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qhtcp-workflow/apps/r/PairwiseLK.R
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895
qhtcp-workflow/apps/r/PairwiseLK.R
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# This R script performs GTA L and K Pairwise Compares for user specified pairs of Experiments
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library("ggplot2")
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library("plotly")
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library("htmlwidgets")
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library("extrafont")
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library("grid")
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library("ggthemes")
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args <- commandArgs(TRUE)
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exp1_name <- args[1]
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exp1_file <- args[2]
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exp2_name <- args[3]
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exp2_file <- args[4]
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output_dir <- args[5]
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pairDirL <- file.path(output_dir, paste0("PairwiseCompareL_", exp1_name, "-", exp2_name))
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pairDirK <- file.path(output_dir, paste0("PairwiseCompareK_", exp1_name, "-", exp2_name))
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# Pairwise L
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# outputPlotly <- "../GTAresults/PairwiseCompareL/" #"/GTAresults/PairwiseCompareL/"
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# Theme elements for plots
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theme_Publication <- function(base_size = 14, base_family = "sans") {
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(theme_foundation(base_size = base_size, base_family = base_family) +
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theme(
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plot.title = element_text(face = "bold", size = rel(1.2), hjust = 0.5),
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text = element_text(),
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panel.background = element_rect(colour = NA),
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plot.background = element_rect(colour = NA),
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panel.border = element_rect(colour = NA),
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axis.title = element_text(face = "bold", size = rel(1)),
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axis.title.y = element_text(angle = 90, vjust = 2),
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axis.title.x = element_text(vjust = -0.2),
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axis.text = element_text(),
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axis.line = element_line(colour = "black"),
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axis.ticks = element_line(),
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panel.grid.major = element_line(colour = "#f0f0f0"),
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panel.grid.minor = element_blank(),
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legend.key = element_rect(colour = NA),
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legend.position = "bottom",
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legend.direction = "horizontal",
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legend.key.size = unit(0.2, "cm"),
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legend.spacing = unit(0, "cm"),
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legend.title = element_text(face = "italic"),
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plot.margin = unit(c(10, 5, 5, 5), "mm"),
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strip.background = element_rect(colour = "#f0f0f0", fill = "#f0f0f0"),
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strip.text = element_text(face = "bold")
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)
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)
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}
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theme_Publication_legend_right <- function(base_size = 14, base_family = "sans") {
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(theme_foundation(base_size = base_size, base_family = base_family) +
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theme(
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plot.title = element_text(face = "bold", size = rel(1.2), hjust = 0.5),
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text = element_text(),
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panel.background = element_rect(colour = NA),
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plot.background = element_rect(colour = NA),
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panel.border = element_rect(colour = NA),
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axis.title = element_text(face = "bold", size = rel(1)),
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axis.title.y = element_text(angle = 90, vjust = 2),
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axis.title.x = element_text(vjust = -0.2),
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axis.text = element_text(),
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axis.line = element_line(colour = "black"),
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axis.ticks = element_line(),
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panel.grid.major = element_line(colour = "#f0f0f0"),
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panel.grid.minor = element_blank(),
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legend.key = element_rect(colour = NA),
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legend.position = "right",
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legend.direction = "vertical",
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legend.key.size = unit(0.5, "cm"),
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legend.spacing = unit(0, "cm"),
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legend.title = element_text(face = "italic"),
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plot.margin = unit(c(10, 5, 5, 5), "mm"),
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strip.background = element_rect(colour = "#f0f0f0", fill = "#f0f0f0"),
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strip.text = element_text(face = "bold")
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)
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)
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}
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scale_fill_Publication <- function(...) {
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discrete_scale("fill", "Publication", manual_pal(
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values = c("#386cb0", "#fdb462", "#7fc97f", "#ef3b2c", "#662506",
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"#a6cee3", "#fb9a99", "#984ea3", "#ffff33")), ...)
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}
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scale_colour_Publication <- function(...) {
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discrete_scale("colour", "Publication", manual_pal(
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values = c("#386cb0", "#fdb462", "#7fc97f", "#ef3b2c", "#662506",
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"#a6cee3", "#fb9a99", "#984ea3", "#ffff33")), ...)
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}
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X1 <- read.csv(file = exp1_file, stringsAsFactors = FALSE, header = TRUE)
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X2 <- read.csv(file = exp2_file, stringsAsFactors = FALSE, header = TRUE)
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X <- merge(X1, X2, by = "Term_Avg", all = TRUE, suffixes = c("_X1", "_X2"))
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gg <- ggplot(data = X, aes(
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x = Z_lm_L_Avg_X1,
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y = Z_lm_L_Avg_X2,
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color = Ontology_Avg_X1,
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Term = Term_Avg,
