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• 15:58, 17 March 2023 Brb talk contribs created page File:Svg4.svg (<pre> svg("svg4.svg", width=4, height=4) plot(1:10, main="width=4, height=4") dev.off() </pre>)
• 15:58, 17 March 2023 Brb talk contribs uploaded File:Svg4.svg (<pre> svg("svg4.svg", width=4, height=4) plot(1:10, main="width=4, height=4") dev.off() </pre>)
• 09:44, 11 March 2023 Brb talk contribs created page File:RStudioVisualMode.png
• 09:44, 11 March 2023 Brb talk contribs uploaded File:RStudioVisualMode.png
• 15:01, 8 March 2023 Brb talk contribs created page File:Pca directly2.png
• 15:01, 8 March 2023 Brb talk contribs uploaded File:Pca directly2.png
• 10:11, 11 February 2023 Brb talk contribs created page File:MultipleProbes.PNG
• 10:11, 11 February 2023 Brb talk contribs uploaded File:MultipleProbes.PNG
• 10:10, 11 February 2023 Brb talk contribs created page File:ClassPredictionOptions.PNG
• 10:10, 11 February 2023 Brb talk contribs uploaded File:ClassPredictionOptions.PNG
• 10:08, 11 February 2023 Brb talk contribs created page File:ClassPrediction.PNG
• 10:08, 11 February 2023 Brb talk contribs uploaded File:ClassPrediction.PNG
• 20:01, 28 January 2023 Brb talk contribs created page File:Pca factoextra.png
• 20:01, 28 January 2023 Brb talk contribs uploaded File:Pca factoextra.png
• 19:34, 28 January 2023 Brb talk contribs created page File:Pca autoplot.png
• 19:34, 28 January 2023 Brb talk contribs uploaded File:Pca autoplot.png
• 19:34, 28 January 2023 Brb talk contribs created page File:Pca directly.png
• 19:34, 28 January 2023 Brb talk contribs uploaded File:Pca directly.png
• 09:21, 25 January 2023 Brb talk contribs created page File:VscodeEnergy.png
• 09:21, 25 January 2023 Brb talk contribs uploaded File:VscodeEnergy.png
• 21:26, 14 January 2023 Brb talk contribs created page File:RbdGeom.png (<pre> require(ggplot2) aggregate( .~ treatment +block,FUN=median, data = data) |> ggplot(aes(treatment, yield)) + geom_line(aes(group = block, color = block), linewidth = 1.2) + geom_point(aes(color = block), shape = 15, size=2.6) </pre>)
• 21:26, 14 January 2023 Brb talk contribs uploaded File:RbdGeom.png (<pre> require(ggplot2) aggregate( .~ treatment +block,FUN=median, data = data) |> ggplot(aes(treatment, yield)) + geom_line(aes(group = block, color = block), linewidth = 1.2) + geom_point(aes(color = block), shape = 15, size=2.6) </pre>)
• 20:51, 14 January 2023 Brb talk contribs created page File:RbdBlock.png (<pre> set.seed(1234) block <- as.factor(rep(1:5, each=6)) treatment <- rep(c("A","B","C"),5) block_shift <- rnorm(5, mean = 0, sd = 2) treatment_shift <- c(A=0, B=4, C=2) random_effect <- rnorm(30, mean = 0, sd = 1) yield <- rnorm(30, mean = 10, sd = 2) + treatment_shift[as.integer(factor(treatment))] + block_shift[as.numeric(block)] + random_effect data <- data.frame(block, treatment, yield) summary(fm1 <- aov(yield ~ treatment + block, data = data)) # Df Sum Sq Mean Sq...)
• 20:51, 14 January 2023 Brb talk contribs uploaded File:RbdBlock.png (<pre> set.seed(1234) block <- as.factor(rep(1:5, each=6)) treatment <- rep(c("A","B","C"),5) block_shift <- rnorm(5, mean = 0, sd = 2) treatment_shift <- c(A=0, B=4, C=2) random_effect <- rnorm(30, mean = 0, sd = 1) yield <- rnorm(30, mean = 10, sd = 2) + treatment_shift[as.integer(factor(treatment))] + block_shift[as.numeric(block)] + random_effect data <- data.frame(block, treatment, yield) summary(fm1 <- aov(yield ~ treatment + block, data = data)) # Df Sum Sq Mean Sq...)
