Rollup for java clustering
This commit is contained in:
@@ -39,8 +39,8 @@ Name2 <- Labels[expNumber2, 2]
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go_terms_file <- "Average_GOTerms_All.csv"
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input_file1 <- file.path(output_dir, exp_name, go_terms_file)
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input_file2 <- file.path(output_dir, exp_name2, go_terms_file)
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pairDirL <- file.path(output_dir, paste("PairwiseCompareL_", exp_name, "-", exp_name2, sep = ""))
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pairDirK <- file.path(output_dir, paste("PairwiseCompareK_", exp_name, "-", exp_name2, sep = ""))
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pairDirL <- file.path(output_dir, paste0("PairwiseCompareL_", exp_name, "-", exp_name2))
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pairDirK <- file.path(output_dir, paste0("PairwiseCompareK_", exp_name, "-", exp_name2))
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# Pairwise L
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# outputPlotly <- "../GTAresults/PairwiseCompareL/" #"/GTAresults/PairwiseCompareL/"
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@@ -146,7 +146,7 @@ gg <- ggplot(data = X, aes(
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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 ", Name1, sep = "")) +
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xlab(paste("GO Term Avg lm Z for", Name1)) +
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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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@@ -156,12 +156,12 @@ gg <- ggplot(data = X, aes(
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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 ", Name2, sep = "")) +
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ggtitle(paste("Comparing Average GO Term Z lm for ", Name1, " vs. ", Name2, sep = "")) +
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ylab(paste("GO Term Avg lm Z for", Name2)) +
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ggtitle(paste("Comparing Average GO Term Z lm for", Name1, " vs. ", Name2) +
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theme_Publication_legend_right()
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pdf(
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file.path(pairDirL, paste("Scatter_lm_GTA_Averages_", Name1, "_vs_", Name2, "_All_ByOntology.pdf", sep = "")),
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file.path(pairDirL, paste0("Scatter_lm_GTA_Averages_", Name1, "_vs_", Name2, "_All_ByOntology.pdf")),
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width = 12,
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height = 8
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)
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@@ -169,7 +169,7 @@ pdf(
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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, paste("Scatter_lm_GTA_Averages_", Name1, "_vs_", Name2, "_All_byOntology.html", sep = ""))
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fname <- file.path(pairDirL, paste0("Scatter_lm_GTA_Averages_", Name1, "_vs_", Name2, "_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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@@ -209,7 +209,7 @@ gg <- ggplot(data = X, aes(
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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 ", Name1, sep = "")) +
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xlab(paste("GO Term Avg lm Z for", Name1)) +
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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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@@ -219,12 +219,12 @@ gg <- ggplot(data = X, aes(
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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 ", Name2, sep = "")) +
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ggtitle(paste("Comparing Average GO Term Z lm for ", Name1, " vs. ", Name2, sep = "")) +
