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Add GLM coefficient output to Placement-Factorization
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Submodule genesis
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,109 @@ | ||
| #!/usr/bin/env Rscript | ||
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| # gappa - Genesis Applications for Phylogenetic Placement Analysis | ||
| # Copyright (C) 2017-2024 Lucas Czech | ||
| # | ||
| # This program is free software: you can redistribute it and/or modify | ||
| # it under the terms of the GNU General Public License as published by | ||
| # the Free Software Foundation, either version 3 of the License, or | ||
| # (at your option) any later version. | ||
| # | ||
| # This program is distributed in the hope that it will be useful, | ||
| # but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| # GNU General Public License for more details. | ||
| # | ||
| # You should have received a copy of the GNU General Public License | ||
| # along with this program. If not, see <http://www.gnu.org/licenses/>. | ||
| # | ||
| # Contact: | ||
| # Lucas Czech <[email protected]> | ||
| # Department of Plant Biology, Carnegie Institution For Science | ||
| # 260 Panama Street, Stanford, CA 94305, USA | ||
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| # Load packages | ||
| library(tidyr) | ||
| library(ggplot2) | ||
| library(cowplot) | ||
| theme_set(theme_cowplot()) | ||
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| # Get input and output files from command line, or use defaults. | ||
| meta_file = "meta.csv" | ||
| balances_file = "factor_balances.csv" | ||
| coeffs_file = "factor_glm_coefficients.csv" | ||
| out_pref = "pf-glm-coeffs-" | ||
| args = commandArgs(trailingOnly=TRUE) | ||
| if (length(args) >= 1) { | ||
| meta_file = args[1] | ||
| } | ||
| if (length(args) >= 2) { | ||
| balances_file = args[2] | ||
| } | ||
| if (length(args) >= 3) { | ||
| coeffs_file = args[3] | ||
| } | ||
| if (length(args) <= 4) { | ||
| out_pref = args[4] | ||
| } else { | ||
| stop( "Usage: plot-pf-glm-coeffs.R [meta-data] [balances] [glm-coefficients] [out-prefix]") | ||
| } | ||
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| print(paste("balances: ", balances_file)) | ||
| print(paste("glm-coefficients: ", coeffs_file)) | ||
| print(paste("meta-data: ", meta_file)) | ||
| print(paste("out-prefix: ", out_pref)) | ||
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| Balances <- read.table(balances_file, sep="\t", header=TRUE) | ||
| Coefficients <- read.table(coeffs_file, sep="\t", header=TRUE) | ||
| Meta <- read.table(meta_file, sep="\t", header=TRUE) | ||
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| # Match the Samples between Meta and Balances | ||
| # The Meta table might not have the first column named Samples, | ||
| # so we just take whatever is the first column here. | ||
| matched_samples <- match(Meta[, colnames(Meta)[1]], Balances$Sample) | ||
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| # Loop through each row in the Coefficients table | ||
| for(i in 1:nrow(Coefficients)) { | ||
| print(paste("Factor", i)) | ||
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| # Extract the current row's coefficients and intercept | ||
| # Exclude Factor and Intercept columns | ||
| current_coefficients <- as.numeric(Coefficients[i, -c(1, 2)]) | ||
| current_intercept <- Coefficients$Intercept[i] | ||
|
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| # Compute the dot product for the current coefficients against all Meta rows | ||
| # Then add the current intercept | ||
| result <- as.matrix(Meta[, -1]) %*% current_coefficients + current_intercept | ||
|
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| # Find the corresponding column in the Balances table | ||
| balance_column_name <- paste("Factor", i, sep = "_") | ||
| if(!(balance_column_name %in% names(Balances))) { | ||
| print(paste("Invalid column", balance_column_name)) | ||
| next | ||
| } | ||
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| # Create a data frame for plotting. | ||
| # Add the result with the corresponding balance value. | ||
| # Note: Ensure that the matched_samples indices are valid and there are no NAs | ||
| df <- data.frame( | ||
| Result = result, | ||
| Balance = Balances[matched_samples, balance_column_name] | ||
| ) | ||
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| # Generate the scatter plot. | ||
| p <- ggplot(df, aes(x = Balance, y = Result)) + | ||
| geom_point() + | ||
| # geom_smooth(method = "lm", color = "red", se = FALSE, formula="y~x", orientation = "y") + | ||
| labs( | ||
| title = balance_column_name, | ||
| x = "Balance Value", | ||
| y = "GLM Prediction" | ||
| ) + | ||
| geom_abline(slope=1, intercept=0, color='#6666FF') + | ||
| coord_fixed() + | ||
| theme(legend.title=element_blank()) | ||
|
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| # Display the plot | ||
| # print(p) | ||
| ggsave(paste0(out_pref, i,".png"), width=12, height=8) | ||
| } |
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