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  • 20:06, 24 August 2024 Brb talk contribs created page File:R-squared.png
  • 20:06, 24 August 2024 Brb talk contribs uploaded File:R-squared.png
  • 14:54, 13 August 2024 Brb talk contribs created page File:Geom bar reorder.png (<syntaxhighlight lang='r'> library(ggplot2) library(forcats) data <- data.frame( category = c("A", "B", "C", "D"), value = c(3, 5, 2, 8) ) data$category <- fct_reorder(data$category, data$value) levels(data$category) # [1] "C" "A" "B" "D" ggplot(data, aes(x = category, y = value, fill = category)) + geom_bar(stat = "identity") + coord_flip() + labs(x = "Category", y = "Value") + theme_minimal() </syntaxhighlight>)
  • 14:54, 13 August 2024 Brb talk contribs uploaded File:Geom bar reorder.png (<syntaxhighlight lang='r'> library(ggplot2) library(forcats) data <- data.frame( category = c("A", "B", "C", "D"), value = c(3, 5, 2, 8) ) data$category <- fct_reorder(data$category, data$value) levels(data$category) # [1] "C" "A" "B" "D" ggplot(data, aes(x = category, y = value, fill = category)) + geom_bar(stat = "identity") + coord_flip() + labs(x = "Category", y = "Value") + theme_minimal() </syntaxhighlight>)
  • 14:47, 13 August 2024 Brb talk contribs created page File:Geom bar simple.png (<syntaxhighlight lang='r'> library(ggplot2) data <- data.frame( category = c("A", "B", "C", "D"), value = c(3, 5, 2, 8) ) ggplot(data, aes(x = category, y = value, fill = category)) + geom_bar(stat = "identity") + coord_flip() + labs(x = "Category", y = "Value") + # scale_fill_manual(values = c("A" = "red", "B" = "blue", "C" = "green", "D" = "purple")) theme_minimal() </syntaxhighlight>)
  • 14:47, 13 August 2024 Brb talk contribs uploaded File:Geom bar simple.png (<syntaxhighlight lang='r'> library(ggplot2) data <- data.frame( category = c("A", "B", "C", "D"), value = c(3, 5, 2, 8) ) ggplot(data, aes(x = category, y = value, fill = category)) + geom_bar(stat = "identity") + coord_flip() + labs(x = "Category", y = "Value") + # scale_fill_manual(values = c("A" = "red", "B" = "blue", "C" = "green", "D" = "purple")) theme_minimal() </syntaxhighlight>)
  • 12:44, 12 August 2024 Brb talk contribs created page File:Nomogram.png
  • 12:44, 12 August 2024 Brb talk contribs uploaded File:Nomogram.png
  • 14:56, 15 July 2024 Brb talk contribs created page File:GfortranMac.png
  • 14:56, 15 July 2024 Brb talk contribs uploaded File:GfortranMac.png
  • 07:24, 22 June 2024 Brb talk contribs created page File:Verizonont.jpg
  • 07:24, 22 June 2024 Brb talk contribs uploaded File:Verizonont.jpg
  • 12:38, 14 June 2024 Brb talk contribs created page File:CredoError.png
  • 12:38, 14 June 2024 Brb talk contribs uploaded File:CredoError.png
  • 13:31, 8 June 2024 Brb talk contribs created page File:Add camera.png
  • 13:31, 8 June 2024 Brb talk contribs uploaded File:Add camera.png
  • 14:12, 27 May 2024 Brb talk contribs created page File:Gganimation.gif (<syntaxhighlight lang='r'> library(gganimate) library(ggplot2) library(tidyverse) library(ggimage) data_link <- "https://raw.githubusercontent.com/goodekat/presentations/master/2019-isugg-gganimate-spooky/bat-data/bats-subset.csv" bats <- read.csv(data_link) %>% mutate(id = factor(id)) bat_image_link <- "https://upload.wikimedia.org/wikipedia/en/a/a9/MarioNSMBUDeluxe.png" animation <- bats %>% mutate(image = bat_image_link) %>% filter(id == 1) %>% ggplot(aes(x = longitude, y = la...)
  • 14:12, 27 May 2024 Brb talk contribs uploaded File:Gganimation.gif (<syntaxhighlight lang='r'> library(gganimate) library(ggplot2) library(tidyverse) library(ggimage) data_link <- "https://raw.githubusercontent.com/goodekat/presentations/master/2019-isugg-gganimate-spooky/bat-data/bats-subset.csv" bats <- read.csv(data_link) %>% mutate(id = factor(id)) bat_image_link <- "https://upload.wikimedia.org/wikipedia/en/a/a9/MarioNSMBUDeluxe.png" animation <- bats %>% mutate(image = bat_image_link) %>% filter(id == 1) %>% ggplot(aes(x = longitude, y = la...)
