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Switch from theme_gray() to theme_foundation()

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Bryan Roessler
2024-09-25 18:28:44 -04:00
parent a4d08ad1a2
commit 302110bb9b
2 changed files with 22 additions and 18 deletions
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33
qhtcp-workflow/apps/r/calculate_interaction_zscores.R
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@@ -76,15 +76,15 @@ args <- parse_arguments()
# dir.create(file.path(args$out_dir, "zscores", "qc"), showWarnings = FALSE)
# Define themes and scales
library(ggthemes)
theme_publication <- function(base_size = 14, base_family = "sans", legend_position = "bottom") {
theme_foundation <- ggplot2::theme_grey(base_size = base_size, base_family = base_family)
theme_foundation <- ggthemes::theme_foundation(base_size = base_size, base_family = base_family)
theme_foundation %+replace%
theme(
plot.title = element_text(face = "bold", size = rel(1.2), hjust = 0.5),
text = element_text(),
panel.background = element_rect(colour = NA),
plot.background = element_rect(colour = NA),
panel.border = element_rect(colour = NA),
axis.title = element_text(face = "bold", size = rel(1)),
axis.title.y = element_text(angle = 90, vjust = 2, size = 18),
@@ -1119,7 +1119,7 @@ main <- function() {
x_var = "delta_bg",
y_var = NULL,
plot_type = "density",
title = "Plate analysis by Drug Conc for Delta Background before quality control",
title = "Density plot for Delta Background by Conc All Data",
color_var = "conc_num_factor",
x_label = "Delta Background",
y_label = "Density",
@@ -1130,7 +1130,7 @@ main <- function() {
x_var = "delta_bg",
y_var = NULL,
plot_type = "bar",
title = "Plate analysis by Drug Conc for Delta Background before quality control",
title = "Bar plot for Delta Background by Conc All Data",
color_var = "conc_num_factor",
x_label = "Delta Background",
y_label = "Count",
@@ -1215,9 +1215,7 @@ main <- function() {
)
)
message("Generating quality control plots")
# TODO trying out some parallelization
message("Generating quality control plots in parallel")
# future::plan(future::multicore, workers = parallel::detectCores())
future::plan(future::multisession, workers = 3) # generate 3 plots in parallel
@@ -1368,7 +1366,7 @@ main <- function() {
file = file.path(out_dir, "zscore_interaction_deletion_enhancers_and_suppressors_K.csv"), row.names = FALSE)
# Handle linear model based enhancers and suppressors
lm_threshold <- 2
lm_threshold <- 2 # TODO add to study config?
enhancers_lm_L <- zscore_interactions[zscore_interactions$Z_lm_L >= lm_threshold, ]
suppressors_lm_L <- zscore_interactions[zscore_interactions$Z_lm_L <= -lm_threshold, ]
enhancers_lm_K <- zscore_interactions[zscore_interactions$Z_lm_K >= lm_threshold, ]
@@ -1406,19 +1404,20 @@ main <- function() {
plot_configs = rank_lm_plot_configs, grid_layout = list(ncol = 3, nrow = 2))
message("Filtering and reranking plots")
interaction_threshold <- 2 # TODO add to study config?
# Formerly X_NArm
zscore_interactions_filtered <- zscore_interactions_joined %>%
filter(!is.na(Z_lm_L) & !is.na(Avg_Zscore_L)) %>%
mutate(
Overlap = case_when(
Z_lm_L >= 2 & Avg_Zscore_L >= 2 ~ "Deletion Enhancer Both",
Z_lm_L <= -2 & Avg_Zscore_L <= -2 ~ "Deletion Suppressor Both",
Z_lm_L >= 2 & Avg_Zscore_L <= 2 ~ "Deletion Enhancer lm only",
Z_lm_L <= 2 & Avg_Zscore_L >= 2 ~ "Deletion Enhancer Avg Zscore only",
Z_lm_L <= -2 & Avg_Zscore_L >= -2 ~ "Deletion Suppressor lm only",
Z_lm_L >= -2 & Avg_Zscore_L <= -2 ~ "Deletion Suppressor Avg Zscore only",
Z_lm_L >= 2 & Avg_Zscore_L <= -2 ~ "Deletion Enhancer lm, Deletion Suppressor Avg Z score",
Z_lm_L <= -2 & Avg_Zscore_L >= 2 ~ "Deletion Suppressor lm, Deletion Enhancer Avg Z score",
Z_lm_L >= interaction_threshold & Avg_Zscore_L >= interaction_threshold ~ "Deletion Enhancer Both",
Z_lm_L <= -interaction_threshold & Avg_Zscore_L <= -interaction_threshold ~ "Deletion Suppressor Both",
Z_lm_L >= interaction_threshold & Avg_Zscore_L <= interaction_threshold ~ "Deletion Enhancer lm only",
Z_lm_L <= interaction_threshold & Avg_Zscore_L >= interaction_threshold ~ "Deletion Enhancer Avg Zscore only",
Z_lm_L <= -interaction_threshold & Avg_Zscore_L >= -interaction_threshold ~ "Deletion Suppressor lm only",
Z_lm_L >= -interaction_threshold & Avg_Zscore_L <= -interaction_threshold ~ "Deletion Suppressor Avg Zscore only",
Z_lm_L >= interaction_threshold & Avg_Zscore_L <= -interaction_threshold ~ "Deletion Enhancer lm, Deletion Suppressor Avg Z score",
Z_lm_L <= -interaction_threshold & Avg_Zscore_L >= interaction_threshold ~ "Deletion Suppressor lm, Deletion Enhancer Avg Z score",
TRUE ~ "No Effect"
),
lm_R_squared_L = summary(lm(Z_lm_L ~ Avg_Zscore_L))$r.squared,

5
qhtcp-workflow/qhtcp-workflow
View File

@@ -1430,6 +1430,11 @@ wrapper calculate_interaction_zscores
# TODO
#
# * More variables can be read in from the config file to allow more configuration
# * sd thresholds
# * lm thresholds
# * interaction thresholds
# * reference gene(s)
# * background genes
# * Add gene names, other threshold values, etc.
# * Dataframe columns and output file columns should be standardized in calculate_interactions()
# * Need to decide if conc_num_factor is numeric or factor