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ylab(paste("GO Term Avg lm Z for", Name2)) +
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ggtitle(paste("Comparing Average GO Term Z lm for", Name1, " vs. ", Name2)) +
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theme_Publication_legend_right()
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pdf(
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file.path(pairDirL, paste("Scatter_lm_GTA_Averages_", Name1, "_vs_", Name2, "_All_ByOverlap.pdf", sep = "")),
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file.path(pairDirL, paste0("Scatter_lm_GTA_Averages_", Name1, "_vs_", Name2, "_All_ByOverlap.pdf")),
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width = 12,
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height = 8
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)
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@@ -232,7 +232,7 @@ pdf(
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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, paste("Scatter_lm_GTA_Averages_", Name1, "_vs_", Name2, "_All_byOverlap.html", sep = ""))
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fname <- file.path(pairDirL, paste0("Scatter_lm_GTA_Averages_", Name1, "_vs_", Name2, "_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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@@ -249,15 +249,15 @@ gg <- ggplot(data = x_rem2_gene, aes(
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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 ", Name1, sep = "")) +
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xlab(paste("GO Term Avg lm Z for", Name1)) +
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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 ", Name2, sep = "")) +
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ggtitle(paste("Comparing Average GO Term Z lm for ", Name1, " vs. ", Name2, sep = "")) +
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ylab(paste("GO Term Avg lm Z for", Name2)) +
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ggtitle(paste("Comparing Average GO Term Z lm for", Name1, "vs.", Name2)) +
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theme_Publication_legend_right()
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pdf(
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file.path(pairDirL, paste("Scatter_lm_GTA_Averages_", Name1, "_vs_", Name2, "_All_ByOverlap_above2genes.pdf", sep = "")),
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file.path(pairDirL, paste0("Scatter_lm_GTA_Averages_", Name1, "_vs_", Name2, "_All_ByOverlap_above2genes.pdf")),
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width = 12,
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height = 8
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)
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@@ -266,7 +266,7 @@ 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, paste("Scatter_lm_GTA_Averages_", Name1, "_vs_", Name2, "_All_byOverlap_above2genes.html", sep = ""))
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fname <- file.path(pairDirL, paste0("Scatter_lm_GTA_Averages_", Name1, "_vs_", Name2, "_All_byOverlap_above2genes.html"))
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htmlwidgets::saveWidget(pgg, fname)
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#4
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@@ -282,15 +282,15 @@ gg <- ggplot(data = X_overlap_nothresold, aes(
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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 ", Name1, sep = "")) +
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xlab(paste("GO Term Avg lm Z for", Name1)) +
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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 ", Name2, sep = "")) +
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ggtitle(paste("Comparing Average GO Term Z lm for ", Name1, " vs. ", Name2, sep = "")) +
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ylab(paste("GO Term Avg lm Z for", Name2)) +
