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KarinSchorkKarinSchork
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fix paths
1 parent 7a4be58 commit c7591ad

4 files changed

Lines changed: 37 additions & 37 deletions

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‎R/MA_Plot.R‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -130,8 +130,8 @@ MA_Plots <- function(D,
130130
num <- 0
131131
pb <- utils::txtProgressBar(min = 0,max = number_plots,char = "#",style = 3)
132132

133-
filname <- paste0("MA_Plots", suffix, ".pdf")
134-
grDevices::pdf(paste0(file.path(output_path, "MA_Plots", suffix), ".pdf"), height = plot_height/2.54, width = plot_width/2.54)
133+
filename <- paste0("MA_Plots", suffix, ".pdf")
134+
grDevices::pdf(file.path(output_path, filename), height = plot_height/2.54, width = plot_width/2.54)
135135

136136
for(i in 1:(ncol(D)-1)) {
137137
for (j in (i + 1):ncol(D)) {

‎R/workflow_ANOVA.R‎

Lines changed: 16 additions & 16 deletions
Original file line numberDiff line numberDiff line change
@@ -113,7 +113,7 @@ workflow_ANOVA <- function(data_path,
113113
paired = paired, var.equal = var.equal,
114114
log_before_test = log_before_test, delog_for_FC = delog_for_FC, log_base = 2,
115115
min_obs_per_group = min_obs_per_group, min_perc_per_group = NULL)
116-
openxlsx::write.xlsx(ANOVA_results, paste0(file.path(output_path, "results_ANOVA", suffix), ".xlsx"), keepNA = TRUE)
116+
openxlsx::write.xlsx(ANOVA_results, file.path(output_path, paste0("results_ANOVA", suffix, ".xlsx")), keepNA = TRUE)
117117
mess <- paste0(mess, "ANOVA calculated. \n")
118118

119119

@@ -151,7 +151,7 @@ workflow_ANOVA <- function(data_path,
151151

152152
mess <- paste0(mess, length(volcano_plots), " volcano plots calculated. \n")
153153

154-
grDevices::pdf(paste0(file.path(output_path, "volcano_plots", suffix),".pdf"), height = plot_height, width = plot_width)
154+
grDevices::pdf(file.path(output_path, paste0("volcano_plots", suffix,".pdf")), height = plot_height, width = plot_width)
155155
for (v_plot in volcano_plots) {
156156
graphics::plot(x = v_plot)
157157
}
@@ -164,7 +164,7 @@ workflow_ANOVA <- function(data_path,
164164
columnname_FC = colnames(ANOVA_results)[[fc_columns[[1]]]],
165165
base_size = volcano_base_size)
166166

167-
grDevices::pdf(paste0(file.path(output_path, "histograms", suffix) ,".pdf"),
167+
grDevices::pdf(file.path(output_path, paste0("histograms", suffix,".pdf")),
168168
height = plot_height, width = plot_width)
169169
graphics::plot(x = histograms[["histogram_p_value"]])
170170
graphics::plot(x = histograms[["histogram_adjusted_p_value"]])
@@ -235,7 +235,7 @@ workflow_ANOVA <- function(data_path,
235235
cluster_columns = FALSE,
236236
group_colours = group_colours)
237237

238-
grDevices::pdf(paste0(file.path(output_path, "heatmap", suffix), ".pdf"), height = plot_height, width = plot_width)
238+
grDevices::pdf(file.path(output_path, paste0("heatmap", suffix, ".pdf")), height = plot_height, width = plot_width)
239239
graphics::plot(t_heatmap) # [["heatmap"]]
240240
grDevices::dev.off()
241241

