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• 10:31, 30 August 2022 Brb talk contribs uploaded File:ViridisDefault.png (<pre> library(viridis) n = 200 image( 1:n, 1, as.matrix(1:n), col = viridis(n, option = "D"), xlab = "viridis n", ylab = "", xaxt = "n", yaxt = "n", bty = "n" ) </pre>)
• 10:31, 30 August 2022 Brb talk contribs created page File:ViridisDefault.png (<pre> library(viridis) n = 200 image( 1:n, 1, as.matrix(1:n), col = viridis(n, option = "D"), xlab = "viridis n", ylab = "", xaxt = "n", yaxt = "n", bty = "n" ) </pre>)
• 10:08, 30 August 2022 Brb talk contribs uploaded File:ScaleFillViridisDiscrete.png (See https://r-graph-gallery.com/79-levelplot-with-ggplot2.html <pre> library(ggplot2) # library(hrbrthemes) # Dummy data x <- LETTERS[1:20] y <- paste0("var", seq(1,20)) data <- expand.grid(X=x, Y=y) data$Z <- runif(400, 0, 5) library(viridis) ggplot(data, aes(X, Y, fill= Z)) + geom_tile() + scale_fill_viridis(discrete=FALSE) </pre>)
• 10:08, 30 August 2022 Brb talk contribs created page File:ScaleFillViridisDiscrete.png (See https://r-graph-gallery.com/79-levelplot-with-ggplot2.html <pre> library(ggplot2) # library(hrbrthemes) # Dummy data x <- LETTERS[1:20] y <- paste0("var", seq(1,20)) data <- expand.grid(X=x, Y=y) data$Z <- runif(400, 0, 5) library(viridis) ggplot(data, aes(X, Y, fill= Z)) + geom_tile() + scale_fill_viridis(discrete=FALSE) </pre>)
• 14:19, 29 August 2022 Brb talk contribs uploaded File:Rbiomirgs barall.png
• 14:19, 29 August 2022 Brb talk contribs created page File:Rbiomirgs barall.png
• 14:17, 29 August 2022 Brb talk contribs uploaded File:Rbiomirgs bar.png
• 14:17, 29 August 2022 Brb talk contribs created page File:Rbiomirgs bar.png
• 14:17, 29 August 2022 Brb talk contribs uploaded File:Rbiomirgs volcano.png
• 14:17, 29 August 2022 Brb talk contribs created page File:Rbiomirgs volcano.png
• 07:08, 27 August 2022 Brb talk contribs uploaded File:FgseaPlotTop.png
• 07:08, 27 August 2022 Brb talk contribs created page File:FgseaPlotTop.png
• 06:34, 27 August 2022 Brb talk contribs uploaded File:FgseaPlotSmall2.png
• 06:34, 27 August 2022 Brb talk contribs created page File:FgseaPlotSmall2.png
• 06:34, 27 August 2022 Brb talk contribs uploaded File:FgseaPlotSmall.png
• 06:34, 27 August 2022 Brb talk contribs created page File:FgseaPlotSmall.png
• 06:33, 27 August 2022 Brb talk contribs uploaded File:FgseaPlot.png
• 06:33, 27 August 2022 Brb talk contribs created page File:FgseaPlot.png
• 15:02, 23 August 2022 Brb talk contribs uploaded File:ComplexHeatmap1.png (<pre> library(ComplexHeatmap) set.seed(123) ng <- 10; n <- 10 mat = matrix(rnorm(ng * n), n) rownames(mat) = paste0("R", 1:ng) colnames(mat) = paste0("C", 1:n) bin <- sample(c("resistant", "sensitive"), n, replace = TRUE) tgi <- runif(n) # sort the columns by tgi ord <- order(tgi) col_fun = circlize::colorRamp2(range(tgi), c("#DEEBF7", "#084594")) column_ha = HeatmapAnnotation(tgi = tgi[ord], bin = bin[ord], col = list(tgi = col_fun,...)
• 15:02, 23 August 2022 Brb talk contribs created page File:ComplexHeatmap1.png (<pre> library(ComplexHeatmap) set.seed(123) ng <- 10; n <- 10 mat = matrix(rnorm(ng * n), n) rownames(mat) = paste0("R", 1:ng) colnames(mat) = paste0("C", 1:n) bin <- sample(c("resistant", "sensitive"), n, replace = TRUE) tgi <- runif(n) # sort the columns by tgi ord <- order(tgi) col_fun = circlize::colorRamp2(range(tgi), c("#DEEBF7", "#084594")) column_ha = HeatmapAnnotation(tgi = tgi[ord], bin = bin[ord], col = list(tgi = col_fun,...)
• 14:19, 22 August 2022 Brb talk contribs uploaded File:Doubledip.png (<pre> ng <- 1000 # number of genes ns <- 100 # number of samples k <- 2 # number of groups alpha <- .001 # cutoff of selecting sig genes set.seed(1) x = matrix(rnorm(ng * ns), nr= ns) # samples x features hc = hclust(dist(x)) plot(hc) grp = cutree(hc, k=k) # vector of group membership ex <- t(x) r1 <- genefilter::rowttests(ex, factor(grp)) sum(r1$p.value < alpha) # 2 hist(r1$p.value) i <- which(r1$p.value < alpha) i1 <- i[1] ; i2 <- i[2] plot(x[, i1], x[, i2], col = grp, pch= 16, cex=1...)