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ggtitle(paste("Comparing Average GO Term Z lm for", Name1, "vs.", Name2)) +
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theme_Publication_legend_right()
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pdf(
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file.path(pairDirL, paste("Scatter_lm_GTA_Averages_", Name1, "_vs_", Name2, "_Above2SD_ByOverlap.pdf", sep = "")),
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file.path(pairDirL, paste0("Scatter_lm_GTA_Averages_", Name1, "_vs_", Name2, "_Above2SD_ByOverlap.pdf")),
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width = 12,
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height = 8
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)
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@@ -299,7 +299,7 @@ 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, paste("Scatter_lm_GTA_Averages_", Name1, "_vs_", Name2, "_Above2SD_ByOverlap.html", sep = ""))
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fname <- file.path(pairDirL, paste0("Scatter_lm_GTA_Averages_", Name1, "_vs_", Name2, "_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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@@ -345,15 +345,15 @@ gg <- ggplot(data = X_abovethreshold, aes(
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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 ", Name1, sep = "")) +
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xlab(paste("GO Term Avg lm Z for", Name1)) +
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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 ", Name2, sep = "")) +
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ggtitle(paste("Comparing Average GO Term Z lm for ", Name1, " vs. ", Name2, sep = "")) +
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ylab(paste("GO Term Avg lm Z for", Name2)) +
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ggtitle(paste("Comparing Average GO Term Z lm for", Name1, " vs. ", Name2)) +
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theme_Publication_legend_right()
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pdf(
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file.path(pairDirL, paste("Scatter_lm_GTA_Averages_", Name1, "_vs_", Name2, "_All_ByOverlap_AboveThreshold.pdf", sep = "")),
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file.path(pairDirL, paste0("Scatter_lm_GTA_Averages_", Name1, "_vs_", Name2, "_All_ByOverlap_AboveThreshold.pdf")),
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width = 12,
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height = 8
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)
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@@ -362,7 +362,7 @@ 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, paste("Scatter_lm_GTA_Averages_", Name1, "_vs_", Name2, "_All_ByOverlap_AboveThreshold.html", sep = ""))
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fname <- file.path(pairDirL, paste0("Scatter_lm_GTA_Averages_", Name1, "_vs_", Name2, "_All_ByOverlap_AboveThreshold.html"))
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htmlwidgets::saveWidget(pgg, fname)
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#6
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@@ -377,16 +377,16 @@ gg <- ggplot(data = X_abovethreshold, aes(
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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 ", Name1, sep = "")) +
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xlab(paste("GO Term Avg lm Z for", Name1)) +
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geom_text(aes(label = Term_Avg), nudge_y = 0.25, size = 2) +
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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, size = 3) +
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ylab(paste("GO Term Avg lm Z for ", Name2, sep = "")) +
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ggtitle(paste("Comparing Average GO Term Z lm for ", Name1, " vs. ", Name2, sep = "")) +
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ylab(paste("GO Term Avg lm Z for", Name2)) +
