48 lines
2.7 KiB
R
48 lines
2.7 KiB
R
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## -----------------------------------------------------------------------------
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library(gapmap)
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data("sample_tcga")
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library(RColorBrewer)
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RdBu = rev(brewer.pal(11, name="RdBu"))
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RdYlBu = rev(brewer.pal(11, name="RdYlBu"))
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## -----------------------------------------------------------------------------
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#transpose
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dataTable <- t(sample_tcga)
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#calculate the correlation based distance
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row_dist <- as.dist(1-cor(t(dataTable), method = "pearson"))
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col_dist <- as.dist(1-cor(dataTable, method = "pearson"))
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#hierarchical clustering
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col_hc <- hclust(col_dist, method = "complete")
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row_hc <- hclust(row_dist, method = "complete")
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col_d <- as.dendrogram(col_hc)
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row_d <- as.dendrogram(row_hc)
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## ---- fig.height=5, fig.width=7-----------------------------------------------
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gapmap(m = as.matrix(dataTable), d_row = rev(row_d), d_col = col_d, ratio = 0, verbose=FALSE, col=RdBu,
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label_size=2, v_ratio= c(0.1,0.8,0.1), h_ratio=c(0.1,0.8,0.1))
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## ---- fig.height=5, fig.width=7-----------------------------------------------
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gapmap(m = as.matrix(dataTable), d_row = rev(row_d), d_col = col_d, mode = "quantitative", mapping="exponential", col=RdBu,
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ratio = 0.3, verbose=FALSE, scale = 0.5, label_size=2, v_ratio= c(0.1,0.8,0.1), h_ratio=c(0.1,0.8,0.1))
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## ---- fig.height=5, fig.width=7-----------------------------------------------
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gapmap(m = as.matrix(dataTable), d_row = rev(row_d), d_col = col_d, mode = "quantitative", mapping="exponential", col=RdYlBu,
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ratio = 0.3, verbose=FALSE, scale = 0.5, label_size=2, v_ratio= c(0.1,0.8,0.1), h_ratio=c(0.1,0.8,0.1))
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## ---- fig.height=5, fig.width=7-----------------------------------------------
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library(dendsort)
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gapmap(m = as.matrix(dataTable), d_row = rev(dendsort(row_d, type = "average")), d_col = dendsort(col_d, type = "average"),
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mode = "quantitative", mapping="exponential", ratio = 0.3, verbose=FALSE, scale = 0.5, v_ratio= c(0.1,0.8,0.1),
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h_ratio=c(0.1,0.8,0.1), label_size=2, show_legend=TRUE, col=RdBu)
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## ---- fig.height=5, fig.width=7-----------------------------------------------
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row_data <- gap_data(d= row_d, mode = "quantitative", mapping="exponential", ratio=0.3, scale= 0.5)
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dend <- gap_dendrogram(data = row_data, leaf_labels = TRUE, rotate_label = TRUE)
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dend + theme(axis.ticks.length= grid::unit(0,"lines") )+ theme(axis.ticks.margin = grid::unit(-0.8, "lines"))
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## ---- fig.height=5, fig.width=7-----------------------------------------------
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row_data <- gap_data(d= dendsort(row_d, type = "average"), mode = "quantitative", mapping="exponential", ratio=0.3, scale= 0.5)
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dend <- gap_dendrogram(data = row_data, leaf_labels = TRUE, rotate_label = TRUE)
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dend + theme(axis.ticks.length= grid::unit(0,"lines") )+ theme(axis.ticks.margin = grid::unit(-0.8, "lines"))
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