• 20:50, 14 January 2023 Brb talk contribs created page File:RbdTreat.png (<pre> set.seed(1234) block <- as.factor(rep(1:5, each=6)) treatment <- rep(c("A","B","C"),5) block_shift <- rnorm(5, mean = 0, sd = 2) treatment_shift <- c(A=0, B=4, C=2) random_effect <- rnorm(30, mean = 0, sd = 1) yield <- rnorm(30, mean = 10, sd = 2) + treatment_shift[as.integer(factor(treatment))] + block_shift[as.numeric(block)] + random_effect data <- data.frame(block, treatment, yield) summary(fm1 <- aov(yield ~ treatment + block, data = data)) # Df Sum Sq Mean Sq...)
• 20:50, 14 January 2023 Brb talk contribs uploaded File:RbdTreat.png (<pre> set.seed(1234) block <- as.factor(rep(1:5, each=6)) treatment <- rep(c("A","B","C"),5) block_shift <- rnorm(5, mean = 0, sd = 2) treatment_shift <- c(A=0, B=4, C=2) random_effect <- rnorm(30, mean = 0, sd = 1) yield <- rnorm(30, mean = 10, sd = 2) + treatment_shift[as.integer(factor(treatment))] + block_shift[as.numeric(block)] + random_effect data <- data.frame(block, treatment, yield) summary(fm1 <- aov(yield ~ treatment + block, data = data)) # Df Sum Sq Mean Sq...)
• 11:18, 12 January 2023 Brb talk contribs created page File:GseaTable2.png (An example of a plot from 10 non-enriched pathways. <pre> data(examplePathways) data(exampleRanks) fgseaRes <- fgsea(examplePathways, exampleRanks, nperm=1000, minSize=15, maxSize=100) fgseaRes[order(pval, decreasing = T),][1:10, c('NES', 'pval')] # NES pval # 1: -0.4050950 1.0000000 # 2: -0.4050950 1.0000000 # 3: -0.4966664 0.9932584 # 4: 0.4804114 0.9870610 # 5: 0.4804114 0.9870610 # 6: 0.4804114 0.9870610 # 7: 0.4804114 0.9870610 # 8: 0.4955139 0.9854...)
• 11:18, 12 January 2023 Brb talk contribs uploaded File:GseaTable2.png (An example of a plot from 10 non-enriched pathways. <pre> data(examplePathways) data(exampleRanks) fgseaRes <- fgsea(examplePathways, exampleRanks, nperm=1000, minSize=15, maxSize=100) fgseaRes[order(pval, decreasing = T),][1:10, c('NES', 'pval')] # NES pval # 1: -0.4050950 1.0000000 # 2: -0.4050950 1.0000000 # 3: -0.4966664 0.9932584 # 4: 0.4804114 0.9870610 # 5: 0.4804114 0.9870610 # 6: 0.4804114 0.9870610 # 7: 0.4804114 0.9870610 # 8: 0.4955139 0.9854...)
• 11:01, 12 January 2023 Brb talk contribs created page File:GseaTable.png (<pre> data(examplePathways) data(exampleRanks) fgseaRes <- fgsea(examplePathways, exampleRanks, nperm=1000, minSize=15, maxSize=100) # I pick 5 pathways with + NES and 5 pathways with - NES. fgseaRes[order(pval), ][62:71, c('pathway', 'NES')] # pathway NES # 1: 5992282_ECM_proteoglycans 1.984081 # 2: 5992219_Regulation_of_cholesterol_biosynthesis_by_SREBP_SREBF_ 1.95...)
• 11:01, 12 January 2023 Brb talk contribs uploaded File:GseaTable.png (<pre> data(examplePathways) data(exampleRanks) fgseaRes <- fgsea(examplePathways, exampleRanks, nperm=1000, minSize=15, maxSize=100) # I pick 5 pathways with + NES and 5 pathways with - NES. fgseaRes[order(pval), ][62:71, c('pathway', 'NES')] # pathway NES # 1: 5992282_ECM_proteoglycans 1.984081 # 2: 5992219_Regulation_of_cholesterol_biosynthesis_by_SREBP_SREBF_ 1.95...)
