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| ^.*\.Rproj$ | ||
| ^\.Rproj\.user$ |
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| .Rproj.user | ||
| .Rhistory | ||
| .RData | ||
| .Ruserdata | ||
| src/*.o | ||
| src/*.so | ||
| src/*.dll |
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| plot_sections <- function(merfish.anno, | ||
| meta.f, | ||
| meta.col, | ||
| select.cells, | ||
| coord.to.use = "corrected", | ||
| negative.y = T, | ||
| frac.overlap = 0.05, | ||
| sections, | ||
| ncol=length(sections), | ||
| layout=NULL, | ||
| plot.option=c("all","left","right","folded","crop"), | ||
| label.top=4, | ||
| fg.alpha=1, | ||
| fg.cex=1, | ||
| combine.plots=TRUE, | ||
| frac.crop = c(0,0,0,0), #crop x(l), x(r), y(t), y(b) | ||
| label.cex = 1, | ||
| plot.ccf = NULL, | ||
| ccf.column = "CCF_acronym", | ||
| ...) | ||
| { | ||
| x_coord <- paste0(coord.to.use,"_x") | ||
| y_coord <- paste0(coord.to.use,"_y") | ||
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| rd.dat = as.data.frame(merfish.anno[,c(x_coord,y_coord)]) | ||
| if(isTRUE(negative.y)){ | ||
| rd.dat[,2] = - rd.dat[,2] | ||
| } | ||
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| #xlims <- c(min(rd.dat[,1]), max(rd.dat[,1])) | ||
| #ylims <- c(min(rd.dat[,2]), max(rd.dat[,2])) | ||
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| row.names(rd.dat) = merfish.anno$cell_id | ||
| meta = setNames(merfish.anno[[meta.f]], merfish.anno$cell_id) | ||
| meta.section = merfish.anno %>% filter(cell_id %in% select.cells & section %in% sections) %>% select(one_of(c(meta.f, "section"))) %>% group_by_at(vars(one_of(meta.f))) %>% summarise(select.section = names(which.max(table(section)))) | ||
| select.meta.section = setNames(meta.section[["select.section"]],meta.section[[meta.f]]) | ||
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| g.list=list() | ||
| for(sec in sections){ | ||
| # print(sec) | ||
| all.cells = intersect(merfish.anno %>% filter(section==sec) %>% pull(cell_id),row.names(rd.dat)) | ||
| select.rd.dat = rd.dat[all.cells,] | ||
| if(plot.option=="folded"){ | ||
| select.rd.dat[,1] =abs(select.rd.dat[,1]) | ||
| } else if(plot.option=="left"){ | ||
| #cutoff = rearrr::centroid(select.rd.dat[,x_coord]) + (rearrr::centroid(select.rd.dat[,x_coord])*frac.overlap) | ||
| cutoff = mean(select.rd.dat[,x_coord]) + mean(select.rd.dat[,x_coord])*frac.overlap | ||
| select.rd.dat = select.rd.dat[select.rd.dat[,1]<=cutoff,,drop=F] | ||
| } else if(plot.option=="right"){ | ||
| cutoff = mean(select.rd.dat[,x_coord]) - mean(select.rd.dat[,x_coord])*frac.overlap | ||
| select.rd.dat = select.rd.dat[select.rd.dat[,1]>= cutoff,,drop=F] | ||
| } else if(plot.option == "crop"){ | ||
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| min.x = min(select.rd.dat[,x_coord]) | ||
| max.x = max(select.rd.dat[,x_coord]) | ||
| cutoff.xl = min.x + ((max.x-min.x)*frac.crop[1]) | ||
| cutoff.xr = min.x + ((max.x-min.x)*(1-frac.crop[2]) ) | ||
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| select.rd.dat = select.rd.dat[select.rd.dat[,x_coord]>=cutoff.xl,,drop=F] | ||
| select.rd.dat = select.rd.dat[select.rd.dat[,x_coord]<=cutoff.xr,,drop=F] | ||
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| min.y = min(select.rd.dat[,y_coord]) | ||
| max.y = max(select.rd.dat[,y_coord]) | ||
| cutoff.yb = min.y + ((max.y-min.y)*frac.crop[4]) | ||
| cutoff.yt = min.y + ((max.y-min.y)*(1-frac.crop[3]) ) | ||
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| select.rd.dat = select.rd.dat[select.rd.dat[,y_coord]>=cutoff.yb,,drop=F] | ||
| select.rd.dat = select.rd.dat[select.rd.dat[,y_coord]<=cutoff.yt,,drop=F] | ||
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| } | ||
