## ----echo = FALSE------------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----eval=FALSE,include=TRUE,results="hide",message=FALSE,warning=FALSE------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("scBFA") ## ----include=TRUE,results="hide",message=FALSE,warning=FALSE------------------ library(zinbwave) library(SingleCellExperiment) library(ggplot2) library(scBFA) ## ----------------------------------------------------------------------------- # raw counts matrix with rows are genes and columns are cells data("exprdata") # a vector specify the ground truth of cell types provided by conquer database data("celltype") ## ----------------------------------------------------------------------------- sce <- SingleCellExperiment(assay = list(counts = exprdata)) ## ----include=TRUE,results="hide",message=FALSE-------------------------------- bfa_model = scBFA(scData = sce, numFactors = 2) ## ----fig.width=8, fig.height=6------------------------------------------------ set.seed(5) df = as.data.frame(bfa_model$ZZ) df$celltype = celltype p1 <- ggplot(df,aes(x = V1,y = V2,colour = celltype)) p1 <- p1 + geom_jitter(size=2.5,alpha = 0.8) colorvalue <- c("#43d5f9","#24b71f","#E41A1C", "#ffc935","#3d014c","#39ddb2", "slateblue2","maroon","#f7df27","palevioletred1","olivedrab3", "#377EB8","#5043c1","blue","aquamarine2","chartreuse4", "burlywood2","indianred1","mediumorchid1") p1 <- p1 + xlab("tsne axis 1") + ylab("tsne axis 2") p1 <- p1 + scale_color_manual(values = colorvalue) p1 <- p1 + theme(panel.background = element_blank(), legend.position = "right", axis.text=element_blank(), axis.line.x = element_line(color="black"), axis.line.y = element_line(color="black"), plot.title = element_blank() ) p1 ## ----------------------------------------------------------------------------- bpca = BinaryPCA(scData = sce) ## ----fig.width=8, fig.height=6------------------------------------------------ df = as.data.frame(bpca$x[,c(1:2)]) colnames(df) = c("V1","V2") df$celltype = celltype p1 <- ggplot(df,aes(x = V1,y = V2,colour = celltype)) p1 <- p1 + geom_jitter(size=2.5,alpha = 0.8) colorvalue <- c("#43d5f9","#24b71f","#E41A1C", "#ffc935","#3d014c","#39ddb2", "slateblue2","maroon","#f7df27","palevioletred1","olivedrab3", "#377EB8","#5043c1","blue","aquamarine2","chartreuse4", "burlywood2","indianred1","mediumorchid1") p1 <- p1 + xlab("tsne axis 1") + ylab("tsne axis 2") p1 <- p1 + scale_color_manual(values = colorvalue) p1 <- p1 + theme(panel.background = element_blank(), legend.position = "right", axis.text=element_blank(), axis.line.x = element_line(color="black"), axis.line.y = element_line(color="black"), plot.title = element_blank() ) p1 ## ----------------------------------------------------------------------------- sessionInfo()