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Combined display of all available logs of 太極. You can narrow down the view by selecting a log type, the username (case-sensitive), or the affected page (also case-sensitive).
- 17:26, 19 October 2022 Brb talk contribs created page File:NC better kNN.png (The green color is a new observation (Sensitive). By using the kNN method, it will be assigned to Resistant b/c it is closer to the Resistant group. However, using the NC, the distance of it to the Resistant group centroid is 8.42 which is larger than the distance of it to the Sensitive groups centroid 7.31. So NC classified it to Sensitive. Color annotation: green=LOO obs, black=centroid in each class.)
- 17:26, 19 October 2022 Brb talk contribs uploaded File:NC better kNN.png (The green color is a new observation (Sensitive). By using the kNN method, it will be assigned to Resistant b/c it is closer to the Resistant group. However, using the NC, the distance of it to the Resistant group centroid is 8.42 which is larger than the distance of it to the Sensitive groups centroid 7.31. So NC classified it to Sensitive. Color annotation: green=LOO obs, black=centroid in each class.)
- 11:03, 12 October 2022 Brb talk contribs created page File:Foldchangefilter.png (<pre> LFC <- log2(1.5) x <- c(0, 0, 0, 0, 0, 0, 0, 0, 3.22, 0, 0, 0, 8.09, 0, 0.65, 0, 0, 0, 0, 0, 3.38, 0, 5.63, 7.46, 0, 0, 4.38, 0) plot(x, y = 1:28, xlab="log2 intensity", ylab="samples") abline(v=LFC, lty="dashed") axis(side=3,at=LFC, labels="LFC", tick=FALSE, line=0) </pre>)
- 11:03, 12 October 2022 Brb talk contribs uploaded File:Foldchangefilter.png (<pre> LFC <- log2(1.5) x <- c(0, 0, 0, 0, 0, 0, 0, 0, 3.22, 0, 0, 0, 8.09, 0, 0.65, 0, 0, 0, 0, 0, 3.38, 0, 5.63, 7.46, 0, 0, 4.38, 0) plot(x, y = 1:28, xlab="log2 intensity", ylab="samples") abline(v=LFC, lty="dashed") axis(side=3,at=LFC, labels="LFC", tick=FALSE, line=0) </pre>)
- 16:39, 11 October 2022 Brb talk contribs created page File:Cvglmnetplot.png (<pre> n <- 100 set.seed(1) x1 <- rnorm(n) e <- rnorm(n)*.01 y <- x1 + e x4 <- x fit <- cv.glmnet(x=cbind(x1, x4, matrix(rnorm(n*10), nr=n)), y=y) plot (fit) </pre>)
- 16:39, 11 October 2022 Brb talk contribs uploaded File:Cvglmnetplot.png (<pre> n <- 100 set.seed(1) x1 <- rnorm(n) e <- rnorm(n)*.01 y <- x1 + e x4 <- x fit <- cv.glmnet(x=cbind(x1, x4, matrix(rnorm(n*10), nr=n)), y=y) plot (fit) </pre>)
- 07:57, 7 October 2022 Brb talk contribs created page Prediction (Created page with "= Gradient boost = * https://en.wikipedia.org/wiki/Gradient_boosting * [https://datascienceplus.com/gradient-boosting-in-r/ Gradient boosting in R] == GBDT: Gradient Boosting...")
- 14:12, 6 October 2022 Brb talk contribs created page File:Greedypairs.png
- 14:12, 6 October 2022 Brb talk contribs uploaded File:Greedypairs.png
- 11:11, 6 October 2022 Brb talk contribs uploaded a new version of File:Barplot base.png
- 11:06, 6 October 2022 Brb talk contribs created page File:Barplot ggplot2.png
- 11:06, 6 October 2022 Brb talk contribs uploaded File:Barplot ggplot2.png
- 11:06, 6 October 2022 Brb talk contribs created page File:Barplot base.png
- 11:06, 6 October 2022 Brb talk contribs uploaded File:Barplot base.png
- 11:50, 30 August 2022 Brb talk contribs created page File:Geomcolviridis.png (Modify the example from https://datavizpyr.com/re-ordering-bars-in-barplot-in-r/ to allow filled colors and facet. <pre> library(tidyverse) library(gapminder) library(viridis) theme_set(theme_bw(base_size=16)) pop_df <- gapminder %>% filter(year==2007)%>% group_by(continent) %>% summarize(pop_in_millions=sum(pop)/1e06) pop_df2 <- tibble(class=rbinom(nrow(pop_df), 1, .5), pop_df) pop_df2 <- pop_df2 |> mutate(pop_in_millions = pop_in_millions-1900) pop_df2 %>% ggplot(aes...)