  • 08:58, 23 May 2024 Brb talk contribs created page File:Pca ggplot2.png (<syntaxhighlight lang='r'> df <- iris[, 1:4] # exclude "Species" column pca_res <- prcomp(df, scale = TRUE) ggplot(iris, aes(x = pca_res$x[,1], y = pca_res$x[,2], color = Species)) + geom_point() + stat_ellipse() </syntaxhighlight>)
  • 08:58, 23 May 2024 Brb talk contribs uploaded File:Pca ggplot2.png (<syntaxhighlight lang='r'> df <- iris[, 1:4] # exclude "Species" column pca_res <- prcomp(df, scale = TRUE) ggplot(iris, aes(x = pca_res$x[,1], y = pca_res$x[,2], color = Species)) + geom_point() + stat_ellipse() </syntaxhighlight>)
  • 14:18, 8 May 2024 Brb talk contribs created page File:Rtools44.png
  • 14:18, 8 May 2024 Brb talk contribs uploaded File:Rtools44.png
  • 16:31, 23 April 2024 Brb talk contribs created page File:Polygon.png (<syntaxhighlight lang='r'> plot(c(1, 9), 1:2, type = "n") polygon(1:9, c(2,1,2,1,NA,2,1,2,1), col = c("red", "blue"), border = c("green", "yellow"), lwd = 3, lty = c("dashed", "solid")) </syntaxhighlight>)
  • 16:31, 23 April 2024 Brb talk contribs uploaded File:Polygon.png (<syntaxhighlight lang='r'> plot(c(1, 9), 1:2, type = "n") polygon(1:9, c(2,1,2,1,NA,2,1,2,1), col = c("red", "blue"), border = c("green", "yellow"), lwd = 3, lty = c("dashed", "solid")) </syntaxhighlight>)
  • 13:49, 23 April 2024 Brb talk contribs created page File:Venn4.png (<syntaxhighlight lang='r'> library(venn) set.seed(12345) x <- list(First = 1:40, Second = 15:60, Third = sample(25:50, 25), Fourth=sample(15:65, 35)) venn(x, ilabels = "counts", zcolor = "style") </syntaxhighlight>)
  • 13:49, 23 April 2024 Brb talk contribs uploaded File:Venn4.png (<syntaxhighlight lang='r'> library(venn) set.seed(12345) x <- list(First = 1:40, Second = 15:60, Third = sample(25:50, 25), Fourth=sample(15:65, 35)) venn(x, ilabels = "counts", zcolor = "style") </syntaxhighlight>)
  • 14:53, 17 April 2024 Brb talk contribs created page File:Tiv-demo.png
  • 14:53, 17 April 2024 Brb talk contribs uploaded File:Tiv-demo.png
  • 19:17, 12 March 2024 Brb talk contribs created page File:Filtered R mean.png (Use sample mean instead of variance for each gene as the filter statistic. <syntaxhighlight lang='r'> # Follow the previous code chunks M2 <- rowMeans(exprs(ALL_bcrneg)) theta <- seq(0, .80, .01) R_BH <- filtered_R(alpha=.10, M2, p2, theta, method="BH") which.max(R_BH) # 10% <---- so theta=0.1 is the optimal; only 10% genes are removed # 11 max(R_BH) # [1] 270 plot(theta, R_BH, type="l", xlab=expression(theta), ylab="Rejections", main="BH cutoff = 0.1") abline(v=.1, lty=2) <...)
  • 19:17, 12 March 2024 Brb talk contribs uploaded File:Filtered R mean.png (Use sample mean instead of variance for each gene as the filter statistic. <syntaxhighlight lang='r'> # Follow the previous code chunks M2 <- rowMeans(exprs(ALL_bcrneg)) theta <- seq(0, .80, .01) R_BH <- filtered_R(alpha=.10, M2, p2, theta, method="BH") which.max(R_BH) # 10% <---- so theta=0.1 is the optimal; only 10% genes are removed # 11 max(R_BH) # [1] 270 plot(theta, R_BH, type="l", xlab=expression(theta), ylab="Rejections", main="BH cutoff = 0.1") abline(v=.1, lty=2) <...)