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ggtitle(paste("Comparing Average GO Term Z lm for", Name1, "vs.", Name2)) +
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theme_Publication_legend_right()
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pdf(
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file.path(pairDirL, paste("Scatter_lm_GTA_Averages_", Name1, "_vs_", Name2, "_All_ByOverlap_AboveThreshold_names.pdf", sep = "")),
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file.path(pairDirL, paste0("Scatter_lm_GTA_Averages_", Name1, "_vs_", Name2, "_All_ByOverlap_AboveThreshold_names.pdf")),
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width = 20,
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height = 20
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)
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@@ -395,7 +395,7 @@ 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, paste("Scatter_lm_GTA_Averages_", Name1, "_vs_", Name2, "_All_ByOverlap_AboveThreshold_names.html", sep = ""))
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fname <- file.path(pairDirL, paste0("Scatter_lm_GTA_Averages_", Name1, "_vs_", Name2, "_All_ByOverlap_AboveThreshold_names.html"))
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htmlwidgets::saveWidget(pgg, fname)
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X_abovethreshold$X1_Rank <- NA
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@@ -415,16 +415,16 @@ gg <- ggplot(data = X_abovethreshold, aes(
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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 ", Name1, sep = "")) +
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xlab(paste("GO Term Avg lm Z for", Name1)) +
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geom_text(aes(label = X1_Rank), nudge_y = 0.25, size = 4) +
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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, size = 3) +
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ylab(paste("GO Term Avg lm Z for ", Name2, sep = "")) +
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ggtitle(paste("Comparing Average GO Term Z lm for ", Name1, " vs. ", Name2, sep = "")) +
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ylab(paste("GO Term Avg lm Z for", Name2)) +
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ggtitle(paste("Comparing Average GO Term Z lm for", Name1, "vs.", Name2)) +
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theme_Publication_legend_right()
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pdf(
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file.path(pairDirL, paste("Scatter_lm_GTA_Averages_", Name1, "_vs_", Name2, "_All_ByOverlap_AboveThreshold_numberedX1.pdf", sep = "")),
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file.path(pairDirL, paste0("Scatter_lm_GTA_Averages_", Name1, "_vs_", Name2, "_All_ByOverlap_AboveThreshold_numberedX1.pdf")),
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width = 15,
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height = 15
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)
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@@ -435,7 +435,7 @@ pgg <- ggplotly(gg)
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#pgg
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fname <-
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file.path(pairDirL, paste("Scatter_lm_GTA_Averages_", Name1, "_vs_", Name2, "_All_ByOverlap_AboveThreshold_numberedX1.html", sep = ""))
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file.path(pairDirL, paste0("Scatter_lm_GTA_Averages_", Name1, "_vs_", Name2, "_All_ByOverlap_AboveThreshold_numberedX1.html"))
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htmlwidgets::saveWidget(pgg, fname)
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#8
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@@ -450,16 +450,16 @@ gg <- ggplot(data = X_abovethreshold, aes(
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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 ", Name1, sep = "")) +