- 11:50, 30 August 2022 Brb talk contribs uploaded File:Geomcolviridis.png (Modify the example from https://datavizpyr.com/re-ordering-bars-in-barplot-in-r/ to allow filled colors and facet. <pre> library(tidyverse) library(gapminder) library(viridis) theme_set(theme_bw(base_size=16)) pop_df <- gapminder %>% filter(year==2007)%>% group_by(continent) %>% summarize(pop_in_millions=sum(pop)/1e06) pop_df2 <- tibble(class=rbinom(nrow(pop_df), 1, .5), pop_df) pop_df2 <- pop_df2 |> mutate(pop_in_millions = pop_in_millions-1900) pop_df2 %>% ggplot(aes...)
- 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>)
- 10:31, 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>)
- 10:08, 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$Z <- runif(400, 0, 5) library(viridis) ggplot(data, aes(X, Y, fill= Z)) + geom_tile() + scale_fill_viridis(discrete=FALSE) </pre>)
- 10:08, 30 August 2022 Brb talk contribs uploaded File:ScaleFillViridisDiscrete.png (See https://r-graph-gallery.com/79-levelplot-with-ggplot2.html <pre> library(ggplot2) # library(hrbrthemes) # Dummy data x <- LETTERS[1:20] y <- paste0("var", seq(1,20)) data <- expand.grid(X=x, Y=y) data$Z <- runif(400, 0, 5) library(viridis) ggplot(data, aes(X, Y, fill= Z)) + geom_tile() + scale_fill_viridis(discrete=FALSE) </pre>)
- 14:19, 29 August 2022 Brb talk contribs created page File:Rbiomirgs barall.png
- 14:19, 29 August 2022 Brb talk contribs uploaded File:Rbiomirgs barall.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 bar.png
- 14:17, 29 August 2022 Brb talk contribs created page File:Rbiomirgs volcano.png
- 14:17, 29 August 2022 Brb talk contribs uploaded File:Rbiomirgs volcano.png
- 07:08, 27 August 2022 Brb talk contribs created page File:FgseaPlotTop.png
- 07:08, 27 August 2022 Brb talk contribs uploaded File:FgseaPlotTop.png
- 06:34, 27 August 2022 Brb talk contribs created page File:FgseaPlotSmall2.png
- 06:34, 27 August 2022 Brb talk contribs uploaded File:FgseaPlotSmall2.png
- 06:34, 27 August 2022 Brb talk contribs created page File:FgseaPlotSmall.png
- 06:34, 27 August 2022 Brb talk contribs uploaded File:FgseaPlotSmall.png
- 06:33, 27 August 2022 Brb talk contribs created page File:FgseaPlot.png
- 06:33, 27 August 2022 Brb talk contribs uploaded File:FgseaPlot.png
- 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,...)
- 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,...)
- 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$p.value < alpha) i1 <- i[1] ; i2 <- i[2] plot(x[, i1], x[, i2], col = grp, pch= 16, cex=1...)
- 14:19, 22 August 2022 Brb talk contribs uploaded File:Doubledip.png (<pre> ng <- 1000 # number of genes ns <- 100 # number of samples k <- 2 # number of groups alpha <- .001 # cutoff of selecting sig genes set.seed(1) x = matrix(rnorm(ng * ns), nr= ns) # samples x features hc = hclust(dist(x)) plot(hc) grp = cutree(hc, k=k) # vector of group membership ex <- t(x) r1 <- genefilter::rowttests(ex, factor(grp)) sum(r1$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...)
- 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))
- 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))
- 19:55, 23 June 2022 Brb talk contribs created page File:Tidyheatmap.png
- 19:55, 23 June 2022 Brb talk contribs uploaded File:Tidyheatmap.png
- 15:22, 21 June 2022 Brb talk contribs created page File:BatchqcPCA.png
- 15:22, 21 June 2022 Brb talk contribs uploaded File:BatchqcPCA.png
- 15:22, 21 June 2022 Brb talk contribs created page File:BatchqcDE.png
- 15:22, 21 June 2022 Brb talk contribs uploaded File:BatchqcDE.png
- 15:21, 21 June 2022 Brb talk contribs created page File:BatchqcVariation.png
- 15:21, 21 June 2022 Brb talk contribs uploaded File:BatchqcVariation.png
- 15:20, 21 June 2022 Brb talk contribs created page File:BatchqcSummary.png
- 15:20, 21 June 2022 Brb talk contribs uploaded File:BatchqcSummary.png