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Genes = Genes_Avg_X1,
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NumGenes = NumGenes_Avg_X1,
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AllPossibleGenes = AllPossibleGenes_Avg_X1,
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SD_1 = Z_lm_L_SD_X1,
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SD_2 = Z_lm_L_SD_X2
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)) +
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xlab(paste("GO Term Avg lm Z for", exp1_name)) +
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geom_rect(
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aes(xmin = -2, xmax = 2, ymin = -2, ymax = 2),
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color = "grey20",
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size = 0.25,
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alpha = 0.1,
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inherit.aes = FALSE,
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fill = NA
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) +
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geom_point(shape = 3) +
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ylab(paste("GO Term Avg lm Z for", exp2_name)) +
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ggtitle(paste("Comparing Average GO Term Z lm for", exp1_name, " vs. ", exp2_name)) +
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theme_Publication_legend_right()
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pdf(
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file.path(pairDirL, paste0("Scatter_lm_GTA_Averages_", exp1_name, "_vs_", exp2_name, "_All_ByOntology.pdf")),
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width = 12,
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height = 8
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)
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gg
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dev.off()
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pgg <- ggplotly(gg)
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fname <- file.path(pairDirL, paste0("Scatter_lm_GTA_Averages_", exp1_name, "_vs_", exp2_name, "_All_byOntology.html"))
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htmlwidgets::saveWidget(pgg, fname)
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# ID aggravators and alleviators, regardless of whether they meet 2SD threshold
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X1_Specific_Aggravators <- X[which(X$Z_lm_L_Avg_X1 >= 2 & X$Z_lm_L_Avg_X2 < 2), ]
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X1_Specific_Alleviators <- X[which(X$Z_lm_L_Avg_X1 <= -2 & X$Z_lm_L_Avg_X2 > -2), ]
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X2_Specific_Aggravators <- X[which(X$Z_lm_L_Avg_X2 >= 2 & X$Z_lm_L_Avg_X1 < 2), ]
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X2_Specific_Alleviators <- X[which(X$Z_lm_L_Avg_X2 <= -2 & X$Z_lm_L_Avg_X1 > -2), ]
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Overlap_Aggravators <- X[which(X$Z_lm_L_Avg_X1 >= 2 & X$Z_lm_L_Avg_X2 >= 2), ]
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Overlap_Alleviators <- X[which(X$Z_lm_L_Avg_X1 <= -2 & X$Z_lm_L_Avg_X2 <= -2), ]
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X2_Specific_Aggravators_X1_Alleviatiors <- X[which(X$Z_lm_L_Avg_X2 >= 2 & X$Z_lm_L_Avg_X1 <= -2), ]
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X2_Specific_Alleviators_X1_Aggravators <- X[which(X$Z_lm_L_Avg_X2 <= -2 & X$Z_lm_L_Avg_X1 >= 2), ]
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X$Overlap_Avg <- NA
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try(X[X$Term_Avg %in% X1_Specific_Aggravators$Term_Avg, ]$Overlap_Avg <-
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paste(exp1_name, "Specific_Deletion_Enhancers", sep = "_"))
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try(X[X$Term_Avg %in% X1_Specific_Alleviators$Term_Avg, ]$Overlap_Avg <-
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paste(exp1_name, "Specific_Deletion_Suppresors", sep = "_"))
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try(X[X$Term_Avg %in% X2_Specific_Aggravators$Term_Avg, ]$Overlap_Avg <-
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paste(exp2_name, "Specific_Deletion_Enhancers", sep = "_"))
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try(X[X$Term_Avg %in% X2_Specific_Alleviators$Term_Avg, ]$Overlap_Avg <-
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paste(exp2_name, "Specific_Deletion_Suppressors", sep = "_"))
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try(X[X$Term_Avg %in% Overlap_Aggravators$Term_Avg, ]$Overlap_Avg <- "Overlapping_Deletion_Enhancers")
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try(X[X$Term_Avg %in% Overlap_Alleviators$Term_Avg, ]$Overlap_Avg <- "Overlapping_Deletion_Suppressors")
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try(X[X$Term_Avg %in% X2_Specific_Aggravators_X1_Alleviatiors$Term_Avg, ]$Overlap_Avg <-
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paste(exp2_name, "Deletion_Enhancers", exp1_name, "Deletion_Suppressors", sep = "_"))
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try(X[X$Term_Avg %in% X2_Specific_Alleviators_X1_Aggravators$Term_Avg, ]$Overlap_Avg <-
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paste(exp2_name, "Deletion_Suppressors", exp1_name, "Deletion_Enhancers", sep = "_"))
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gg <- ggplot(data = X, aes(
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x = Z_lm_L_Avg_X1,
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y = Z_lm_L_Avg_X2,
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color = Overlap_Avg,
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Term = Term_Avg,
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Genes = Genes_Avg_X1,
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NumGenes = NumGenes_Avg_X1,
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AllPossibleGenes = AllPossibleGenes_Avg_X1,
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SD_1 = Z_lm_L_SD_X1,
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SD_2 = Z_lm_L_SD_X2
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)) +
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xlab(paste("GO Term Avg lm Z for", exp1_name)) +
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geom_rect(
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aes(xmin = -2, xmax = 2, ymin = -2, ymax = 2),
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color = "grey20",
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size = 0.25,
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alpha = 0.1,
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inherit.aes = FALSE,
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fill = NA
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) +
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geom_point(shape = 3) +
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ylab(paste("GO Term Avg lm Z for", exp2_name)) +
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ggtitle(paste("Comparing Average GO Term Z lm for", exp1_name, " vs. ", exp2_name)) +
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theme_Publication_legend_right()
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pdf(
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file.path(pairDirL, paste0("Scatter_lm_GTA_Averages_", exp1_name, "_vs_", exp2_name, "_All_ByOverlap.pdf")),
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width = 12,
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height = 8
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)
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gg
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dev.off()
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pgg <- ggplotly(gg)
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fname <- file.path(pairDirL, paste0("Scatter_lm_GTA_Averages_", exp1_name, "_vs_", exp2_name, "_All_byOverlap.html"))
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htmlwidgets::saveWidget(pgg, fname)
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x_rem2_gene <- X[X$NumGenes_Avg_X1 >= 2 & X$NumGenes_Avg_X2 >= 2, ]
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#3
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gg <- ggplot(data = x_rem2_gene, aes(
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x = Z_lm_L_Avg_X1,
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y = Z_lm_L_Avg_X2,