• 14:19, 22 August 2022 Brb talk contribs created page File:Doubledip.png (<pre> ng <- 1000 # number of genes ns <- 100 # number of samples k <- 2 # number of groups alpha <- .001 # cutoff of selecting sig genes set.seed(1) x = matrix(rnorm(ng * ns), nr= ns) # samples x features hc = hclust(dist(x)) plot(hc) grp = cutree(hc, k=k) # vector of group membership ex <- t(x) r1 <- genefilter::rowttests(ex, factor(grp)) sum(r1$p.value < alpha) # 2 hist(r1$p.value) i <- which(r1$p.value < alpha) i1 <- i[1] ; i2 <- i[2] plot(x[, i1], x[, i2], col = grp, pch= 16, cex=1...)
• 10:21, 10 August 2022 Brb talk contribs uploaded File:Ruspini.png (library(cluster) # ruspini is 75 x 2 data(ruspini) hc <- hclust(dist(ruspini), "ave"); plot(hc) # si <- silhouette(groups, dist(ruspini)) # plot(si, main = paste("k = ", 4)) op <- par(mfrow= c(3,2), oma= c(0,0, 3, 0), mgp= c(1.6,.8,0), mar= .1+c(4,2,2,2)) plot(hc) for(k in 2:6) { groups<- cutree(hc, k=k) si <- silhouette(groups, dist(ruspini)) plot(si, main = paste("k = ", k)) } par(op))
• 10:21, 10 August 2022 Brb talk contribs created page File:Ruspini.png (library(cluster) # ruspini is 75 x 2 data(ruspini) hc <- hclust(dist(ruspini), "ave"); plot(hc) # si <- silhouette(groups, dist(ruspini)) # plot(si, main = paste("k = ", 4)) op <- par(mfrow= c(3,2), oma= c(0,0, 3, 0), mgp= c(1.6,.8,0), mar= .1+c(4,2,2,2)) plot(hc) for(k in 2:6) { groups<- cutree(hc, k=k) si <- silhouette(groups, dist(ruspini)) plot(si, main = paste("k = ", k)) } par(op))
• 19:55, 23 June 2022 Brb talk contribs uploaded File:Tidyheatmap.png
• 19:55, 23 June 2022 Brb talk contribs created page File:Tidyheatmap.png
• 15:22, 21 June 2022 Brb talk contribs uploaded File:BatchqcPCA.png
• 15:22, 21 June 2022 Brb talk contribs created page File:BatchqcPCA.png
• 15:22, 21 June 2022 Brb talk contribs uploaded File:BatchqcDE.png
• 15:22, 21 June 2022 Brb talk contribs created page File:BatchqcDE.png
• 15:21, 21 June 2022 Brb talk contribs uploaded File:BatchqcVariation.png
• 15:21, 21 June 2022 Brb talk contribs created page File:BatchqcVariation.png
• 15:20, 21 June 2022 Brb talk contribs uploaded File:BatchqcSummary.png
• 15:20, 21 June 2022 Brb talk contribs created page File:BatchqcSummary.png
• 20:43, 8 June 2022 Brb talk contribs created page Fstab (Created page with "* man fstab * https://help.ubuntu.com/community/Fstab ** Format: [Device] [Mount Point] [File System Type] [Options] [Dump] [Pass] ** <dump> Enable or disable backing up of th...")
• 18:02, 4 June 2022 Brb talk contribs uploaded File:Heatmap rdylbu.png
• 18:02, 4 June 2022 Brb talk contribs created page File:Heatmap rdylbu.png
• 15:02, 4 June 2022 Brb talk contribs created page Self hosting (Created page with "= Resource = * [https://github.com/mycroftwilde/portainer_templates Helpful Youtube Channels for Self-Hosting] = [http://www.proxmox.com/en/ Proxmox Virtual Environment] = *...")
• 10:06, 27 May 2022 Brb talk contribs uploaded File:Inter gg2.png
• 10:06, 27 May 2022 Brb talk contribs created page File:Inter gg2.png
• 09:51, 27 May 2022 Brb talk contribs uploaded File:Inter gg.png
• 09:51, 27 May 2022 Brb talk contribs created page File:Inter gg.png
• 09:51, 27 May 2022 Brb talk contribs uploaded File:Inter base.png
• 09:51, 27 May 2022 Brb talk contribs created page File:Inter base.png
• 09:16, 27 May 2022 Brb talk contribs uploaded a new version of File:Inter base.svg
• 09:04, 27 May 2022 Brb talk contribs uploaded File:Inter base.svg
• 09:04, 27 May 2022 Brb talk contribs created page File:Inter base.svg
• 10:08, 26 May 2022 Brb talk contribs uploaded File:LogisticFail.svg (> set.seed(1234); n <- 16; mu=3; x <- c(rnorm(n), rnorm(n, mu)); y <- rep(0:1, each=n) > summary(glm(y ~ x, family = binomial)); plot(x, y))
• 10:08, 26 May 2022 Brb talk contribs created page File:LogisticFail.svg (> set.seed(1234); n <- 16; mu=3; x <- c(rnorm(n), rnorm(n, mu)); y <- rep(0:1, each=n) > summary(glm(y ~ x, family = binomial)); plot(x, y))
• 13:35, 16 May 2022 Brb talk contribs created page Batch effect (Created page with "= Merging two gene expression studies, ComBat = * [https://www.coursera.org/lecture/statistical-genomics/module-2-overview-1-12-cbqYZ Statistics for Genomic Data Science] (Cou...")