  • 07:54, 12 March 2024 Brb talk contribs created page File:Rainbow v05.png
  • 07:54, 12 March 2024 Brb talk contribs uploaded File:Rainbow v05.png
  • 07:53, 12 March 2024 Brb talk contribs created page File:Rainbow s05.png
  • 07:53, 12 March 2024 Brb talk contribs uploaded File:Rainbow s05.png
  • 07:52, 12 March 2024 Brb talk contribs created page File:Rainbow default.png (<syntaxhighlight lang='r'> library(shiny) # Define the UI ui <- fluidPage( titlePanel("Rainbow Color Palette"), sidebarLayout( sidebarPanel( sliderInput("s_value", "Saturation (s):", min = 0, max = 1, value = 1, step = 0.01), sliderInput("v_value", "Value (v):", min = 0, max = 1, value = 1, step = 0.01) ), mainPanel( plotOutput("rainbow_plot") ) ) ) # Define the server server <- function(input, output) { output$rainbow_plot <- renderPlot({ s <-...)
  • 07:52, 12 March 2024 Brb talk contribs uploaded File:Rainbow default.png (<syntaxhighlight lang='r'> library(shiny) # Define the UI ui <- fluidPage( titlePanel("Rainbow Color Palette"), sidebarLayout( sidebarPanel( sliderInput("s_value", "Saturation (s):", min = 0, max = 1, value = 1, step = 0.01), sliderInput("v_value", "Value (v):", min = 0, max = 1, value = 1, step = 0.01) ), mainPanel( plotOutput("rainbow_plot") ) ) ) # Define the server server <- function(input, output) { output$rainbow_plot <- renderPlot({ s <-...)
  • 20:41, 11 March 2024 Brb talk contribs created page File:Filtered R.png (<syntaxhighlight lang='r'> theta <- seq(0, .80, .01) R_BH <- filtered_R(alpha=.10, S2, p2, theta, method="BH") which.max(R_BH) # 60% <---- so theta=0.6 is the optimal filtering threshold # 61 max(R_BH) # [1] 380 plot(theta, R_BH, type="l", xlab=expression(theta), ylab="Rejections", main="BH cutoff = 0.1") abline(v=.6, lty=2) </syntaxhighlight>)
  • 20:41, 11 March 2024 Brb talk contribs uploaded File:Filtered R.png (<syntaxhighlight lang='r'> theta <- seq(0, .80, .01) R_BH <- filtered_R(alpha=.10, S2, p2, theta, method="BH") which.max(R_BH) # 60% <---- so theta=0.6 is the optimal filtering threshold # 61 max(R_BH) # [1] 380 plot(theta, R_BH, type="l", xlab=expression(theta), ylab="Rejections", main="BH cutoff = 0.1") abline(v=.6, lty=2) </syntaxhighlight>)
  • 20:35, 11 March 2024 Brb talk contribs created page File:Filtered p.png (Note: # x-axis "p cutoff" should be "BH cutoff" or "FDR cutoff". # Each curve represents theta (filtering threshold). For example, theta=.1 means 10% of genes are filtered out before we do multiple testing (or BH adjustment). # It is seen the larger the theta, the more hypotheses are rejected at the same FDR cutoff. For example, #* if theta=0, 251 hypotheses are rejected at FDR=.1 #* if theta=.5, 355 hypotheses are rejected at FDR=.1. <syntaxhighlight lang='r'> BiocManager::install("ALL")...)
  • 20:35, 11 March 2024 Brb talk contribs uploaded File:Filtered p.png (Note: # x-axis "p cutoff" should be "BH cutoff" or "FDR cutoff". # Each curve represents theta (filtering threshold). For example, theta=.1 means 10% of genes are filtered out before we do multiple testing (or BH adjustment). # It is seen the larger the theta, the more hypotheses are rejected at the same FDR cutoff. For example, #* if theta=0, 251 hypotheses are rejected at FDR=.1 #* if theta=.5, 355 hypotheses are rejected at FDR=.1. <syntaxhighlight lang='r'> BiocManager::install("ALL")...)
  • 15:49, 8 March 2024 Brb talk contribs created page File:DataOutliers2.png ({{Pre}} puree <- read.csv("https://gist.githubusercontent.com/arraytools/e851ed88c7456779557fbf3ed67b157a/raw/9971c61fea1db99acbd9de17ea82679ba9811358/dataOutliers2.csv", header=F) plot(puree[,1], puree[, 2], xlab="X", ylab="Y") abline(lm(V2 ~ V1, data = puree)) # robust regression require(MASS) summary(rlm(V2 ~ V1, data = puree)) abline(rr.huber <- rlm(V2 ~ V1, data = puree), col = "blue") # quantile regression library(quantreg) abline(rq(V2 ~ V1, data=puree, tau = 0.5), col = "red") # theil...)