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color = Overlap_Avg,
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Term = Term_Avg,
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Genes = Genes_Avg_X1,
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NumGenes = NumGenes_Avg_X1,
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AllPossibleGenes = AllPossibleGenes_Avg_X1,
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SD_1 = Z_lm_L_SD_X1,
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SD_2 = Z_lm_L_SD_X2
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)) +
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xlab(paste("GO Term Avg lm Z for", exp1_name)) +
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geom_rect(aes(xmin = -2, xmax = 2, ymin = -2, ymax = 2), color = "grey20", size = 0.25, alpha = 0.1, inherit.aes = FALSE, fill = NA) +
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geom_point(shape = 3) +
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ylab(paste("GO Term Avg lm Z for", exp2_name)) +
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ggtitle(paste("Comparing Average GO Term Z lm for", exp1_name, "vs.", exp2_name)) +
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theme_Publication_legend_right()
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pdf(
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file.path(pairDirL, paste0("Scatter_lm_GTA_Averages_", exp1_name, "_vs_", exp2_name, "_All_ByOverlap_above2genes.pdf")),
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width = 12,
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height = 8
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)
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gg
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dev.off()
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pgg <- ggplotly(gg)
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#pgg
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fname <- file.path(pairDirL, paste0("Scatter_lm_GTA_Averages_", exp1_name, "_vs_", exp2_name, "_All_byOverlap_above2genes.html"))
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htmlwidgets::saveWidget(pgg, fname)
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#4
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X_overlap_nothresold <- X[!(is.na(X$Overlap_Avg)), ]
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gg <- ggplot(data = X_overlap_nothresold, aes(
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x = Z_lm_L_Avg_X1,
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y = Z_lm_L_Avg_X2,
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color = Overlap_Avg,
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Term = Term_Avg,
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Genes = Genes_Avg_X1,
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NumGenes = NumGenes_Avg_X1,
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AllPossibleGenes = AllPossibleGenes_Avg_X1,
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SD_1 = Z_lm_L_SD_X1,
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SD_2 = Z_lm_L_SD_X2
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)) +
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xlab(paste("GO Term Avg lm Z for", exp1_name)) +
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geom_rect(aes(xmin = -2, xmax = 2, ymin = -2, ymax = 2), color = "grey20", size = 0.25, alpha = 0.1, inherit.aes = FALSE, fill = NA) +
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geom_point(shape = 3) +
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ylab(paste("GO Term Avg lm Z for", exp2_name)) +
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ggtitle(paste("Comparing Average GO Term Z lm for", exp1_name, "vs.", exp2_name)) +
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theme_Publication_legend_right()
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pdf(
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file.path(pairDirL, paste0("Scatter_lm_GTA_Averages_", exp1_name, "_vs_", exp2_name, "_Above2SD_ByOverlap.pdf")),
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width = 12,
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height = 8
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)
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gg
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dev.off()
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pgg <- ggplotly(gg)
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#pgg
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fname <- file.path(pairDirL, paste0("Scatter_lm_GTA_Averages_", exp1_name, "_vs_", exp2_name, "_Above2SD_ByOverlap.html"))
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htmlwidgets::saveWidget(pgg, fname)
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# Only output GTA terms where average score is still above 2 after subtracting the SD
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# Z1 will ID aggravators, Z2 alleviators
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Z1 <- X
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Z1$L_Subtract_SD_X1 <- Z1$Z_lm_L_Avg_X1 - Z1$Z_lm_L_SD_X1
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Z1$L_Subtract_SD_X2 <- Z1$Z_lm_L_Avg_X2 - Z1$Z_lm_L_SD_X2
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Z2 <- X
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Z2$L_Subtract_SD_X1 <- Z1$Z_lm_L_Avg_X1 + Z1$Z_lm_L_SD_X1
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Z2$L_Subtract_SD_X2 <- Z1$Z_lm_L_Avg_X2 + Z1$Z_lm_L_SD_X2
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X1_Specific_Aggravators2 <- Z1[which(Z1$L_Subtract_SD_X1 >= 2 & Z1$L_Subtract_SD_X2 < 2), ]
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X1_Specific_Alleviators2 <- Z2[which(Z2$L_Subtract_SD_X1 <= -2 & Z2$L_Subtract_SD_X2 > -2), ]
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X2_Specific_Aggravators2 <- Z1[which(Z1$L_Subtract_SD_X2 >= 2 & Z1$L_Subtract_SD_X1 < 2), ]
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X2_Specific_Alleviators2 <- Z2[which(Z2$L_Subtract_SD_X2 <= -2 & Z2$L_Subtract_SD_X1 > -2), ]
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Overlap_Aggravators2 <- Z1[which(Z1$L_Subtract_SD_X1 >= 2 & Z1$L_Subtract_SD_X2 >= 2), ]
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Overlap_Alleviators2 <- Z2[which(Z2$L_Subtract_SD_X2 <= -2 & Z2$L_Subtract_SD_X1 <= -2), ]
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X2_Specific_Aggravators2_X1_Alleviatiors2 <- Z1[which(Z1$L_Subtract_SD_X2 >= 2 & Z2$L_Subtract_SD_X1 <= -2), ]
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X2_Specific_Alleviators2_X1_Aggravators2 <- Z2[which(Z2$L_Subtract_SD_X2 <= -2 & Z1$L_Subtract_SD_X1 >= 2), ]
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X$Overlap <- NA
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try(X[X$Term_Avg %in% X1_Specific_Aggravators2$Term_Avg, ]$Overlap <- paste(exp1_name, "Specific_Deletion_Enhancers", sep = "_"))
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try(X[X$Term_Avg %in% X1_Specific_Alleviators2$Term_Avg, ]$Overlap <- paste(exp1_name, "Specific_Deletion_Suppresors", sep = "_"))
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try(X[X$Term_Avg %in% X2_Specific_Aggravators2$Term_Avg, ]$Overlap <- paste(exp2_name, "Specific_Deletion_Enhancers", sep = "_"))
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try(X[X$Term_Avg %in% X2_Specific_Alleviators2$Term_Avg, ]$Overlap <- paste(exp2_name, "Specific_Deletion_Suppressors", sep = "_"))
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try(X[X$Term_Avg %in% Overlap_Aggravators2$Term_Avg, ]$Overlap <- "Overlapping_Deletion_Enhancers")
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try(X[X$Term_Avg %in% Overlap_Alleviators2$Term_Avg, ]$Overlap <- "Overlapping_Deletion_Suppressors")
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try(X[X$Term_Avg %in% X2_Specific_Aggravators2_X1_Alleviatiors2$Term_Avg, ]$Overlap <-
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paste(exp2_name, "Deletion_Enhancers", exp1_name, "Deletion_Suppressors", sep = "_"))
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try(X[X$Term_Avg %in% X2_Specific_Alleviators2_X1_Aggravators2$Term_Avg, ]$Overlap <-
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paste(exp2_name, "Deletion_Suppressors", exp1_name, "Deletion_Enhancers", sep = "_"))
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#5
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X_abovethreshold <- X[!(is.na(X$Overlap)), ]