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xlab(paste("GO Term Avg lm Z for", Name1)) +
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geom_text(aes(label = X2_Rank), nudge_y = 0.25, size = 4) +
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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, size = 3) +
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ylab(paste("GO Term Avg lm Z for ", Name2, sep = "")) +
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ggtitle(paste("Comparing Average GO Term Z lm for ", Name1, " vs. ", Name2, sep = "")) +
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ylab(paste("GO Term Avg lm Z for", Name2)) +
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ggtitle(paste("Comparing Average GO Term Z lm for", Name1, "vs.", Name2)) +
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theme_Publication_legend_right()
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pdf(
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file.path(pairDirL, paste("Scatter_lm_GTA_Averages_", Name1, "_vs_", Name2, "_All_ByOverlap_AboveThreshold_numberedX2.pdf", sep = "")),
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file.path(pairDirL, paste0("Scatter_lm_GTA_Averages_", Name1, "_vs_", Name2, "_All_ByOverlap_AboveThreshold_numberedX2.pdf")),
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width = 15,
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height = 15
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)
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@@ -469,18 +469,18 @@ dev.off()
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pgg <- ggplotly(gg)
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#pgg
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fname <-
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file.path(pairDirL, paste("Scatter_lm_GTA_Averages_", Name1, "_vs_", Name2, "_All_ByOverlap_AboveThreshold_numberedX2.html", sep = ""))
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file.path(pairDirL, paste0("Scatter_lm_GTA_Averages_", Name1, "_vs_", Name2, "_All_ByOverlap_AboveThreshold_numberedX2.html"))
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htmlwidgets::saveWidget(pgg, fname)
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write.csv(
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x = X,
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file.path(pairDirL, paste("All_GTA_Avg_Scores_", Name1, "_vs_", Name2, ".csv", sep = "")),
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file.path(pairDirL, paste0("All_GTA_Avg_Scores_", Name1, "_vs_", Name2, ".csv")),
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row.names = FALSE
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)
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write.csv(
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x = X_abovethreshold,
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file = file.path(pairDirL, paste("AboveThreshold_GTA_Avg_Scores_", Name1, "_vs_", Name2, ".csv", sep = "")),
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file = file.path(pairDirL, paste0("AboveThreshold_GTA_Avg_Scores_", Name1, "_vs_", Name2, ".csv")),
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row.names = FALSE
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)
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@@ -599,15 +599,15 @@ gg <- ggplot(data = X, aes(
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SD_1 = Z_lm_K_SD_X1,
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SD_2 = Z_lm_K_SD_X2
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)) +
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xlab(paste("GO Term Avg lm Z for ", Name1, sep = "")) +
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xlab(paste("GO Term Avg lm Z for", Name1)) +
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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 ", Name2, sep = "")) +
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ggtitle(paste("Comparing Average GO Term Z lm for ", Name1, " vs. ", Name2, sep = "")) +
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ylab(paste("GO Term Avg lm Z for", Name2)) +