  • 15:49, 8 March 2024 Brb talk contribs uploaded File:DataOutliers2.png ({{Pre}} puree <- read.csv("https://gist.githubusercontent.com/arraytools/e851ed88c7456779557fbf3ed67b157a/raw/9971c61fea1db99acbd9de17ea82679ba9811358/dataOutliers2.csv", header=F) plot(puree[,1], puree[, 2], xlab="X", ylab="Y") abline(lm(V2 ~ V1, data = puree)) # robust regression require(MASS) summary(rlm(V2 ~ V1, data = puree)) abline(rr.huber <- rlm(V2 ~ V1, data = puree), col = "blue") # quantile regression library(quantreg) abline(rq(V2 ~ V1, data=puree, tau = 0.5), col = "red") # theil...)
  • 14:27, 7 March 2024 Brb talk contribs created page File:DataOutliers.png ({{Pre}} puree <- read.csv("https://gist.githubusercontent.com/arraytools/47d3a46ae1f9a9cd47db350ae2bd2338/raw/b5cccc8e566ff3bef81b1b371e8bfa174c98ef38/dataOutliers.csv", header = FALSE) plot(puree[,1], puree[, 2], xlim=c(0,1), ylim=c(0,1), xlab="X", ylab="Y") abline(0,1, lty=2) abline(lm(V2 ~ V1, data = puree)) # robust regression require(MASS) summary(rlm(V2 ~ V1, data = puree)) abline(rr.huber <- rlm(V2 ~ V1, data = puree), col = "blue") # almost overlapped with lm() # quantile regressio...)
  • 14:27, 7 March 2024 Brb talk contribs uploaded File:DataOutliers.png ({{Pre}} puree <- read.csv("https://gist.githubusercontent.com/arraytools/47d3a46ae1f9a9cd47db350ae2bd2338/raw/b5cccc8e566ff3bef81b1b371e8bfa174c98ef38/dataOutliers.csv", header = FALSE) plot(puree[,1], puree[, 2], xlim=c(0,1), ylim=c(0,1), xlab="X", ylab="Y") abline(0,1, lty=2) abline(lm(V2 ~ V1, data = puree)) # robust regression require(MASS) summary(rlm(V2 ~ V1, data = puree)) abline(rr.huber <- rlm(V2 ~ V1, data = puree), col = "blue") # almost overlapped with lm() # quantile regressio...)
  • 21:41, 10 February 2024 Brb talk contribs created page File:R162.png
  • 21:41, 10 February 2024 Brb talk contribs uploaded File:R162.png
  • 21:53, 8 February 2024 Brb talk contribs created page File:Jitterbox.png (<syntaxhighlight lang='r'> nc <- 5 assy <- LETTERS[1:nc] pal <- ggpubr::get_palette("default", nc) set.seed(1) nr <- 5 mat <- matrix(runif(nr*length(assy)), nrow = nr, ncol = length(assy)) set.seed(1) cutoffs <- runif(nc) colnames(mat) <- assy par(mar=c(5,4,1,1)+.1) plot(1, 1, xlim = c(0.5, nc + .5), ylim = c(0,1), type = "n", xlab = "Assay", ylab = "Score", xaxt = 'n') for (i in 1:nc) { rect(i - 0.25, 0, i + 0.25, 1, col = pal[i]) lines(x = c(i - 0.25, i + 0.25), y = c(cutof...)
  • 21:53, 8 February 2024 Brb talk contribs uploaded File:Jitterbox.png (<syntaxhighlight lang='r'> nc <- 5 assy <- LETTERS[1:nc] pal <- ggpubr::get_palette("default", nc) set.seed(1) nr <- 5 mat <- matrix(runif(nr*length(assy)), nrow = nr, ncol = length(assy)) set.seed(1) cutoffs <- runif(nc) colnames(mat) <- assy par(mar=c(5,4,1,1)+.1) plot(1, 1, xlim = c(0.5, nc + .5), ylim = c(0,1), type = "n", xlab = "Assay", ylab = "Score", xaxt = 'n') for (i in 1:nc) { rect(i - 0.25, 0, i + 0.25, 1, col = pal[i]) lines(x = c(i - 0.25, i + 0.25), y = c(cutof...)
  • 10:25, 19 January 2024 Brb talk contribs created page File:RStudioAbort.png
  • 10:25, 19 January 2024 Brb talk contribs uploaded File:RStudioAbort.png
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