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gg <- ggplot(data = X_abovethreshold, aes(
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x = Z_lm_L_Avg_X1,
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y = Z_lm_L_Avg_X2,
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color = Overlap,
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Term = Term_Avg,
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Genes = Genes_Avg_X1,
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NumGenes = NumGenes_Avg_X1,
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AllPossibleGenes = AllPossibleGenes_Avg_X1,
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SD_1 = Z_lm_L_SD_X1,
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SD_2 = Z_lm_L_SD_X2
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)) +
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xlab(paste("GO Term Avg lm Z for", exp1_name)) +
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geom_rect(aes(xmin = -2, xmax = 2, ymin = -2, ymax = 2), color = "grey20", size = 0.25, alpha = 0.1, inherit.aes = FALSE, fill = NA) +
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geom_point(shape = 3) +
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ylab(paste("GO Term Avg lm Z for", exp2_name)) +
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ggtitle(paste("Comparing Average GO Term Z lm for", exp1_name, " vs. ", exp2_name)) +
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theme_Publication_legend_right()
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pdf(
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file.path(pairDirL, paste0("Scatter_lm_GTA_Averages_", exp1_name, "_vs_", exp2_name, "_All_ByOverlap_AboveThreshold.pdf")),
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width = 12,
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height = 8
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)
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gg
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dev.off()
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pgg <- ggplotly(gg)
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#pgg
|
||||
fname <- file.path(pairDirL, paste0("Scatter_lm_GTA_Averages_", exp1_name, "_vs_", exp2_name, "_All_ByOverlap_AboveThreshold.html"))
|
||||
htmlwidgets::saveWidget(pgg, fname)
|
||||
|
||||
#6
|
||||
gg <- ggplot(data = X_abovethreshold, aes(
|
||||
x = Z_lm_L_Avg_X1,
|
||||
y = Z_lm_L_Avg_X2,
|
||||
color = Overlap,
|
||||
Term = Term_Avg,
|
||||
Genes = Genes_Avg_X1,
|
||||
NumGenes = NumGenes_Avg_X1,
|
||||
AllPossibleGenes = AllPossibleGenes_Avg_X1,
|
||||
SD_1 = Z_lm_L_SD_X1,
|
||||
SD_2 = Z_lm_L_SD_X2
|
||||
)) +
|
||||
xlab(paste("GO Term Avg lm Z for", exp1_name)) +
|
||||
geom_text(aes(label = Term_Avg), nudge_y = 0.25, size = 2) +
|
||||
geom_rect(aes(xmin = -2, xmax = 2, ymin = -2, ymax = 2), color = "grey20", size = 0.25, alpha = 0.1, inherit.aes = FALSE, fill = NA) +
|
||||
geom_point(shape = 3, size = 3) +
|
||||
ylab(paste("GO Term Avg lm Z for", exp2_name)) +
|
||||
ggtitle(paste("Comparing Average GO Term Z lm for", exp1_name, "vs.", exp2_name)) +
|
||||
theme_Publication_legend_right()
|
||||
|
||||
pdf(
|
||||
file.path(pairDirL, paste0("Scatter_lm_GTA_Averages_", exp1_name, "_vs_", exp2_name, "_All_ByOverlap_AboveThreshold_names.pdf")),
|
||||
width = 20,
|
||||
height = 20
|
||||
)
|
||||
|
||||
gg
|
||||
dev.off()
|
||||
pgg <- ggplotly(gg)
|
||||
#pgg
|
||||
fname <- file.path(pairDirL, paste0("Scatter_lm_GTA_Averages_", exp1_name, "_vs_", exp2_name, "_All_ByOverlap_AboveThreshold_names.html"))
|
||||
htmlwidgets::saveWidget(pgg, fname)
|
||||
|
||||
X_abovethreshold$X1_Rank <- NA
|
||||
X_abovethreshold$X1_Rank <- rank(-X_abovethreshold$Z_lm_L_Avg_X1, ties.method = "random")
|
||||
X_abovethreshold$X2_Rank <- NA
|
||||
X_abovethreshold$X2_Rank <- rank(-X_abovethreshold$Z_lm_L_Avg_X2, ties.method = "random")
|
||||
|
||||
#7
|
||||
gg <- ggplot(data = X_abovethreshold, aes(
|
||||
x = Z_lm_L_Avg_X1,
|
||||
y = Z_lm_L_Avg_X2,
|
||||
color = Overlap,
|
||||
Term = Term_Avg,
|
||||
Genes = Genes_Avg_X1,
|
||||
NumGenes = NumGenes_Avg_X1,
|
||||
AllPossibleGenes = AllPossibleGenes_Avg_X1,
|
||||
SD_1 = Z_lm_L_SD_X1,
|
||||
SD_2 = Z_lm_L_SD_X2
|
||||
)) +
|
||||
xlab(paste("GO Term Avg lm Z for", exp1_name)) +
|
||||
geom_text(aes(label = X1_Rank), nudge_y = 0.25, size = 4) +
|
||||
geom_rect(aes(xmin = -2, xmax = 2, ymin = -2, ymax = 2), color = "grey20", size = 0.25, alpha = 0.1, inherit.aes = FALSE, fill = NA) +
|
||||
geom_point(shape = 3, size = 3) +
|
||||
ylab(paste("GO Term Avg lm Z for", exp2_name)) +
|
||||
ggtitle(paste("Comparing Average GO Term Z lm for", exp1_name, "vs.", exp2_name)) +
|
||||
theme_Publication_legend_right()
|
||||
|
||||
pdf(
|
||||
file.path(pairDirL, paste0("Scatter_lm_GTA_Averages_", exp1_name, "_vs_", exp2_name, "_All_ByOverlap_AboveThreshold_numberedX1.pdf")),
|
||||
width = 15,
|
||||
height = 15
|
||||
)
|
||||
|
||||
gg
|
||||
dev.off()
|
||||
pgg <- ggplotly(gg)
|
||||
#pgg
|
||||
|
||||
fname <-
|
||||
file.path(pairDirL, paste0("Scatter_lm_GTA_Averages_", exp1_name, "_vs_", exp2_name, "_All_ByOverlap_AboveThreshold_numberedX1.html"))
|
||||
htmlwidgets::saveWidget(pgg, fname)
|
||||
|
||||
#8
|
||||
gg <- ggplot(data = X_abovethreshold, aes(
|
||||
x = Z_lm_L_Avg_X1,
|
||||
y = Z_lm_L_Avg_X2,
|
||||
color = Overlap,
|
||||
Term = Term_Avg,
|
||||
Genes = Genes_Avg_X1,
|
||||
NumGenes = NumGenes_Avg_X1,
|
||||
AllPossibleGenes = AllPossibleGenes_Avg_X1,
|
||||
SD_1 = Z_lm_L_SD_X1,
|
||||
SD_2 = Z_lm_L_SD_X2
|
||||
)) +
|
||||
xlab(paste("GO Term Avg lm Z for", exp1_name)) +
|
||||
geom_text(aes(label = X2_Rank), nudge_y = 0.25, size = 4) +
|
||||
geom_rect(aes(xmin = -2, xmax = 2, ymin = -2, ymax = 2), color = "grey20", size = 0.25, alpha = 0.1, inherit.aes = FALSE, fill = NA) +
|
||||
geom_point(shape = 3, size = 3) +
|
||||
ylab(paste("GO Term Avg lm Z for", exp2_name)) +
|
||||
ggtitle(paste("Comparing Average GO Term Z lm for", exp1_name, "vs.", exp2_name)) +
|
||||
theme_Publication_legend_right()
|
||||
|
||||
pdf(
|
||||
file.path(pairDirL, paste0("Scatter_lm_GTA_Averages_", exp1_name, "_vs_", exp2_name, "_All_ByOverlap_AboveThreshold_numberedX2.pdf")),
|
||||
width = 15,
|
||||
height = 15
|
||||
)
|
||||
|
||||
gg
|
||||
dev.off()
|
||||
pgg <- ggplotly(gg)
|
||||
#pgg
|
||||
fname <-
|
||||
file.path(pairDirL, paste0("Scatter_lm_GTA_Averages_", exp1_name, "_vs_", exp2_name, "_All_ByOverlap_AboveThreshold_numberedX2.html"))
|
||||
htmlwidgets::saveWidget(pgg, fname)
|
||||
|
||||
write.csv(
|
||||
x = X,
|
||||
file.path(pairDirL, paste0("All_GTA_Avg_Scores_", exp1_name, "_vs_", exp2_name, ".csv")),
|
||||
row.names = FALSE
|
||||
)
|
||||
|
||||
write.csv(
|
||||
x = X_abovethreshold,
|
||||
file = file.path(pairDirL, paste0("AboveThreshold_GTA_Avg_Scores_", exp1_name, "_vs_", exp2_name, ".csv")),
|
||||
row.names = FALSE
|
||||
)
|
||||
|
||||
# Begin Pairwsise K
|
||||
# Theme elements for plots
|
||||
theme_Publication <- function(base_size = 14, base_family = "sans") {
|
||||
(theme_foundation(base_size = base_size, base_family = base_family) +
|
||||
theme(
|
||||
plot.title = element_text(face = "bold", size = rel(1.2), hjust = 0.5),
|
||||
text = element_text(),
|
||||
panel.background = element_rect(colour = NA),
|
||||
plot.background = element_rect(colour = NA),
|
||||
panel.border = element_rect(colour = NA),
|
||||
axis.title = element_text(face = "bold", size = rel(1)),
|
||||
axis.title.y = element_text(angle = 90, vjust = 2),
|
||||
axis.title.x = element_text(vjust = -0.2),
|
||||
axis.text = element_text(),
|
||||
axis.line = element_line(colour = "black"),
|
||||
axis.ticks = element_line(),
|
||||
panel.grid.major = element_line(colour = "#f0f0f0"),
|
||||
panel.grid.minor = element_blank(),
|
||||
legend.key = element_rect(colour = NA),
|
||||
legend.position = "bottom",
|
||||
legend.direction = "horizontal",
|
||||
legend.key.size = unit(0.2, "cm"),
|
||||
legend.spacing = unit(0, "cm"),
|
||||
legend.title = element_text(face = "italic"),
|
||||
plot.margin = unit(c(10, 5, 5, 5), "mm"),
|
||||
strip.background = element_rect(colour = "#f0f0f0", fill = "#f0f0f0"),
|
||||
strip.text = element_text(face = "bold")
|
||||
)
|
||||
)
|
||||
}
|
||||
|
||||
scale_fill_Publication <- function(...) {
|
||||
library("scales")
|
||||
discrete_scale(
|
||||
"fill",
|
||||
"Publication",
|
||||
manual_pal(values = c("#386cb0", "#fdb462", "#7fc97f", "#ef3b2c", "#662506", "#a6cee3", "#fb9a99", "#984ea3", "#ffff33")),
|
||||
...