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ggtitle(paste("Comparing Average GO Term Z lm for", Name1, "vs.", Name2)) +
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theme_Publication_legend_right()
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pdf(
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file.path(pairDirK, paste("Scatter_lm_GTF_Averages_", Name1, "_vs_", Name2, "_All_ByOntology.pdf", sep = "")),
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file.path(pairDirK, paste0("Scatter_lm_GTF_Averages_", Name1, "_vs_", Name2, "_All_ByOntology.pdf")),
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width = 12,
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height = 8
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)
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@@ -616,7 +616,7 @@ 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(pairDirK, paste("Scatter_lm_GTA_Averages_", Name1, "_vs_", Name2, "_All_byOntology.html", sep = ""))
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fname <- file.path(pairDirK, paste0("Scatter_lm_GTA_Averages_", Name1, "_vs_", Name2, "_All_byOntology.html"))
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htmlwidgets::saveWidget(pgg, fname)
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#2
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@@ -648,7 +648,7 @@ try(X[X$Term_Avg %in% X2_Specific_Aggravators_X1_Alleviatiors$Term_Avg, ]$Overla
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try(X[X$Term_Avg %in% X2_Specific_Alleviators_X1_Aggravators$Term_Avg, ]$Overlap_Avg <-
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paste(Name2, "Deletion_Enhancers", Name1, "Deletion_Suppressors", sep = "_"))
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plotly_path <- file.path(pairDirK, paste("Scatter_lm_GTF_Averages_", Name1, "_vs_", Name2, "_All_byOverlap.html", sep = ""))
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plotly_path <- file.path(pairDirK, paste0("Scatter_lm_GTF_Averages_", Name1, "_vs_", Name2, "_All_byOverlap.html"))
|
||||
gg <- ggplot(data = X, aes(
|
||||
x = Z_lm_K_Avg_X1,
|
||||
y = Z_lm_K_Avg_X2,
|
||||
@@ -660,15 +660,15 @@ gg <- ggplot(data = X, aes(
|
||||
SD_1 = Z_lm_K_SD_X1,
|
||||
SD_2 = Z_lm_K_SD_X2
|
||||
)) +
|
||||
xlab(paste("GO Term Avg lm Z for ", Name1, sep = "")) +
|
||||
xlab(paste("GO Term Avg lm Z for", Name1)) +
|
||||
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 ", Name2, sep = "")) +
|
||||
ggtitle(paste("Comparing Average GO Term Z lm for ", Name1, " vs. ", Name2, sep = "")) +
|
||||
ylab(paste("GO Term Avg lm Z for", Name2)) +
|
||||
ggtitle(paste("Comparing Average GO Term Z lm for", Name1, "vs.", Name2)) +
|
||||
theme_Publication_legend_right()
|
||||
|
||||
pdf(
|
||||
file.path(pairDirK, paste("Scatter_lm_GTF_Averages_", Name1, "_vs_", Name2, "_All_ByOverlap.pdf", sep = "")),
|
||||
file.path(pairDirK, paste0("Scatter_lm_GTF_Averages_", Name1, "_vs_", Name2, "_All_ByOverlap.pdf")),
|
||||
width = 12,
|
||||
height = 8
|
||||
)
|
||||
@@ -678,12 +678,12 @@ dev.off()
|
||||
pgg <- ggplotly(gg)
|
||||
|
||||
#2
|
||||
fname <- file.path(pairDirK, paste("Scatter_lm_GTA_Averages_", Name1, "_vs_", Name2, "_All_byOverlap.html", sep = ""))
|
||||
fname <- file.path(pairDirK, paste0("Scatter_lm_GTA_Averages_", Name1, "_vs_", Name2, "_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, paste("Scatter_lm_GTF_Averages_", Name1, "_vs_", Name2, "_All_byOverlap_above2genes.html", sep = ""))
|
||||
plotly_path <- file.path(pairDirK, paste0("Scatter_lm_GTF_Averages_", Name1, "_vs_", Name2, "_All_byOverlap_above2genes.html"))
|
||||
gg <- ggplot(data = x_rem2_gene, aes(
|
||||
x = Z_lm_K_Avg_X1,
|
||||
y = Z_lm_K_Avg_X2,
|
||||
@@ -695,15 +695,15 @@ gg <- ggplot(data = x_rem2_gene, aes(
|
||||
SD_1 = Z_lm_K_SD_X1,
|
||||
SD_2 = Z_lm_K_SD_X2
|
||||
)) +
|
||||
xlab(paste("GO Term Avg lm Z for ", Name1, sep = "")) +
|
||||
xlab(paste("GO Term Avg lm Z for", Name1)) +
|
||||
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 ", Name2, sep = "")) +
|
||||
ggtitle(paste("Comparing Average GO Term Z lm for ", Name1, " vs. ", Name2, sep = "")) +