• 11:15, 8 January 2023 Brb talk contribs created page File:Reorder.dendrogram.png (<pre> set.seed(123) x <- rnorm(20) hc <- hclust(dist(x)) dd <- as.dendrogram(hc) par(mfrow=c(3, 1)) plot(dd, main = "random dendrogram 'dd'") # not the same as reorder(dd, 1:20) plot(reorder(dd, 20:1), main = 'reorder(dd, 20:1, sum)') plot(reorder(dd, 20:1, mean), main = 'reorder(dd, 20:1, mean)') </pre>)
• 11:15, 8 January 2023 Brb talk contribs uploaded File:Reorder.dendrogram.png (<pre> set.seed(123) x <- rnorm(20) hc <- hclust(dist(x)) dd <- as.dendrogram(hc) par(mfrow=c(3, 1)) plot(dd, main = "random dendrogram 'dd'") # not the same as reorder(dd, 1:20) plot(reorder(dd, 20:1), main = 'reorder(dd, 20:1, sum)') plot(reorder(dd, 20:1, mean), main = 'reorder(dd, 20:1, mean)') </pre>)
• 20:37, 7 January 2023 Brb talk contribs created page File:ComplexHeatmap2.png (<syntaxhighlight lang="rsplus"> # Simulate data library(ComplexHeatmap) ng <- 30; ns <- 20 set.seed(1) mat <- matrix(rnorm(ng*ns), nr=ng, nc=ns) colnames(mat) <- 1:ns rownames(mat) <- 1:ng # color bar on RHS ind_e <- 1:round(ng/3) ind_m <- (1+round(ng/3)):ng epimes <- rep(c("epi", "mes"), c(length(ind_e), length(ind_m))) row_ha <- rowAnnotation(epimes = epimes, col = list(epimes = c("epi" = "orange", "mes" = "darkgreen"))) # color bar on Top tumortype <- rep(c("carcinoma", "sarcoma"...)
• 20:37, 7 January 2023 Brb talk contribs uploaded File:ComplexHeatmap2.png (<syntaxhighlight lang="rsplus"> # Simulate data library(ComplexHeatmap) ng <- 30; ns <- 20 set.seed(1) mat <- matrix(rnorm(ng*ns), nr=ng, nc=ns) colnames(mat) <- 1:ns rownames(mat) <- 1:ng # color bar on RHS ind_e <- 1:round(ng/3) ind_m <- (1+round(ng/3)):ng epimes <- rep(c("epi", "mes"), c(length(ind_e), length(ind_m))) row_ha <- rowAnnotation(epimes = epimes, col = list(epimes = c("epi" = "orange", "mes" = "darkgreen"))) # color bar on Top tumortype <- rep(c("carcinoma", "sarcoma"...)
• 11:37, 6 January 2023 Brb talk contribs created page File:Fgsea3plots.png (<pre> par(mfrow=c(1,3)) with(fgseaRes, plot(abs(ES), pval)) with(fgseaRes, plot(abs(NES), pval)) with(fgseaRes, plot(ES, NES)) </pre>)
• 11:37, 6 January 2023 Brb talk contribs uploaded File:Fgsea3plots.png (<pre> par(mfrow=c(1,3)) with(fgseaRes, plot(abs(ES), pval)) with(fgseaRes, plot(abs(NES), pval)) with(fgseaRes, plot(ES, NES)) </pre>)
• 13:58, 31 December 2022 Brb talk contribs created page File:Filebrowser.png
• 13:58, 31 December 2022 Brb talk contribs uploaded File:Filebrowser.png
• 19:07, 25 December 2022 Brb talk contribs created page File:DisableDropbox4pm.png
• 19:07, 25 December 2022 Brb talk contribs uploaded File:DisableDropbox4pm.png
• 14:40, 15 December 2022 Brb talk contribs created page File:Geom smooth ex.png (<pre> library(dplyr) #group the data by cyl and create the plots mpg %>% group_by(cyl) %>% ggplot(aes(x=displ, y=hwy, color=factor(cyl))) + geom_point() + geom_smooth(method = "lm", se = FALSE) + theme(legend.position="none") </pre>)