|
||||
)
|
||||
}
|
||||
|
||||
scale_colour_Publication <- function(...) {
|
||||
discrete_scale(
|
||||
"colour",
|
||||
"Publication",
|
||||
manual_pal(values = c("#386cb0", "#fdb462", "#7fc97f", "#ef3b2c", "#662506", "#a6cee3", "#fb9a99", "#984ea3", "#ffff33")),
|
||||
...
|
||||
)
|
||||
}
|
||||
|
||||
theme_Publication_legend_right <- function(base_size = 14, base_family = "sans") {
|
||||
(theme_foundation(base_size = base_size, base_family = base_family) +
|
||||
theme(
|
||||
plot.title = element_text(face = "bold",
|
||||
size = rel(1.2), hjust = 0.5),
|
||||
text = element_text(),
|
||||
panel.background = element_rect(colour = NA),
|
||||
plot.background = element_rect(colour = NA),
|
||||
panel.border = element_rect(colour = NA),
|
||||
axis.title = element_text(face = "bold", size = rel(1)),
|
||||
axis.title.y = element_text(angle = 90, vjust = 2),
|
||||
axis.title.x = element_text(vjust = -0.2),
|
||||
axis.text = element_text(),
|
||||
axis.line = element_line(colour = "black"),
|
||||
axis.ticks = element_line(),
|
||||
panel.grid.major = element_line(colour = "#f0f0f0"),
|
||||
panel.grid.minor = element_blank(),
|
||||
legend.key = element_rect(colour = NA),
|
||||
legend.position = "right",
|
||||
legend.direction = "vertical",
|
||||
legend.key.size = unit(0.5, "cm"),
|
||||
legend.spacing = unit(0, "cm"),
|
||||
legend.title = element_text(face = "italic"),
|
||||
plot.margin = unit(c(10, 5, 5, 5), "mm"),
|
||||
strip.background = element_rect(colour = "#f0f0f0", fill = "#f0f0f0"),
|
||||
strip.text = element_text(face = "bold")
|
||||
)
|
||||
)
|
||||
}
|
||||
|
||||
scale_fill_Publication <- function(...) {
|
||||
discrete_scale(
|
||||
"fill",
|
||||
"Publication",
|
||||
manual_pal(values = c("#386cb0", "#fdb462", "#7fc97f", "#ef3b2c", "#662506", "#a6cee3", "#fb9a99", "#984ea3", "#ffff33")),
|
||||
...
|
||||
)
|
||||
}
|
||||
|
||||
scale_colour_Publication <- function(...) {
|
||||
discrete_scale(
|
||||
"colour",
|
||||
"Publication",
|
||||
manual_pal(values = c("#386cb0", "#fdb462", "#7fc97f", "#ef3b2c", "#662506", "#a6cee3", "#fb9a99", "#984ea3", "#ffff33")),
|
||||
...
|
||||
)
|
||||
}
|
||||
|
||||
X1 <- read.csv(file = exp1_file, stringsAsFactors = FALSE, header = TRUE)
|
||||
X2 <- read.csv(file = exp2_file, stringsAsFactors = FALSE, header = TRUE)
|
||||
|
||||
#1
|
||||
X <- merge(X1, X2, by = "Term_Avg", all = TRUE, suffixes = c("_X1", "_X2"))
|
||||
|
||||
gg <- ggplot(data = X, aes(
|
||||
x = Z_lm_K_Avg_X1,
|
||||
y = Z_lm_K_Avg_X2,
|
||||
color = Ontology_Avg_X1,
|
||||
Term = Term_Avg,
|
||||
Genes = Genes_Avg_X1,
|
||||
NumGenes = NumGenes_Avg_X1,
|
||||
AllPossibleGenes = AllPossibleGenes_Avg_X1,
|
||||
SD_1 = Z_lm_K_SD_X1,
|
||||
SD_2 = Z_lm_K_SD_X2
|
||||
)) +
|
||||
xlab(paste("GO Term Avg lm Z for", exp1_name)) +
|
||||
geom_rect(aes(xmin = -2, xmax = 2, ymin = -2, ymax = 2), color = "grey20", size = 0.25, alpha = 0.1, inherit.aes = FALSE, fill = NA) +
|
||||
geom_point(shape = 3) +
|
||||
ylab(paste("GO Term Avg lm Z for", exp2_name)) +
|
||||
ggtitle(paste("Comparing Average GO Term Z lm for", exp1_name, "vs.", exp2_name)) +
|
||||
theme_Publication_legend_right()
|
||||
|
||||
pdf(
|
||||
file.path(pairDirK, paste0("Scatter_lm_GTF_Averages_", exp1_name, "_vs_", exp2_name, "_All_ByOntology.pdf")),
|
||||
width = 12,
|
||||
height = 8
|
||||
)
|
||||
|
||||
gg
|
||||
dev.off()
|
||||
pgg <- ggplotly(gg)
|
||||
#pgg
|
||||
fname <- file.path(pairDirK, paste0("Scatter_lm_GTA_Averages_", exp1_name, "_vs_", exp2_name, "_All_byOntology.html"))
|
||||
htmlwidgets::saveWidget(pgg, fname)
|
||||
|
||||
#2
|
||||
# ID aggravators and alleviators, regardless of whether they meet 2SD threshold
|
||||
X1_Specific_Aggravators <- X[which(X$Z_lm_K_Avg_X1 >= 2 & X$Z_lm_K_Avg_X2 < 2), ]
|
||||
X1_Specific_Alleviators <- X[which(X$Z_lm_K_Avg_X1 <= -2 & X$Z_lm_K_Avg_X2 > -2), ]
|
||||
X2_Specific_Aggravators <- X[which(X$Z_lm_K_Avg_X2 >= 2 & X$Z_lm_K_Avg_X1 < 2), ]
|
||||
X2_Specific_Alleviators <- X[which(X$Z_lm_K_Avg_X2 <= -2 & X$Z_lm_K_Avg_X1 > -2), ]
|
||||
Overlap_Aggravators <- X[which(X$Z_lm_K_Avg_X1 >= 2 & X$Z_lm_K_Avg_X2 >= 2), ]
|
||||
Overlap_Alleviators <- X[which(X$Z_lm_K_Avg_X1 <= -2 & X$Z_lm_K_Avg_X2 <= -2), ]
|
||||
X2_Specific_Aggravators_X1_Alleviatiors <- X[which(X$Z_lm_K_Avg_X2 >= 2 & X$Z_lm_K_Avg_X1 <= -2), ]
|
||||
X2_Specific_Alleviators_X1_Aggravators <- X[which(X$Z_lm_K_Avg_X2 <= -2 & X$Z_lm_K_Avg_X1 >= 2), ]
|
||||
X$Overlap_Avg <- NA
|
||||
|
||||
