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b/R/DIscBIO-generic-plotExptSNE.R |
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#' @title Highlighting gene expression in the t-SNE map |
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#' @description The t-SNE map representation can also be used to analyze |
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#' expression of a gene or a group of genes, to investigate cluster specific |
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#' gene expression patterns |
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#' @param object \code{DISCBIO} class object. |
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#' @param g Individual gene name or vector with a group of gene names |
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#' corresponding to a subset of valid row names of the \code{ndata} slot of |
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#' the \code{DISCBIO} object. |
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#' @param n String of characters representing the title of the plot. Default is |
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#' NULL and the first element of \code{g} is chosen. |
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#' @return t-SNE plot for one particular gene |
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setGeneric("plotExptSNE", function(object, g, n = NULL) { |
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standardGeneric("plotExptSNE") |
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}) |
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#' @export |
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#' @rdname plotExptSNE |
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setMethod( |
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"plotExptSNE", |
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signature = "DISCBIO", |
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definition = function(object, g, n = NULL) { |
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# ====================================================================== |
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# Validation |
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# ====================================================================== |
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ran_k <- length(object@tsne) > 0 |
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ran_m <- length(object@MBtsne) > 0 |
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if (ran_k) { |
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x <- object@tsne |
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} else if (ran_m) { |
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x <- object@MBtsne |
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} else { |
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stop("run comptSNE before plotExptSNE") |
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} |
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if (length(intersect(g, rownames(object@ndata))) < length(unique(g))) { |
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stop( |
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"second argument does not correspond to set of rownames slot", |
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"ndata of SCseq object" |
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) |
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} |
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if (is.null(n)) n <- g[1] |
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# ====================================================================== |
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# Plotting |
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# ====================================================================== |
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logObj <- log(object@ndata) |
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l <- apply(logObj[g, ] - .1, 2, sum) + .1 |
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mi <- min(l, na.rm = TRUE) |
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ma <- max(l, na.rm = TRUE) |
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ColorRamp <- colorRampPalette( |
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rev(brewer.pal(n = 7, name = "RdYlBu")) |
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)(100) |
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ColorLevels <- seq(mi, ma, length = length(ColorRamp)) |
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v <- round((l - mi) / (ma - mi) * 99 + 1, 0) |
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layout( |
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matrix( |
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data = c(1, 3, 2, 4), |
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nrow = 2, |
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ncol = 2 |
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), |
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widths = c(5, 1, 5, 1), |
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heights = c(5, 1, 1, 1) |
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) |
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opar <- withr::local_par(mar = c(3, 5, 2.5, 2)) |
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on.exit(withr::local_par(opar)) |
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plot( |
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x, |
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xlab = "Dim 1", |
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ylab = "Dim 2", |
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main = n, |
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pch = 20, |
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cex = 0, |
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col = "grey", |
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las = 1 |
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) |
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for (k in seq_len(length(v))) { |
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points( |
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x[k, 1], |
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x[k, 2], |
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col = ColorRamp[v[k]], |
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pch = 20, |
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cex = 1.5 |
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) |
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} |
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opar <- withr::local_par(mar = c(3, 2.5, 2.5, 2)) |
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on.exit(withr::local_par(opar)) |
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image( |
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1, |
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ColorLevels, |
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matrix( |
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data = ColorLevels, |
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ncol = length(ColorLevels), |
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nrow = 1 |
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), |
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col = ColorRamp, |
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xlab = "", |
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ylab = "", |
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las = 1, |
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xaxt = "n" |
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) |
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layout(1) |
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} |
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) |