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Add some debug for rank plots

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Bryan Roessler
2024-09-15 18:37:42 -04:00
parent f848a60871
commit eb2e1ae7d6
1 changed files with 9 additions and 5 deletions
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14
qhtcp-workflow/apps/r/calculate_interaction_zscores.R
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@@ -585,13 +585,16 @@ adjust_missing_and_rank <- function(df, variables) {
df[[z_lm_col]] <- if_else(is.na(df[[z_lm_col]]), 0.001, df[[z_lm_col]]) df[[z_lm_col]] <- if_else(is.na(df[[z_lm_col]]), 0.001, df[[z_lm_col]])
# Compute ranks and create new columns # Compute ranks and create new columns
df[[rank_col]] <- rank(df[[avg_zscore_col]], na.last = "keep") df[[rank_col]] <- rank(df[[avg_zscore_col]])
df[[rank_lm_col]] <- rank(df[[z_lm_col]], na.last = "keep") df[[rank_lm_col]] <- rank(df[[z_lm_col]])
} else { } else {
warning(paste("Columns", avg_zscore_col, "or", z_lm_col, "not found in data frame")) warning(paste("Columns", avg_zscore_col, "or", z_lm_col, "not found in data frame"))
} }
# Print some debugging output
print(df %>% select("OrfRep", "Gene", "conc_num", "conc_num_factor",
avg_zscore_col, z_lm_col, rank_col, rank_lm_col))
} }
return(df) return(df)
} }
@@ -771,8 +774,7 @@ generate_rank_plot_configs <- function(df, rank_var, zscore_var, var, is_lm = FA
enhancer_label = NULL, enhancer_label = NULL,
suppressor_label = NULL, suppressor_label = NULL,
shape = 3, shape = 3,
size = 0.1, size = 0.1
position = "jitter"
) )
return(configs) return(configs)
@@ -1213,8 +1215,10 @@ main <- function() {
file = file.path(out_dir, "ZScores_Interaction_Deletion_Suppressors_K_lm.csv"), row.names = FALSE) file = file.path(out_dir, "ZScores_Interaction_Deletion_Suppressors_K_lm.csv"), row.names = FALSE)
# TODO needs explanation # TODO needs explanation
message("Adjusting and ranking interactions scores")
zscores_interactions_adjusted <- adjust_missing_and_rank(zscores_interactions, variables = interaction_vars) zscores_interactions_adjusted <- adjust_missing_and_rank(zscores_interactions, variables = interaction_vars)
message("Generating rank plots")
rank_plot_configs <- c( rank_plot_configs <- c(
generate_rank_plot_configs(zscores_interactions_adjusted, "Rank_L", "Avg_Zscore_L", "L"), generate_rank_plot_configs(zscores_interactions_adjusted, "Rank_L", "Avg_Zscore_L", "L"),
generate_rank_plot_configs(zscores_interactions_adjusted, "Rank_K", "Avg_Zscore_K", "K") generate_rank_plot_configs(zscores_interactions_adjusted, "Rank_K", "Avg_Zscore_K", "K")