try(X[X$Term_Avg %in% X1_Specific_Aggravators$Term_Avg, ]$Overlap_Avg <-
|
||||
paste(exp1_name, "Specific_Deletion_Suppressors", sep = "_"))
|
||||
try(X[X$Term_Avg %in% X1_Specific_Alleviators$Term_Avg, ]$Overlap_Avg <-
|
||||
paste(exp1_name, "Specific_Deletion_Enhancers", sep = "_"))
|
||||
try(X[X$Term_Avg %in% X2_Specific_Aggravators$Term_Avg, ]$Overlap_Avg <-
|
||||
paste(exp2_name, "Specific_Deletion_Suppressors", sep = "_"))
|
||||
try(X[X$Term_Avg %in% X2_Specific_Alleviators$Term_Avg, ]$Overlap_Avg <-
|
||||
paste(exp2_name, "Specific_Deletion_Enhancers", sep = "_"))
|
||||
try(X[X$Term_Avg %in% Overlap_Aggravators$Term_Avg, ]$Overlap_Avg <-
|
||||
"Overlapping_Deletion_Suppressors")
|
||||
try(X[X$Term_Avg %in% Overlap_Alleviators$Term_Avg, ]$Overlap_Avg <-
|
||||
"Overlapping_Deletion_Enhancers")
|
||||
try(X[X$Term_Avg %in% X2_Specific_Aggravators_X1_Alleviatiors$Term_Avg, ]$Overlap_Avg <-
|
||||
paste(exp2_name, "Deletion_Suppressors", exp1_name, "Deletion_Enhancers", sep = "_"))
|
||||
try(X[X$Term_Avg %in% X2_Specific_Alleviators_X1_Aggravators$Term_Avg, ]$Overlap_Avg <-
|
||||
paste(exp2_name, "Deletion_Enhancers", exp1_name, "Deletion_Suppressors", sep = "_"))
|
||||
|
||||
plotly_path <- file.path(pairDirK, paste0("Scatter_lm_GTF_Averages_", exp1_name, "_vs_", exp2_name, "_All_byOverlap.html"))
|
||||
gg <- ggplot(data = X, aes(
|
||||
x = Z_lm_K_Avg_X1,
|
||||
y = Z_lm_K_Avg_X2,
|
||||
color = Overlap_Avg,
|
||||
Term = Term_Avg,
|
||||
Genes = Genes_Avg_X1,
|
||||
NumGenes = NumGenes_Avg_X1,
|
||||
AllPossibleGenes = AllPossibleGenes_Avg_X1,
|
||||
SD_1 = Z_lm_K_SD_X1,
|
||||
SD_2 = Z_lm_K_SD_X2
|
||||
)) +
|
||||
xlab(paste("GO Term Avg lm Z for", exp1_name)) +
|
||||
geom_rect(aes(xmin = -2, xmax = 2, ymin = -2, ymax = 2), color = "grey20", size = 0.25, alpha = 0.1, inherit.aes = FALSE, fill = NA) +
|
||||
geom_point(shape = 3) +
|
||||
ylab(paste("GO Term Avg lm Z for", exp2_name)) +
|
||||
ggtitle(paste("Comparing Average GO Term Z lm for", exp1_name, "vs.", exp2_name)) +
|
||||
theme_Publication_legend_right()
|
||||
|
||||
pdf(
|
||||
file.path(pairDirK, paste0("Scatter_lm_GTF_Averages_", exp1_name, "_vs_", exp2_name, "_All_ByOverlap.pdf")),
|
||||
width = 12,
|
||||
height = 8
|
||||
)
|
||||
|
||||
gg
|
||||
dev.off()
|
||||
pgg <- ggplotly(gg)
|
||||
|
||||
#2
|
||||
fname <- file.path(pairDirK, paste0("Scatter_lm_GTA_Averages_", exp1_name, "_vs_", exp2_name, "_All_byOverlap.html"))
|
||||
htmlwidgets::saveWidget(pgg, fname)
|
||||
|
||||
#3
|
||||
x_rem2_gene <- X[X$NumGenes_Avg_X1 >= 2 & X$NumGenes_Avg_X2 >= 2, ]
|
||||
plotly_path <- file.path(pairDirK, paste0("Scatter_lm_GTF_Averages_", exp1_name, "_vs_", exp2_name, "_All_byOverlap_above2genes.html"))
|
||||
gg <- ggplot(data = x_rem2_gene, aes(
|
||||
x = Z_lm_K_Avg_X1,
|
||||
y = Z_lm_K_Avg_X2,
|
||||
color = Overlap_Avg,
|
||||
Term = Term_Avg,
|
||||
Genes = Genes_Avg_X1,
|
||||
NumGenes = NumGenes_Avg_X1,
|
||||
AllPossibleGenes = AllPossibleGenes_Avg_X1,
|
||||
SD_1 = Z_lm_K_SD_X1,
|
||||
SD_2 = Z_lm_K_SD_X2
|
||||
)) +
|
||||
xlab(paste("GO Term Avg lm Z for", exp1_name)) +
|
||||
geom_rect(aes(xmin = -2, xmax = 2, ymin = -2, ymax = 2), color = "grey20", size = 0.25, alpha = 0.1, inherit.aes = FALSE, fill = NA) +
|
||||
geom_point(shape = 3) +
|
||||
ylab(paste("GO Term Avg lm Z for", exp2_name)) +
|
||||
ggtitle(paste("Comparing Average GO Term Z lm for", exp1_name, "vs.", exp2_name)) +
|
||||
theme_Publication_legend_right()
|
||||
|
||||
pdf(
|
||||
file.path(pairDirK, paste0("Scatter_lm_GTF_Averages_", exp1_name, "_vs_", exp2_name, "_All_ByOverlap_above2genes.pdf")),
|
||||
width = 12,
|
||||
height = 8
|
||||
)
|
||||
|
||||
gg
|
||||
dev.off()
|
||||
pgg <- ggplotly(gg)
|
||||
#pgg
|
||||
fname <- file.path(pairDirK, paste0("Scatter_lm_GTA_Averages_", exp1_name, "_vs_", exp2_name, "_All_byOverlap_above2genes.html"))
|
||||
htmlwidgets::saveWidget(pgg, fname)
|
||||
|
||||
#4
|
||||
X_overlap_nothresold <- X[!(is.na(X$Overlap_Avg)), ]
|
||||
gg <- ggplot(data = X_overlap_nothresold, aes(
|
||||
x = Z_lm_K_Avg_X1,
|
||||
y = Z_lm_K_Avg_X2,
|
||||
color = Overlap_Avg,
|
||||
Term = Term_Avg,
|
||||
Genes = Genes_Avg_X1,
|
||||
NumGenes = NumGenes_Avg_X1,
|
||||
AllPossibleGenes = AllPossibleGenes_Avg_X1,
|
||||
SD_1 = Z_lm_K_SD_X1,
|
||||
SD_2 = Z_lm_K_SD_X2
|
||||
)) +
|
||||
xlab(paste("GO Term Avg lm Z for", exp1_name)) +
|
||||
geom_rect(aes(xmin = -2, xmax = 2, ymin = -2, ymax = 2), color = "grey20", size = 0.25, alpha = 0.1, inherit.aes = FALSE, fill = NA) +
|
||||