|
||||
ylab(paste("GO Term Avg lm Z for", Name2)) +
|
||||
ggtitle(paste("Comparing Average GO Term Z lm for", Name1, "vs.", Name2)) +
|
||||
theme_Publication_legend_right()
|
||||
|
||||
pdf(
|
||||
file.path(pairDirK, paste("Scatter_lm_GTF_Averages_", Name1, "_vs_", Name2, "_All_ByOverlap_above2genes.pdf", sep = "")),
|
||||
file.path(pairDirK, paste0("Scatter_lm_GTF_Averages_", Name1, "_vs_", Name2, "_All_ByOverlap_above2genes.pdf")),
|
||||
width = 12,
|
||||
height = 8
|
||||
)
|
||||
@@ -712,7 +712,7 @@ gg
|
||||
dev.off()
|
||||
pgg <- ggplotly(gg)
|
||||
#pgg
|
||||
fname <- file.path(pairDirK, paste("Scatter_lm_GTA_Averages_", Name1, "_vs_", Name2, "_All_byOverlap_above2genes.html", sep = ""))
|
||||
fname <- file.path(pairDirK, paste0("Scatter_lm_GTA_Averages_", Name1, "_vs_", Name2, "_All_byOverlap_above2genes.html"))
|
||||
htmlwidgets::saveWidget(pgg, fname)
|
||||
|
||||
#4
|
||||
@@ -728,15 +728,15 @@ gg <- ggplot(data = X_overlap_nothresold, aes(
|
||||
SD_1 = Z_lm_K_SD_X1,
|
||||
SD_2 = Z_lm_K_SD_X2
|
||||
)) +
|
||||
xlab(paste("GO Term Avg lm Z for ", Name1, sep = "")) +
|
||||
xlab(paste("GO Term Avg lm Z for", Name1)) +
|
||||
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 ", Name2, sep = "")) +
|
||||
ggtitle(paste("Comparing Average GO Term Z lm for ", Name1, " vs. ", Name2, sep = "")) +
|
||||
ylab(paste("GO Term Avg lm Z for", Name2)) +
|
||||
ggtitle(paste("Comparing Average GO Term Z lm for", Name1, "vs.", Name2)) +
|
||||
theme_Publication_legend_right()
|
||||
|
||||
pdf(
|
||||
file.path(pairDirK, paste("Scatter_lm_GTF_Averages_", Name1, "_vs_", Name2, "_Above2SD_ByOverlap.pdf", sep = "")),
|
||||
file.path(pairDirK, paste0("Scatter_lm_GTF_Averages_", Name1, "_vs_", Name2, "_Above2SD_ByOverlap.pdf")),
|
||||
width = 12,
|
||||
height = 8
|
||||
)
|
||||
@@ -746,7 +746,7 @@ dev.off()
|
||||
pgg <- ggplotly(gg)
|
||||
#pgg
|
||||
|
||||
fname <- file.path(pairDirK, paste("Scatter_lm_GTA_Averages_", Name1, "_vs_", Name2, "_Above2SD_ByOverlap.html", sep = ""))
|
||||
fname <- file.path(pairDirK, paste0("Scatter_lm_GTA_Averages_", Name1, "_vs_", Name2, "_Above2SD_ByOverlap.html"))
|
||||
htmlwidgets::saveWidget(pgg, fname)
|
||||
|
||||
#5
|
||||
@@ -797,15 +797,15 @@ gg <- ggplot(data = X_abovethreshold, aes(
|
||||
SD_1 = Z_lm_K_SD_X1,
|
||||
SD_2 = Z_lm_K_SD_X2
|
||||
)) +
|
||||
xlab(paste("GO Term Avg lm Z for ", Name1, sep = "")) +
|
||||
xlab(paste("GO Term Avg lm Z for", Name1)) +
|
||||
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 ", Name2, sep = "")) +
|
||||
ggtitle(paste("Comparing Average GO Term Z lm for ", Name1, " vs. ", Name2, sep = "")) +
|
||||
ylab(paste("GO Term Avg lm Z for", Name2)) +
|
||||
ggtitle(paste("Comparing Average GO Term Z lm for", Name1, "vs.", Name2)) +
|
||||
theme_Publication_legend_right()
|
||||
|
||||
pdf(
|
||||
file.path(pairDirK, paste("Scatter_lm_GTF_Averages_", Name1, "_vs_", Name2, "_All_ByOverlap_AboveThreshold.pdf", sep = "")),
|
||||
file.path(pairDirK, paste0("Scatter_lm_GTF_Averages_", Name1, "_vs_", Name2, "_All_ByOverlap_AboveThreshold.pdf")),
|
||||
width = 12,
|
||||
height = 8
|
||||
)
|
||||
@@ -814,7 +814,7 @@ gg
|
||||
dev.off()
|
||||
pgg <- ggplotly(gg)
|
||||
#pgg
|
||||
fname <- file.path(pairDirK, paste("Scatter_lm_GTA_Averages_", Name1, "_vs_", Name2, "_All_ByOverlap_AboveThreshold.html", sep = ""))
|
||||
fname <- file.path(pairDirK, paste0("Scatter_lm_GTA_Averages_", Name1, "_vs_", Name2, "_All_ByOverlap_AboveThreshold.html"))
|
||||
htmlwidgets::saveWidget(pgg, fname)
|
||||
|
||||
#6
|
||||
@@ -829,16 +829,16 @@ gg <- ggplot(data = X_abovethreshold, aes(
|
||||
SD_1 = Z_lm_K_SD_X1,
|
||||
SD_2 = Z_lm_K_SD_X2
|
||||
)) +
|
||||
xlab(paste("GO Term Avg lm Z for ", Name1, sep = "")) +
|
||||
xlab(paste("GO Term Avg lm Z for", Name1)) +
|
||||
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 ", Name2, sep = "")) +
|
||||
ggtitle(paste("Comparing Average GO Term Z lm for ", Name1, " vs. ", Name2, sep = "")) +
|
||||
ylab(paste("GO Term Avg lm Z for", Name2)) +
|
||||
ggtitle(paste("Comparing Average GO Term Z lm for", Name1, " vs. ", Name2)) +
|
||||
