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Explicitly filter data before plotting to silence ggplot

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This commit is contained in:
Bryan Roessler
2024-09-15 14:32:48 -04:00
parent 6c13182961
commit 5dfa2d1650
1 changed files with 55 additions and 39 deletions
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94
qhtcp-workflow/apps/r/calculate_interaction_zscores.R
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@@ -365,7 +365,7 @@ calculate_interaction_scores <- function(df, max_conc, variables, group_vars = c
}
generate_and_save_plots <- function(output_dir, file_name, plot_configs, grid_layout = NULL) {
message("Generating html and pdf plots for: ", file_name)
message("Generating ", file_name, ".pdf and ", file_name, ".html")
# Prepare lists to collect plots
static_plots <- list()
@@ -456,32 +456,6 @@ generate_and_save_plots <- function(output_dir, file_name, plot_configs, grid_la
}
generate_scatter_plot <- function(plot, config) {
# Check for missing or out-of-range data
missing_data <- config$df %>%
filter(
is.na(!!sym(config$x_var)) | is.na(!!sym(config$y_var)) |
!!sym(config$y_var) < min(config$ylim_vals, na.rm = TRUE) |
!!sym(config$y_var) > max(config$ylim_vals, na.rm = TRUE)
)
# Print the rows with missing or out-of-range data if any
if (nrow(missing_data) > 0) {
message("Missing or out-of-range data for ", config$title, ":")
print(
missing_data %>% select(any_of(
c(
"OrfRep",
"Gene",
"num",
"conc_num",
"conc_num_factor",
config$x_var,
config$y_var
)
)),
n = 100
)
}
if (!is.null(config$delta_bg_point) && config$delta_bg_point) {
plot <- plot + geom_point(
@@ -620,6 +594,10 @@ adjust_missing_and_rank <- function(df, variables) {
generate_interaction_plot_configs <- function(df, variables) {
configs <- list()
# Data frames to collect filtered data and out-of-range data
filtered_data_list <- list()
out_of_range_data_list <- list()
# Define common y-limits for each variable
limits_map <- list(
L = c(-65, 65),
@@ -630,8 +608,8 @@ generate_interaction_plot_configs <- function(df, variables) {
# Define annotation positions and labels
annotation_positions <- list(
Z_Shift = 45,
Z_lm = 25,
ZShift = 45,
lm_ZScore = 25,
NG = -25,
DB = -35,
SM = -45
@@ -639,11 +617,11 @@ generate_interaction_plot_configs <- function(df, variables) {
# Define functions to generate annotation labels
annotation_labels <- list(
Z_Shift = function(df, var) {
ZShift = function(df, var) {
val <- df[[paste0("Z_Shift_", var)]]
paste("ZShift =", round(val, 2))
},
Z_lm = function(df, var) {
lm_ZScore = function(df, var) {
val <- df[[paste0("Z_lm_", var)]]
paste("lm ZScore =", round(val, 2))
},
@@ -678,9 +656,30 @@ generate_interaction_plot_configs <- function(df, variables) {
# Remove NULL annotations
annotations <- Filter(Negate(is.null), annotations)
# Filter the data based on y-limits and missing values
y_var_sym <- sym(variable)
x_var_sym <- sym("conc_num_factor")
# Identify missing data and out-of-range data
missing_data <- df %>% filter(is.na(!!x_var_sym) | is.na(!!y_var_sym))
out_of_range_data <- df %>% filter(
!is.na(!!y_var_sym) &
(!!y_var_sym < min(ylim_vals, na.rm = TRUE) | !!y_var_sym > max(ylim_vals, na.rm = TRUE))
)
# Combine missing data and out-of-range data
data_to_filter_out <- bind_rows(missing_data, out_of_range_data) %>% distinct()
# Filtered data for plotting
filtered_data <- df %>% anti_join(data_to_filter_out, by = names(df))
# Collect the filtered data and out-of-range data
filtered_data_list[[variable]] <- filtered_data
out_of_range_data_list[[variable]] <- data_to_filter_out
# Create scatter plot config
configs[[length(configs) + 1]] <- list(
df = df,
df = filtered_data,
x_var = "conc_num_factor",
y_var = variable,
plot_type = "scatter",
@@ -698,7 +697,7 @@ generate_interaction_plot_configs <- function(df, variables) {
# Create box plot config
configs[[length(configs) + 1]] <- list(
df = df,
df = filtered_data,
x_var = "conc_num_factor",
y_var = variable,
plot_type = "box",
@@ -713,9 +712,15 @@ generate_interaction_plot_configs <- function(df, variables) {
)
}
return(configs)
}
# Combine the filtered data and out-of-range data into data frames
filtered_data_df <- bind_rows(filtered_data_list, .id = "variable")
out_of_range_data_df <- bind_rows(out_of_range_data_list, .id = "variable")
return(list(
configs = configs,
out_of_range_data = out_of_range_data_df
))
}
generate_rank_plot_configs <- function(df, rank_var, zscore_var, var, is_lm = FALSE) {
configs <- list()
@@ -1151,11 +1156,22 @@ main <- function() {
write.csv(zscores_interactions, file = file.path(out_dir, "ZScores_Interaction.csv"), row.names = FALSE)
# Create interaction plots
message("Generating interaction plot configurations")
reference_plot_configs <- generate_interaction_plot_configs(zscores_interactions_reference_joined, interaction_vars)
deletion_plot_configs <- generate_interaction_plot_configs(zscores_interactions_joined, interaction_vars)
message("Generating interaction plots")
message("Generating reference interaction plots")
results <- generate_interaction_plot_configs(zscores_interactions_reference_joined, interaction_vars)
if (nrow(results$out_of_range_data) > 0) {
message("Out-of-range data:")
print(results$out_of_range_data)
}
reference_plot_configs <- results$configs
generate_and_save_plots(out_dir, "RF_interactionPlots", reference_plot_configs, grid_layout = list(ncol = 4, nrow = 3))
message("Generating deletion interaction plots")
results <- generate_interaction_plot_configs(zscores_interactions_joined, interaction_vars)
if (nrow(results$out_of_range_data) > 0) {
message("Out-of-range data:")
print(results$out_of_range_data)
}
deletion_plot_configs <- results$configs
generate_and_save_plots(out_dir, "InteractionPlots", deletion_plot_configs, grid_layout = list(ncol = 4, nrow = 3))
# Define conditions for enhancers and suppressors