geom_point(shape = 3) +
|
||||
ylab(paste("GO Term Avg lm Z for", exp2_name)) +
|
||||
ggtitle(paste("Comparing Average GO Term Z lm for", exp1_name, "vs.", exp2_name)) +
|
||||
theme_Publication_legend_right()
|
||||
|
||||
pdf(
|
||||
file.path(pairDirK, paste0("Scatter_lm_GTF_Averages_", exp1_name, "_vs_", exp2_name, "_Above2SD_ByOverlap.pdf")),
|
||||
width = 12,
|
||||
height = 8
|
||||
)
|
||||
|
||||
gg
|
||||
dev.off()
|
||||
pgg <- ggplotly(gg)
|
||||
#pgg
|
||||
|
||||
fname <- file.path(pairDirK, paste0("Scatter_lm_GTA_Averages_", exp1_name, "_vs_", exp2_name, "_Above2SD_ByOverlap.html"))
|
||||
htmlwidgets::saveWidget(pgg, fname)
|
||||
|
||||
#5
|
||||
# Only output GTA terms where average score is still above 2 after subtracting the SD
|
||||
# Z1 will ID aggravators, Z2 alleviators
|
||||
Z1 <- X
|
||||
Z1$L_Subtract_SD_X1 <- Z1$Z_lm_K_Avg_X1 - Z1$Z_lm_K_SD_X1
|
||||
Z1$L_Subtract_SD_X2 <- Z1$Z_lm_K_Avg_X2 - Z1$Z_lm_K_SD_X2
|
||||
Z2 <- X
|
||||
Z2$L_Subtract_SD_X1 <- Z1$Z_lm_K_Avg_X1 + Z1$Z_lm_K_SD_X1
|
||||
Z2$L_Subtract_SD_X2 <- Z1$Z_lm_K_Avg_X2 + Z1$Z_lm_K_SD_X2
|
||||
X1_Specific_Aggravators2 <- Z1[which(Z1$L_Subtract_SD_X1 >= 2 & Z1$L_Subtract_SD_X2 < 2), ]
|
||||
X1_Specific_Alleviators2 <- Z2[which(Z2$L_Subtract_SD_X1 <= -2 & Z2$L_Subtract_SD_X2 > -2), ]
|
||||
X2_Specific_Aggravators2 <- Z1[which(Z1$L_Subtract_SD_X2 >= 2 & Z1$L_Subtract_SD_X1 < 2), ]
|
||||
X2_Specific_Alleviators2 <- Z2[which(Z2$L_Subtract_SD_X2 <= -2 & Z2$L_Subtract_SD_X1 > -2), ]
|
||||
Overlap_Aggravators2 <- Z1[which(Z1$L_Subtract_SD_X1 >= 2 & Z1$L_Subtract_SD_X2 >= 2), ]
|
||||
Overlap_Alleviators2 <- Z2[which(Z2$L_Subtract_SD_X2 <= -2 & Z2$L_Subtract_SD_X1 <= -2), ]
|
||||
X2_Specific_Aggravators2_X1_Alleviatiors2 <- Z1[which(Z1$L_Subtract_SD_X2 >= 2 & Z2$L_Subtract_SD_X1 <= -2), ]
|
||||
X2_Specific_Alleviators2_X1_Aggravators2 <- Z2[which(Z2$L_Subtract_SD_X2 <= -2 & Z1$L_Subtract_SD_X1 >= 2), ]
|
||||
X$Overlap <- NA
|
||||
|
||||
try(X[X$Term_Avg %in% X1_Specific_Aggravators2$Term_Avg, ]$Overlap <-
|
||||
paste(exp1_name, "Specific_Deletion_Suppressors", sep = "_"))
|
||||
try(X[X$Term_Avg %in% X1_Specific_Alleviators2$Term_Avg, ]$Overlap <-
|
||||
paste(exp1_name, "Specific_Deletion_Enhancers", sep = "_"))
|
||||
try(X[X$Term_Avg %in% X2_Specific_Aggravators2$Term_Avg, ]$Overlap <-
|
||||
paste(exp2_name, "Specific_Deletion_Suppressors", sep = "_"))
|
||||
try(X[X$Term_Avg %in% X2_Specific_Alleviators2$Term_Avg, ]$Overlap <-
|
||||
paste(exp2_name, "Specific_Deletion_Enhancers", sep = "_"))
|
||||
try(X[X$Term_Avg %in% Overlap_Aggravators2$Term_Avg, ]$Overlap <-
|
||||
"Overlapping_Deletion_Suppressors")
|
||||
try(X[X$Term_Avg %in% Overlap_Alleviators2$Term_Avg, ]$Overlap <-
|
||||
"Overlapping_Deletion_Enhancers")
|
||||
try(X[X$Term_Avg %in% X2_Specific_Aggravators2_X1_Alleviatiors2$Term_Avg, ]$Overlap <-
|
||||
paste(exp2_name, "Deletion_Suppressors", exp1_name, "Deletion_Enhancers", sep = "_"))
|
||||
try(X[X$Term_Avg %in% X2_Specific_Alleviators2_X1_Aggravators2$Term_Avg, ]$Overlap <-
|
||||
paste(exp2_name, "Deletion_Enhancers", exp1_name, "Deletion_Suppressors", sep = "_"))
|
||||
|
||||
X_abovethreshold <- X[!(is.na(X$Overlap)), ]
|
||||
gg <- ggplot(data = X_abovethreshold, aes(
|
||||
x = Z_lm_K_Avg_X1,
|
||||
y = Z_lm_K_Avg_X2,
|
||||
color = Overlap,
|
||||
Term = Term_Avg,
|
||||
Genes = Genes_Avg_X1,
|
||||
NumGenes = NumGenes_Avg_X1,
|
||||
AllPossibleGenes = AllPossibleGenes_Avg_X1,
|
||||
SD_1 = Z_lm_K_SD_X1,
|
||||
SD_2 = Z_lm_K_SD_X2
|
||||
)) +
|
||||
xlab(paste("GO Term Avg lm Z for", exp1_name)) +
|
||||
geom_rect(aes(xmin = -2, xmax = 2, ymin = -2, ymax = 2), color = "grey20", size = 0.25, alpha = 0.1, inherit.aes = FALSE, fill = NA) +
|
||||
geom_point(shape = 3) +
|
||||
ylab(paste("GO Term Avg lm Z for", exp2_name)) +
|
||||
ggtitle(paste("Comparing Average GO Term Z lm for", exp1_name, "vs.", exp2_name)) +
|
||||
theme_Publication_legend_right()
|
||||
|
||||
pdf(
|
||||
file.path(pairDirK, paste0("Scatter_lm_GTF_Averages_", exp1_name, "_vs_", exp2_name, "_All_ByOverlap_AboveThreshold.pdf")),
|
||||
width = 12,
|
||||
height = 8
|
||||
)
|
||||
|
||||
gg
|
||||
dev.off()
|
||||
pgg <- ggplotly(gg)
|
||||
#pgg
|
||||
fname <- file.path(pairDirK, paste0("Scatter_lm_GTA_Averages_", exp1_name, "_vs_", exp2_name, "_All_ByOverlap_AboveThreshold.html"))
|
||||
htmlwidgets::saveWidget(pgg, fname)
|
||||
|
||||
#6
|
||||
gg <- ggplot(data = X_abovethreshold, aes(
|
||||
x = Z_lm_K_Avg_X1,
|
||||
y = Z_lm_K_Avg_X2,
|
||||
