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Use precomputed se values with Bessel's correction

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Bryan Roessler
2024-09-26 02:52:09 -04:00
parent fe9dfd9e38
commit 51aa2589be
2 changed files with 14 additions and 8 deletions
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18
qhtcp-workflow/apps/r/calculate_interaction_zscores.R
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@@ -189,7 +189,7 @@ calculate_summary_stats <- function(df, variables, group_vars) {
max = ~ifelse(all(is.na(.)), NA, max(., na.rm = TRUE)), max = ~ifelse(all(is.na(.)), NA, max(., na.rm = TRUE)),
min = ~ifelse(all(is.na(.)), NA, min(., na.rm = TRUE)), min = ~ifelse(all(is.na(.)), NA, min(., na.rm = TRUE)),
sd = ~sd(., na.rm = TRUE), sd = ~sd(., na.rm = TRUE),
se = ~sd(., na.rm = TRUE) / sqrt(N - 1) # TODO non-standard SE, needs explanation se = ~sd(., na.rm = TRUE) / sqrt(N - 1) # Bessel's correction
), ),
.names = "{.fn}_{.col}" .names = "{.fn}_{.col}"
), ),
@@ -581,13 +581,13 @@ generate_scatter_plot <- function(plot, config) {
# Add Error Bars if specified # Add Error Bars if specified
if (!is.null(config$error_bar) && config$error_bar && !is.null(config$y_var)) { if (!is.null(config$error_bar) && config$error_bar && !is.null(config$y_var)) {
y_mean_col <- paste0("mean_", config$y_var) y_mean_col <- paste0("mean_", config$y_var)
y_sd_col <- paste0("sd_", config$y_var) y_se_col <- paste0("se_", config$y_var)
plot <- plot + plot <- plot +
geom_errorbar( geom_errorbar(
aes( aes(
ymin = !!sym(y_mean_col) - !!sym(y_sd_col), ymin = !!sym(y_mean_col) - !!sym(y_se_col),
ymax = !!sym(y_mean_col) + !!sym(y_sd_col) ymax = !!sym(y_mean_col) + !!sym(y_se_col)
), ),
alpha = 0.3 alpha = 0.3
) )
@@ -676,7 +676,8 @@ generate_plate_analysis_plot_configs <- function(variables, stages = c("before",
title = paste("Plate analysis by Drug Conc for", var, stage, "quality control"), title = paste("Plate analysis by Drug Conc for", var, stage, "quality control"),
error_bar = error_bar, error_bar = error_bar,
color_var = "conc_num", color_var = "conc_num",
position = position position = position,
size = 0.2
) )
plots <- append(plots, list(config)) plots <- append(plots, list(config))
} }
@@ -760,7 +761,7 @@ generate_interaction_plot_configs <- function(df, limits_map = NULL) {
x_breaks = levels(df_filtered$conc_num_factor), x_breaks = levels(df_filtered$conc_num_factor),
x_labels = levels(df_filtered$conc_num_factor), x_labels = levels(df_filtered$conc_num_factor),
x_label = unique(df_filtered$Drug[1]), x_label = unique(df_filtered$Drug[1]),
coord_cartesian = y_range coord_cartesian = y_range,
) )
# Scatter plot config # Scatter plot config
@@ -768,7 +769,8 @@ generate_interaction_plot_configs <- function(df, limits_map = NULL) {
plot_type = "scatter", plot_type = "scatter",
title = sprintf("%s %s", df_filtered$OrfRep[1], df_filtered$Gene[1]), title = sprintf("%s %s", df_filtered$OrfRep[1], df_filtered$Gene[1]),
error_bar = TRUE, error_bar = TRUE,
position = "jitter" position = "jitter",
size = 1
)) ))
# Box plot config # Box plot config
@@ -937,7 +939,7 @@ generate_rank_plot_configs <- function(df, variables, is_lm = FALSE, adjust = FA
) )
), ),
shape = 3, shape = 3,
size = 0.1, size = 0.25,
smooth = TRUE, smooth = TRUE,
smooth_color = "black", smooth_color = "black",
lm_line = list(intercept = intercept, slope = slope), lm_line = list(intercept = intercept, slope = slope),

4
qhtcp-workflow/qhtcp-workflow
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@@ -1438,6 +1438,10 @@ wrapper calculate_interaction_zscores
# * Add gene names, other threshold values, etc. # * Add gene names, other threshold values, etc.
# * Dataframe columns and output file columns should be standardized in calculate_interactions() # * Dataframe columns and output file columns should be standardized in calculate_interactions()
# * Need to decide if conc_num_factor is numeric or factor # * Need to decide if conc_num_factor is numeric or factor
# * Do pdfs really need to be all different sizes?
# * We are using standard error bars using the same se values as the data now (includes Bessel's correction)
# * Plate analysis error bars and some others will be slightly different
# * Can be changed back but better to have plots reflect data, no?
# #
# INPUT # INPUT
# #