60,
comment = '#>',
tidy = FALSE)
## ------------------------------------------------------------------------
# Let's load the packages
library(heatmaply)
library(heatmaplyExamples)
## ------------------------------------------------------------------------
center_voom_mat <- voomed_pam50_expression -
apply(voomed_pam50_expression, 1, median)
voom_max <- max(abs(center_voom_mat))
voom_limits <- c(-voom_max, voom_max)
heatmaply(t(center_voom_mat),
row_side_colors=tcga_brca_clinical,
fontsize_col = 7.5,
showticklabels = c(TRUE, FALSE),
col = cool_warm(50),
limits = voom_limits,
main = 'Normalised, centred log2 CPM, PAM50 genes',
plot_method = 'plotly')
## ---- fig.width=13, fig.height=10----------------------------------------
heatmaply_cor(cor(center_voom_mat),
row_side_colors = tcga_brca_clinical,
showticklabels = c(FALSE, FALSE),
main = 'Sample-sample correlation based on centred, normalised PAM50 gene expression',
plot_method = 'plotly')
## ------------------------------------------------------------------------
sessionInfo()
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