Nothing
## ----use-libs, include = FALSE------------------------------------------------
library(mfa)
library(ggplot2)
library(dplyr)
knitr::opts_chunk$set(echo = TRUE, cache = TRUE, fig.width = 6, fig.height = 4,
warning = FALSE, message = FALSE)
## ----install-bioconductor, eval = FALSE---------------------------------------
# if (!requireNamespace("BiocManager", quietly=TRUE))
# install.packages("BiocManager")
# BiocManager::install("mfa")
# library(mfa)
## ----install-github, eval = FALSE---------------------------------------------
# install.packages("devtools") # If not already installed
# devtools::install_github("kieranrcampbell/mfa")
# library(mfa)
## ----synthetic----------------------------------------------------------------
synth <- create_synthetic(C = 100, G = 40)
print(str(synth))
## ----to-tidy------------------------------------------------------------------
df_synth <- as_data_frame(prcomp(synth$X)$x[,1:2]) %>%
mutate(pseudotime = synth$pst,
branch = factor(synth$branch))
## ----pca-rep------------------------------------------------------------------
ggplot(df_synth, aes(x = PC1, y = PC2, color = pseudotime)) + geom_point()
ggplot(df_synth, aes(x = PC1, y = PC2, color = branch)) + geom_point()
## ----run-mfa------------------------------------------------------------------
m <- mfa(synth$X)
print(m)
## ----diagnostics--------------------------------------------------------------
plot_mfa_trace(m)
plot_mfa_autocorr(m)
## ----summary------------------------------------------------------------------
ms <- summary(m)
print(head(ms))
## ----compare-pst--------------------------------------------------------------
qplot(synth$pst, ms$pseudotime, color = factor(synth$branch)) +
xlab('True pseudotime') + ylab('Inferred pseudotime') +
scale_color_discrete(name = 'True\nbranch')
## ----pca-rep-with-branch------------------------------------------------------
mutate(df_synth, inferred_branch = ms[['branch']]) %>%
ggplot(aes(x = PC1, y = PC2, color = inferred_branch)) +
geom_point() +
scale_color_discrete(name = 'Inferred\nbranch')
## ----plot-chi-----------------------------------------------------------------
plot_chi(m)
## ----posterior-mean-chi-------------------------------------------------------
posterior_chi_df <- calculate_chi(m)
head(posterior_chi_df)
## ----str-mfa------------------------------------------------------------------
str(m, max.level = 1)
## ----str-traces---------------------------------------------------------------
print(names(m$traces))
## ----tau----------------------------------------------------------------------
str(m$traces$tau_trace)
## ----print-k------------------------------------------------------------------
str(m$traces$k_trace)
## ----posterior-mean-of-k------------------------------------------------------
pmean_k <- apply(m$traces$k_trace, 3, colMeans)
str(pmean_k)
## ----sess-info----------------------------------------------------------------
sessionInfo()
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