theme_Publication_legend_right()
|
||||
|
||||
pdf(
|
||||
file.path(pairDirK, paste("Scatter_lm_GTF_Averages_", Name1, "_vs_", Name2, "_All_ByOverlap_AboveThreshold_names.pdf", sep = "")),
|
||||
file.path(pairDirK, paste0("Scatter_lm_GTF_Averages_", Name1, "_vs_", Name2, "_All_ByOverlap_AboveThreshold_names.pdf")),
|
||||
width = 20,
|
||||
height = 20
|
||||
)
|
||||
@@ -846,7 +846,7 @@ gg
|
||||
dev.off()
|
||||
pgg <- ggplotly(gg)
|
||||
#pgg
|
||||
fname <- file.path(pairDirK, paste("Scatter_lm_GTA_Averages_", Name1, "_vs_", Name2, "_All_ByOverlap_AboveThreshold_names.html", sep = ""))
|
||||
fname <- file.path(pairDirK, paste0("Scatter_lm_GTA_Averages_", Name1, "_vs_", Name2, "_All_ByOverlap_AboveThreshold_names.html"))
|
||||
htmlwidgets::saveWidget(pgg, fname)
|
||||
|
||||
#7
|
||||
@@ -866,16 +866,16 @@ gg <- ggplot(data = X_abovethreshold, aes(
|
||||
SD_1 = Z_lm_K_SD_X1,
|
||||
SD_2 = Z_lm_K_SD_X2
|
||||
)) +
|
||||
xlab(paste("GO Term Avg lm Z for ", Name1, sep = "")) +
|
||||
xlab(paste("GO Term Avg lm Z for", Name1)) +
|
||||
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 ", Name2, sep = "")) +
|
||||
ggtitle(paste("Comparing Average GO Term Z lm for ", Name1, " vs. ", Name2, sep = "")) +
|
||||
ylab(paste("GO Term Avg lm Z for", Name2)) +
|
||||
ggtitle(paste("Comparing Average GO Term Z lm for", Name1, "vs.", Name2)) +
|
||||
theme_Publication_legend_right()
|
||||
|
||||
pdf(
|
||||
file.path(pairDirK, paste("Scatter_lm_GTF_Averages_", Name1, "_vs_", Name2, "_All_ByOverlap_AboveThreshold_numberedX1.pdf", sep = "")),
|
||||
file.path(pairDirK, paste0("Scatter_lm_GTF_Averages_", Name1, "_vs_", Name2, "_All_ByOverlap_AboveThreshold_numberedX1.pdf")),
|
||||
width = 15,
|
||||
height = 15
|
||||
)
|
||||
@@ -885,7 +885,7 @@ dev.off()
|
||||
pgg <- ggplotly(gg)
|
||||
#pgg
|
||||
fname <-
|
||||
file.path(pairDirK, paste("Scatter_lm_GTA_Averages_", Name1, "_vs_", Name2, "_All_ByOverlap_AboveThreshold_numberedX1.html", sep = ""))
|
||||
file.path(pairDirK, paste0("Scatter_lm_GTA_Averages_", Name1, "_vs_", Name2, "_All_ByOverlap_AboveThreshold_numberedX1.html"))
|
||||
htmlwidgets::saveWidget(pgg, fname)
|
||||
|
||||
#8
|
||||
@@ -900,16 +900,16 @@ gg <- ggplot(data = X_abovethreshold, aes(
|
||||
SD_1 = Z_lm_K_SD_X1,
|
||||
SD_2 = Z_lm_K_SD_X2
|
||||
)) +
|
||||
xlab(paste("GO Term Avg lm Z for ", Name1, sep = "")) +
|
||||
xlab(paste("GO Term Avg lm Z for", Name1)) +
|
||||
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 ", Name2, sep = "")) +
|
||||
ggtitle(paste("Comparing Average GO Term Z lm for ", Name1, " vs. ", Name2, sep = "")) +
|
||||
ylab(paste("GO Term Avg lm Z for", Name2)) +
|
||||
ggtitle(paste("Comparing Average GO Term Z lm for", Name1, "vs.", Name2)) +
|
||||
theme_Publication_legend_right()
|
||||
|
||||
pdf(
|
||||
file.path(pairDirK, paste("Scatter_lm_GTF_Averages_", Name1, "_vs_", Name2, "_All_ByOverlap_AboveThreshold_numberedX2.pdf", sep = "")),
|
||||
file.path(pairDirK, paste0("Scatter_lm_GTF_Averages_", Name1, "_vs_", Name2, "_All_ByOverlap_AboveThreshold_numberedX2.pdf")),
|
||||
width = 15,
|
||||
height = 15
|
||||
)
|
||||
@@ -919,17 +919,17 @@ dev.off()
|
||||
pgg <- ggplotly(gg)
|
||||
#pgg
|
||||
fname <-
|
||||
file.path(pairDirK, paste("Scatter_lm_GTA_Averages_", Name1, "_vs_", Name2, "_All_ByOverlap_AboveThreshold_numberedX2.html", sep = ""))
|
||||
file.path(pairDirK, paste0("Scatter_lm_GTA_Averages_", Name1, "_vs_", Name2, "_All_ByOverlap_AboveThreshold_numberedX2.html"))
|
||||
htmlwidgets::saveWidget(pgg, fname)
|
||||
|
||||
write.csv(
|
||||
x = X,
|
||||
file = file.path(pairDirK, paste("All_GTF_Avg_Scores_", Name1, "_vs_", Name2, ".csv", sep = "")),
|
||||
file = file.path(pairDirK, paste0("All_GTF_Avg_Scores_", Name1, "_vs_", Name2, ".csv")),
|
||||
row.names = FALSE
|
||||
)
|
||||
|
||||
write.csv(
|
||||
x = X_abovethreshold,
|
||||
file = file.path(pairDirK, paste("AboveThreshold_GTF_Avg_Scores_", Name1, "_vs_", Name2, ".csv", sep = "")),
|
||||
file = file.path(pairDirK, paste0("AboveThreshold_GTF_Avg_Scores_", Name1, "_vs_", Name2, ".csv")),
|
||||
row.names = FALSE
|
||||
)
|
||||
|
||||
Reference in New Issue
Block a user