## ---------------------------------------------------------------------------------------------------------------------------------------------------库（MFA）库（GGPLOT2）库（dplyr）knitr :: opts_chunk $ set（echo = true，cache = true，fig.width = 6，fic.height = 4，警告= false，message = false）## ----安装双管仪，eval = false -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------＃＃if（！sireseenamespace（“ biocmanager”，悄悄= true））＃install.packages（“ biocmanager”）＃biocmanager :: install（install（“ mfa”）＃library（mfa）## ----安装github，eval = false ----------------------------------------------------------------------------------------------＃install.packages（“ devtools”）＃如果尚未安装＃devtools :: install_github（“ kieranrcampbell/mfa”）＃library（mfa）## ----------------------------------------------------------------------------------------------------------------------------------------------------------------------合成器< - create_synthetic（c = 100，g = 40）print（str（Synth））## ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- df_synth < - as_data_frame（prcomp（synth $ x）$ x [，1：2]）％>％突变（pseudotime = synth $ pst，branch = factor = factor（synth $ branch））## ---- PCA-REP -------------------------------------------------------------------------------------------------------------------------------------------- ggplot（df_synth，aes（x = pc1，y = pc2，color = pseudotime）） + geom_point（）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()