Upload log

Below is a list of the most recent file uploads. See the gallery of new files for a more visual overview.

• 10:50, 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...)
• 09:31, 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>)
• 09:08, 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$Z <- runif(400, 0, 5) library(viridis) ggplot(data, aes(X, Y, fill= Z)) + geom_tile() + scale_fill_viridis(discrete=FALSE) </pre>)
• 13:19, 29 August 2022 Brb talk contribs uploaded File:Rbiomirgs barall.png
• 13:17, 29 August 2022 Brb talk contribs uploaded File:Rbiomirgs bar.png
• 13:17, 29 August 2022 Brb talk contribs uploaded File:Rbiomirgs volcano.png
• 06:08, 27 August 2022 Brb talk contribs uploaded File:FgseaPlotTop.png
• 05:34, 27 August 2022 Brb talk contribs uploaded File:FgseaPlotSmall2.png
• 05:34, 27 August 2022 Brb talk contribs uploaded File:FgseaPlotSmall.png
• 05:33, 27 August 2022 Brb talk contribs uploaded File:FgseaPlot.png
• 14:02, 23 August 2022 Brb talk contribs uploaded File:ComplexHeatmap1.png (<pre> library(ComplexHeatmap) set.seed(123) ng <- 10; n <- 10 mat = matrix(rnorm(ng * n), n) rownames(mat) = paste0("R", 1:ng) colnames(mat) = paste0("C", 1:n) bin <- sample(c("resistant", "sensitive"), n, replace = TRUE) tgi <- runif(n) # sort the columns by tgi ord <- order(tgi) col_fun = circlize::colorRamp2(range(tgi), c("#DEEBF7", "#084594")) column_ha = HeatmapAnnotation(tgi = tgi[ord], bin = bin[ord], col = list(tgi = col_fun,...)
• 13:19, 22 August 2022 Brb talk contribs uploaded File:Doubledip.png (<pre> ng <- 1000 # number of genes ns <- 100 # number of samples k <- 2 # number of groups alpha <- .001 # cutoff of selecting sig genes set.seed(1) x = matrix(rnorm(ng * ns), nr= ns) # samples x features hc = hclust(dist(x)) plot(hc) grp = cutree(hc, k=k) # vector of group membership ex <- t(x) r1 <- genefilter::rowttests(ex, factor(grp)) sum(r1$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...)
• 09:21, 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))
• 18:55, 23 June 2022 Brb talk contribs uploaded File:Tidyheatmap.png
• 14:22, 21 June 2022 Brb talk contribs uploaded File:BatchqcPCA.png
• 14:22, 21 June 2022 Brb talk contribs uploaded File:BatchqcDE.png
• 14:21, 21 June 2022 Brb talk contribs uploaded File:BatchqcVariation.png
• 14:20, 21 June 2022 Brb talk contribs uploaded File:BatchqcSummary.png
• 17:02, 4 June 2022 Brb talk contribs uploaded File:Heatmap rdylbu.png
• 09:06, 27 May 2022 Brb talk contribs uploaded File:Inter gg2.png
• 08:51, 27 May 2022 Brb talk contribs uploaded File:Inter gg.png
• 08:51, 27 May 2022 Brb talk contribs uploaded File:Inter base.png
• 08:16, 27 May 2022 Brb talk contribs uploaded a new version of File:Inter base.svg
• 08:04, 27 May 2022 Brb talk contribs uploaded File:Inter base.svg
• 09:08, 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))
• 11:56, 10 May 2022 Brb talk contribs uploaded File:ColorRampBlueRed.png
• 18:39, 24 March 2022 Brb talk contribs uploaded File:Rerrorbars.png (<pre> library(ggplot2) df <- ToothGrowth df$dosef <- as.factor(df$dose) library(dplyr) df.summary <- df %>% group_by(dosef) %>% summarise( sd = sd(len, na.rm = TRUE), len = mean(len) ) df.summary p1 <- ggplot(df, aes(dosef, len)) + geom_jitter(position = position_jitter(0.2, seed=1), color = "darkgray") + geom_point(aes(x=dosef, y=len), shape="+", size=8, data=df.summary) + geom_errorbar(aes(ymin = len-sd, ymax = len+sd), width=.2, data = df.summary) df.summary$dose <...)