| fg.cells = intersect(select.cells, row.names(select.rd.dat)) | ||
| cl.size = table(meta[fg.cells]) | ||
| if(length(fg.alpha)>1){ | ||
| select.fg.alpha = fg.alpha[fg.cells] | ||
| } else{ | ||
| select.fg.alpha= fg.alpha | ||
| } | ||
| if(length(fg.cex)>1){ | ||
| select.fg.cex = fg.cex[fg.cells] | ||
| } else{ | ||
| select.fg.cex = fg.cex | ||
| } | ||
| label.meta = names(select.meta.section)[select.meta.section==sec] | ||
| label.meta = union(label.meta, names(tail(sort(cl.size[cl.size > 0]), label.top))) | ||
| g.list[[sec]]=plot_RD_highlight(select.rd.dat, | ||
| meta=meta, | ||
| meta.col=meta.col, | ||
| label.meta = label.meta, | ||
| fg.cells = fg.cells, | ||
| fg.alpha=select.fg.alpha, | ||
| fg.cex=select.fg.cex, | ||
| label.cex=label.cex, | ||
| #xlims = xlims, | ||
| #ylims = ylims, | ||
| ... | ||
| ) | ||
| } | ||
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| if(!is.null(plot.ccf)){ | ||
| require(ggforce) | ||
| for(sect in names(g.list)){ | ||
| print(sect) | ||
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| sel.sect <- sect | ||
| hull.df <- merfish.anno %>% | ||
| filter(section %in% sect) | ||
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| if(isTRUE(negative.y)){ | ||
| hull.df[,y_coord] = - hull.df[,y_coord] | ||
| } | ||
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| plot.meta <- g.list[[sect]][["data"]] | ||
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| plot.meta <- plot.meta %>% | ||
| left_join(hull.df[,c(x_coord,y_coord,"CCF_bin_x", "CCF_bin_y",ccf.column)], by=c("Dim1"=x_coord, "Dim2"=y_coord) ) | ||
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| g.list[[sect]] <- g.list[[sect]] + #theme_bw() + | ||
| ggnewscale::new_scale_color() + | ||
| geom_mark_hull(data = plot.meta %>% ungroup(), inherit.aes = F, | ||
| aes( x=Dim1, y=Dim2, filter = get(ccf.column) %in% plot.ccf), | ||
| lwd = 0.1, | ||
| concavity = 5, | ||
| expand=0, | ||
| radius=0 | ||
| ) | ||
| } | ||
| } | ||
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| if(combine.plots){ | ||
| multiplot(plotlist= g.list, cols = ncol, layout=layout,byrow=TRUE) | ||
| #gridExtra::grid.arrange(grobs=g.list,ncol=ncol,top=textGrob(plotTitle)) | ||
| } | ||
| else{ | ||
| return(g.list) | ||
| } | ||
| } | ||
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| plot_gene_sections <- function(merfish.anno, big.dat=NULL, gene.exp=NULL, gene, sections, ncol=length(sections), colorset= c("#ffffd9","#c7e9b4","#41b6c4","#1d91c0","#225ea8","#081d58"),plot.option=c("left","right","both"),...) | ||
| { | ||
| rd.dat = merfish.anno[,c("global_x","global_y")] | ||
| row.names(rd.dat) = merfish.anno$cell_id | ||
| if(is.null(gene.exp)){ | ||
| gene.exp = get_cols(big.dat, rows=gene, cols = big.dat$col_id,sparse=FALSE) | ||
| } | ||
| meta.bin = setNames(cut(gene.exp[gene,], 100), colnames(gene.exp)) | ||
| meta.col = setNames(colorRampPalette(colorset)(100), levels(meta.bin)) | ||
| g.list=list() | ||
| for(s in sections){ | ||
| all.cells = merfish.anno %>% filter(section==s) %>% pull(cell_id) | ||
| select.rd.dat = rd.dat[all.cells,] | ||
| if(plot.option=="left"){ | ||
| select.rd.dat = select.rd.dat[select.rd.dat[,1]<=0.5,,drop=F] | ||
| }else if(plot.option=="right"){ | ||
| select.rd.dat = select.rd.dat[select.rd.dat[,1]>=-0.5,,drop=F] | ||
| } | ||
| all.cells = row.names(select.rd.dat) | ||
| fg.cells = all.cells[gene.exp[gene, all.cells] > 0] | ||
| g.list[[paste0(s,gene)]] =plot_RD_highlight(select.rd.dat, meta= meta.bin[all.cells], meta.col=meta.col, show.legend="none",raster=TRUE, fg.cells=fg.cells,...) | ||
| } | ||
| return(g.list) | ||
| } | ||
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