color = Overlap,
|
||||
Term = Term_Avg,
|
||||
Genes = Genes_Avg_X1,
|
||||
NumGenes = NumGenes_Avg_X1,
|
||||
AllPossibleGenes = AllPossibleGenes_Avg_X1,
|
||||
SD_1 = Z_lm_K_SD_X1,
|
||||
SD_2 = Z_lm_K_SD_X2
|
||||
)) +
|
||||
xlab(paste("GO Term Avg lm Z for", exp1_name)) +
|
||||
geom_text(aes(label = Term_Avg), nudge_y = 0.25, size = 2) +
|
||||
geom_rect(aes(xmin = -2, xmax = 2, ymin = -2, ymax = 2), color = "grey20", size = 0.25, alpha = 0.1, inherit.aes = FALSE, fill = NA) +
|
||||
geom_point(shape = 3, size = 3) +
|
||||
ylab(paste("GO Term Avg lm Z for", exp2_name)) +
|
||||
ggtitle(paste("Comparing Average GO Term Z lm for", exp1_name, " vs. ", exp2_name)) +
|
||||
theme_Publication_legend_right()
|
||||
|
||||
pdf(
|
||||
file.path(pairDirK, paste0("Scatter_lm_GTF_Averages_", exp1_name, "_vs_", exp2_name, "_All_ByOverlap_AboveThreshold_names.pdf")),
|
||||
width = 20,
|
||||
height = 20
|
||||
)
|
||||
gg
|
||||
dev.off()
|
||||
pgg <- ggplotly(gg)
|
||||
#pgg
|
||||
fname <- file.path(pairDirK, paste0("Scatter_lm_GTA_Averages_", exp1_name, "_vs_", exp2_name, "_All_ByOverlap_AboveThreshold_names.html"))
|
||||
htmlwidgets::saveWidget(pgg, fname)
|
||||
|
||||
#7
|
||||
X_abovethreshold$X1_Rank <- NA
|
||||
X_abovethreshold$X1_Rank <- rank(-X_abovethreshold$Z_lm_K_Avg_X1, ties.method = "random")
|
||||
X_abovethreshold$X2_Rank <- NA
|
||||
X_abovethreshold$X2_Rank <- rank(-X_abovethreshold$Z_lm_K_Avg_X2, ties.method = "random")
|
||||
|
||||
gg <- ggplot(data = X_abovethreshold, aes(
|
||||
x = Z_lm_K_Avg_X1,
|
||||
y = Z_lm_K_Avg_X2,
|
||||
color = Overlap,
|
||||
Term = Term_Avg,
|
||||
Genes = Genes_Avg_X1,
|
||||
NumGenes = NumGenes_Avg_X1,
|
||||
AllPossibleGenes = AllPossibleGenes_Avg_X1,
|
||||
SD_1 = Z_lm_K_SD_X1,
|
||||
SD_2 = Z_lm_K_SD_X2
|
||||
)) +
|
||||
xlab(paste("GO Term Avg lm Z for", exp1_name)) +
|
||||
geom_text(aes(label = X1_Rank), nudge_y = 0.25, size = 4) +
|
||||
geom_rect(aes(xmin = -2, xmax = 2, ymin = -2, ymax = 2), color = "grey20", size = 0.25, alpha = 0.1, inherit.aes = FALSE, fill = NA) +
|
||||
geom_point(shape = 3, size = 3) +
|
||||
ylab(paste("GO Term Avg lm Z for", exp2_name)) +
|
||||
ggtitle(paste("Comparing Average GO Term Z lm for", exp1_name, "vs.", exp2_name)) +
|
||||
theme_Publication_legend_right()
|
||||
|
||||
pdf(
|
||||
file.path(pairDirK, paste0("Scatter_lm_GTF_Averages_", exp1_name, "_vs_", exp2_name, "_All_ByOverlap_AboveThreshold_numberedX1.pdf")),
|
||||
width = 15,
|
||||
height = 15
|
||||
)
|
||||
|
||||
gg
|
||||
dev.off()
|
||||
pgg <- ggplotly(gg)
|
||||
#pgg
|
||||
fname <-
|
||||
file.path(pairDirK, paste0("Scatter_lm_GTA_Averages_", exp1_name, "_vs_", exp2_name, "_All_ByOverlap_AboveThreshold_numberedX1.html"))
|
||||
htmlwidgets::saveWidget(pgg, fname)
|
||||
|
||||
#8
|
||||
gg <- ggplot(data = X_abovethreshold, aes(
|
||||
x = Z_lm_K_Avg_X1,
|
||||
y = Z_lm_K_Avg_X2,
|
||||
color = Overlap,
|
||||
Term = Term_Avg,
|
||||
Genes = Genes_Avg_X1,
|
||||
NumGenes = NumGenes_Avg_X1,
|
||||
AllPossibleGenes = AllPossibleGenes_Avg_X1,
|
||||
SD_1 = Z_lm_K_SD_X1,
|
||||
SD_2 = Z_lm_K_SD_X2
|
||||
)) +
|
||||
xlab(paste("GO Term Avg lm Z for", exp1_name)) +
|
||||
geom_text(aes(label = X2_Rank), nudge_y = 0.25, size = 4) +
|
||||
geom_rect(aes(xmin = -2, xmax = 2, ymin = -2, ymax = 2), color = "grey20", size = 0.25, alpha = 0.1, inherit.aes = FALSE, fill = NA) +
|
||||
geom_point(shape = 3, size = 3) +
|
||||
ylab(paste("GO Term Avg lm Z for", exp2_name)) +
|
||||
ggtitle(paste("Comparing Average GO Term Z lm for", exp1_name, "vs.", exp2_name)) +
|
||||
theme_Publication_legend_right()
|
||||
|
||||
pdf(
|
||||
file.path(pairDirK, paste0("Scatter_lm_GTF_Averages_", exp1_name, "_vs_", exp2_name, "_All_ByOverlap_AboveThreshold_numberedX2.pdf")),
|
||||
width = 15,
|
||||
height = 15
|
||||
)
|
||||
|
||||
gg
|
||||
dev.off()
|
||||
pgg <- ggplotly(gg)
|
||||
#pgg
|
||||
fname <-
|
||||
file.path(pairDirK, paste0("Scatter_lm_GTA_Averages_", exp1_name, "_vs_", exp2_name, "_All_ByOverlap_AboveThreshold_numberedX2.html"))
|
||||
htmlwidgets::saveWidget(pgg, fname)
|
||||
|
||||
write.csv(
|
||||
x = X,
|
||||
file = file.path(pairDirK, paste0("All_GTF_Avg_Scores_", exp1_name, "_vs_", exp2_name, ".csv")),
|
||||
row.names = FALSE
|
||||
)
|
||||
|
||||
write.csv(
|
||||
x = X_abovethreshold,
|
||||
file = file.path(pairDirK, paste0("AboveThreshold_GTF_Avg_Scores_", exp1_name, "_vs_", exp2_name, ".csv")),
|
||||
row.names = FALSE
|
||||
)
|
||||
Reference in New Issue
Block a user