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Add configurable plot filtering

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This commit is contained in:
Bryan Roessler
2024-10-05 22:39:53 -04:00
parent 936a35aadb
commit f335b414e1
1 changed files with 20 additions and 9 deletions
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29
qhtcp-workflow/apps/r/calculate_interaction_zscores.R
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@@ -545,6 +545,13 @@ generate_and_save_plots <- function(out_dir, filename, plot_configs, page_width
)
}
# Filter NAs if specified
if (!is.null(config$na_rm) && config$na_rm) {
df <- df %>%
filter(!is.na(.data[[config$x_var]])) %>%
filter(!is.na(.data[[config$y_var]]))
}
# Set up aes mapping based on plot type
aes_mapping <- if (config$plot_type == "bar") {
if (!is.null(config$color_var)) {
@@ -1092,7 +1099,7 @@ generate_interaction_plot_configs <- function(df_summary, df_interactions, type)
))
}
generate_rank_plot_configs <- function(df, is_lm = FALSE, adjust = FALSE, overlap_color = FALSE) {
generate_rank_plot_configs <- function(df, is_lm = FALSE, adjust = FALSE, na_rm = FALSE, overlap_color = FALSE) {
sd_bands <- c(1, 2, 3)
plot_configs <- list()
@@ -1109,7 +1116,7 @@ generate_rank_plot_configs <- function(df, is_lm = FALSE, adjust = FALSE, overla
}
# Helper function to create a rank plot configuration
create_plot_config <- function(variable, rank_var, zscore_var, y_label, sd_band, with_annotations = TRUE) {
create_plot_config <- function(variable, rank_var, zscore_var, y_label, sd_band, na_rm, with_annotations = TRUE) {
num_enhancers <- sum(df[[zscore_var]] >= sd_band, na.rm = TRUE)
num_suppressors <- sum(df[[zscore_var]] <= -sd_band, na.rm = TRUE)
@@ -1119,6 +1126,7 @@ generate_rank_plot_configs <- function(df, is_lm = FALSE, adjust = FALSE, overla
x_var = rank_var,
y_var = zscore_var,
x_label = "Rank",
y_label = y_label,
plot_type = "scatter",
title = paste(y_label, "vs. Rank for", variable, "above", sd_band, "SD"),
sd_band = sd_band,
@@ -1128,8 +1136,7 @@ generate_rank_plot_configs <- function(df, is_lm = FALSE, adjust = FALSE, overla
alpha_negative = 0.3,
shape = 3,
size = 0.1,
y_label = y_label,
x_label = "Rank",
na_rm = na_rm,
legend_position = "none"
)
@@ -1161,10 +1168,12 @@ generate_rank_plot_configs <- function(df, is_lm = FALSE, adjust = FALSE, overla
# Loop through SD bands
for (sd_band in sd_bands) {
# Create plot with annotations
plot_configs[[length(plot_configs) + 1]] <- create_plot_config(variable, rank_var, zscore_var, y_label, sd_band, with_annotations = TRUE)
plot_configs[[length(plot_configs) + 1]] <-
create_plot_config(variable, rank_var, zscore_var, y_label, sd_band, na_rm, with_annotations = TRUE)
# Create plot without annotations
plot_configs[[length(plot_configs) + 1]] <- create_plot_config(variable, rank_var, zscore_var, y_label, sd_band, with_annotations = FALSE)
plot_configs[[length(plot_configs) + 1]] <-
create_plot_config(variable, rank_var, zscore_var, y_label, sd_band, na_rm, with_annotations = FALSE)
}
}
@@ -1650,21 +1659,23 @@ main <- function() {
generate_and_save_plots(out_dir, "rank_plots_lm", rank_lm_plot_configs,
page_width = 18, page_height = 12)
message("Generating filtered ranked plots")
message("Generating overlapped ranked plots")
rank_plot_filtered_configs <- generate_rank_plot_configs(
df_interactions,
is_lm = FALSE,
adjust = FALSE,
na_rm = TRUE,
overlap_color = TRUE
)
generate_and_save_plots(out_dir, "rank_plots_na_rm", rank_plot_filtered_configs,
page_width = 18, page_height = 12)
message("Generating filtered ranked linear model plots")
message("Generating overlapped ranked linear model plots")
rank_plot_lm_filtered_configs <- generate_rank_plot_configs(
df_interactions,
is_lm = TRUE,
adjust = FALSE,
na_rm = TRUE,
overlap_color = TRUE
)
generate_and_save_plots(out_dir, "rank_plots_lm_na_rm", rank_plot_lm_filtered_configs,
@@ -1672,7 +1683,7 @@ main <- function() {
message("Generating correlation curve parameter pair plots")
correlation_plot_configs <- generate_correlation_plot_configs(
df_interactions_joined
df_interactions
)
generate_and_save_plots(out_dir, "correlation_cpps", correlation_plot_configs,
page_width = 10, page_height = 7)