• 18:37, 24 March 2022 Brb talk contribs uploaded File:Rerrorbar.svg (<pre> library(ggplot2) df <- ToothGrowth df$dosef <- as.factor(df$dose) library(dplyr) df.summary <- df %>% group_by(dosef) %>% summarise( sd = sd(len, na.rm = TRUE), len = mean(len) ) df.summary p1 <- ggplot(df, aes(dosef, len)) + geom_jitter(position = position_jitter(0.2, seed=1), color = "darkgray") + geom_point(aes(x=dosef, y=len), shape="+", size=8, data=df.summary) + geom_errorbar(aes(ymin = len-sd, ymax = len+sd), width=.2, data = df.summary) df.summary$dose <...)
• 13:13, 18 March 2022 Brb talk contribs uploaded File:SnrVScor.png
• 13:10, 18 March 2022 Brb talk contribs uploaded File:CorVSsnr.svg
• 13:15, 5 March 2022 Brb talk contribs uploaded File:AntiX21 mmedia.png
• 21:31, 2 February 2022 Brb talk contribs uploaded File:WewatchJetsonnano-min.png
• 09:11, 17 November 2021 Brb talk contribs uploaded File:Atnormalize.png
• 11:22, 15 September 2021 Brb talk contribs uploaded File:Jupyter.drawio.png
• 08:43, 14 August 2021 Brb talk contribs uploaded File:VscodeR.png
• 15:58, 24 June 2021 Brb talk contribs uploaded File:Infercnv.png
• 09:20, 11 June 2021 Brb talk contribs uploaded File:Hmapseqcolor.png
• 16:07, 30 April 2021 Brb talk contribs uploaded File:BarcodeRanks.png
• 16:01, 30 April 2021 Brb talk contribs uploaded File:Cellrangersum.png
• 19:20, 21 March 2021 Brb talk contribs uploaded File:SsGSEA.png
• 09:50, 24 January 2021 Brb talk contribs uploaded File:Scalefill.png
• 21:29, 2 January 2021 Brb talk contribs uploaded File:Winerating.png
• 20:26, 2 January 2021 Brb talk contribs uploaded File:Rating.png
• 19:56, 2 January 2021 Brb talk contribs uploaded a new version of File:Rating.png
• 19:46, 2 January 2021 Brb talk contribs uploaded File:Rating.png
• 14:28, 7 November 2020 Brb talk contribs uploaded File:Ksnip.png
• 08:43, 26 September 2020 Brb talk contribs uploaded File:Coffeeinteract.png
• 09:48, 24 September 2020 Brb talk contribs uploaded a new version of File:Progpreg.png (<pre> library(magick) u <- c("https://www.ncbi.nlm.nih.gov/books/NBK402284/bin/prognostic_predictive-Image001.jpg", "https://www.ncbi.nlm.nih.gov/books/NBK402284/bin/prognostic_predictive-Image002.jpg", "https://www.ncbi.nlm.nih.gov/books/NBK402284/bin/prognostic_predictive-Image003.jpg", "https://www.ncbi.nlm.nih.gov/books/NBK402284/bin/prognostic_predictive-Image004.jpg", "https://www.ncbi.nlm.nih.gov/books/NBK402284/bin/prognostic_predictive-Image005.jpg", "https://ww...)
• 08:41, 24 September 2020 Brb talk contribs uploaded File:Zlj9991056240002.jpeg
• 08:07, 24 September 2020 Brb talk contribs uploaded File:Progpreg.png (<pre> library(magick) u <- c("https://www.ncbi.nlm.nih.gov/books/NBK402284/bin/prognostic_predictive-Image001.jpg", "https://www.ncbi.nlm.nih.gov/books/NBK402284/bin/prognostic_predictive-Image003.jpg", "https://www.ncbi.nlm.nih.gov/books/NBK402284/bin/prognostic_predictive-Image005.jpg", "https://www.ncbi.nlm.nih.gov/books/NBK402284/bin/prognostic_predictive-Image006.jpg") x1 <- image_read(u[1]) x2 <- image_read(u[2]) x3 <- image_read(u[3]) x4 <- image_read(u[4]) imgU <- image_append(image_s...)