• 14:40, 15 December 2022 Brb talk contribs uploaded File:Geom smooth ex.png (<pre> library(dplyr) #group the data by cyl and create the plots mpg %>% group_by(cyl) %>% ggplot(aes(x=displ, y=hwy, color=factor(cyl))) + geom_point() + geom_smooth(method = "lm", se = FALSE) + theme(legend.position="none") </pre>)
• 14:14, 15 December 2022 Brb talk contribs created page File:Geom bar4.png (<pre> ggplot(mpg, aes(x = class)) + geom_vline(xintercept = mpg$class, color = "grey", linetype = "dashed", size = 1) + geom_bar() + theme_classic() + coord_flip() </pre>)
• 14:14, 15 December 2022 Brb talk contribs uploaded File:Geom bar4.png (<pre> ggplot(mpg, aes(x = class)) + geom_vline(xintercept = mpg$class, color = "grey", linetype = "dashed", size = 1) + geom_bar() + theme_classic() + coord_flip() </pre>)
• 14:08, 15 December 2022 Brb talk contribs created page File:Geom bar3.png (<pre> ggplot(mpg, aes(x=manufacturer)) + geom_bar() + theme(panel.grid.major.x = element_blank(), panel.grid.minor = element_blank()) </pre>)
• 14:08, 15 December 2022 Brb talk contribs uploaded File:Geom bar3.png (<pre> ggplot(mpg, aes(x=manufacturer)) + geom_bar() + theme(panel.grid.major.x = element_blank(), panel.grid.minor = element_blank()) </pre>)
• 13:41, 15 December 2022 Brb talk contribs created page File:Geom bar2.png (<pre> library(ggplot2) library(scales) library(patchwork) dtf <- data.frame(x = c("ETB", "PMA", "PER", "KON", "TRA", "DDR", "BUM", "MAT", "HED", "EXP"), y = c(.02, .11, -.01, -.03, -.03, .02, .1, -.01, -.02, 0.06)) set.seed(1) dtf2 <- data.frame(x = dtf[, 1], y = sample(dtf[, 2])) g1 <- ggplot(dtf, aes(x, y)) + geom_bar(stat = "identity", fill = "#F8767D") + geom_text(aes(label = paste0(y * 100, "%"), hjust = ifelse(y >= 0, 0, 1))) +...)
• 13:41, 15 December 2022 Brb talk contribs uploaded File:Geom bar2.png (<pre> library(ggplot2) library(scales) library(patchwork) dtf <- data.frame(x = c("ETB", "PMA", "PER", "KON", "TRA", "DDR", "BUM", "MAT", "HED", "EXP"), y = c(.02, .11, -.01, -.03, -.03, .02, .1, -.01, -.02, 0.06)) set.seed(1) dtf2 <- data.frame(x = dtf[, 1], y = sample(dtf[, 2])) g1 <- ggplot(dtf, aes(x, y)) + geom_bar(stat = "identity", fill = "#F8767D") + geom_text(aes(label = paste0(y * 100, "%"), hjust = ifelse(y >= 0, 0, 1))) +...)
• 13:39, 15 December 2022 Brb talk contribs created page File:Geom bar1.png (<pre> library(ggplot2) library(scales) library(patchwork) dtf <- data.frame(x = c("ETB", "PMA", "PER", "KON", "TRA", "DDR", "BUM", "MAT", "HED", "EXP"), y = c(.02, .11, -.01, -.03, -.03, .02, .1, -.01, -.02, 0.06)) set.seed(1) dtf2 <- data.frame(x = dtf[, 1], y = sample(dtf[, 2])) g1 <- ggplot(dtf, aes(x, y)) + geom_bar(stat = "identity", aes(fill = x)) + geom_text(aes(label = paste0(y * 100, "%"), hjust = ifelse(y >= 0,...)
• 13:39, 15 December 2022 Brb talk contribs uploaded File:Geom bar1.png (<pre> library(ggplot2) library(scales) library(patchwork) dtf <- data.frame(x = c("ETB", "PMA", "PER", "KON", "TRA", "DDR", "BUM", "MAT", "HED", "EXP"), y = c(.02, .11, -.01, -.03, -.03, .02, .1, -.01, -.02, 0.06)) set.seed(1) dtf2 <- data.frame(x = dtf[, 1], y = sample(dtf[, 2])) g1 <- ggplot(dtf, aes(x, y)) + geom_bar(stat = "identity", aes(fill = x)) + geom_text(aes(label = paste0(y * 100, "%"), hjust = ifelse(y >= 0,...)