@@ -247,17 +247,17 @@ workflow_ANOVA <- function(data_path,
247247

248248
#### Create On-Off Heatmap ####
249249

250-
if (is.null(min_valid_values_on)) {
251-
min_valid_values_on <- length(intensity_columns)
252-
}
253-
254-
on_off <- calculate_onoff(D = data[["D"]],
255-
id = data[["ID"]],
256-
group = data[["group"]],
257-
max_vv_off = max_valid_values_off,
258-
min_vv_on = min_valid_values_on,
259-
protein_names_column = protein_names_column)
260-
openxlsx::write.xlsx(on_off, paste0(file.path(output_path, "table_on_off", suffix), ".xlsx"), keepNA = TRUE)
250+
# if (is.null(min_valid_values_on)) {
251+
# min_valid_values_on <- length(intensity_columns)
252+
# }
253+
#
254+
# on_off <- calculate_onoff(D = data[["D"]],
255+
# id = data[["ID"]],
256+
# group = data[["group"]],
257+
# max_vv_off = max_valid_values_off,
258+
# min_vv_on = min_valid_values_on,
259+
# protein_names_column = protein_names_column)
260+
# openxlsx::write.xlsx(on_off, paste0(file.path(output_path, "table_on_off", suffix), ".xlsx"), keepNA = TRUE)
261261

262262

263263

@@ -269,7 +269,7 @@ workflow_ANOVA <- function(data_path,
269269

270270
#### Save message log ####
271271

272-
cat(mess, file = paste0(file.path(output_path, "message_log_anova", suffix), ".txt"))
272+
cat(mess, file = file.path(output_path, paste0("message_log_anova", suffix, ".txt")))
273273

274274

275275

‎R/workflow_QC.R‎

Lines changed: 12 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -216,21 +216,21 @@ workflow_QC <- function(data_path,
216216

217217
group <- prepared_data$group
218218

219-
utils::write.csv(x = prepared_data$ID, file = paste0(file.path(output_path, "ID", suffix), ".csv"), row.names = FALSE)
220-
utils::write.csv(x = prepared_data$D, file = paste0(file.path(output_path, "D_norm_wide", suffix), ".csv"), row.names = FALSE)
221-
utils::write.csv(x = prepared_data$D_long, file = paste0(file.path(output_path, "D_norm_long", suffix), ".csv"), row.names = FALSE)
219+
utils::write.csv(x = prepared_data$ID, file = file.path(output_path, paste0("ID", suffix, ".csv")), row.names = FALSE)
220+
utils::write.csv(x = prepared_data$D, file = file.path(output_path, paste0("D_norm_wide", suffix, ".csv")), row.names = FALSE)
221+
utils::write.csv(x = prepared_data$D_long, file = file.path(output_path, paste0("D_norm_long", suffix, ".csv")), row.names = FALSE)
222222

223223

224224
if (output_type == "xlsx") {
225-
openxlsx::write.xlsx(x = cbind(prepared_data$ID, prepared_data$D), file = paste0(file.path(output_path, "D_norm_ID", suffix), ".xlsx"),
225+
openxlsx::write.xlsx(x = cbind(prepared_data$ID, prepared_data$D), file = file.path(output_path, paste0("D_norm_ID", suffix, ".xlsx")),
226226
rowNames = FALSE, overwrite = TRUE, keepNA = TRUE, na.string = na_out)
227227
}
228228
if (output_type == "csv") {
229-
utils::write.csv(x = cbind(prepared_data$ID, prepared_data$D), file = paste0(file.path(output_path, "D_norm_ID", suffix), ".csv"),
229+
utils::write.csv(x = cbind(prepared_data$ID, prepared_data$D), file = file.path(output_path, paste0("D_norm_ID", suffix, ".csv")),
230230
row.names = FALSE, na = na_out)
231231
}
232232
if (output_type == "tsv") {
233-
utils::write.table(x = cbind(prepared_data$ID, prepared_data$D), file = paste0(file.path(output_path, "D_norm_ID", suffix), ".tsv"),
233+
utils::write.table(x = cbind(prepared_data$ID, prepared_data$D), file = file.path(output_path, paste0("D_norm_ID", suffix, ".tsv")),
234234
row.names = FALSE, sep = "\t", na = na_out)
235235
}
236236

@@ -250,9 +250,9 @@ workflow_QC <- function(data_path,
250250
mess <- paste0(mess, vv_plot_data[["message"]])
251251

252252

253-
ggplot2::ggsave(paste0(file.path(output_path, "valid_value_plot", suffix), ".", plot_device), plot = vv_plot_data[["plot"]],
253+
ggplot2::ggsave(file.path(output_path, paste0("valid_value_plot", suffix, ".", plot_device)), plot = vv_plot_data[["plot"]],
254254
device = plot_device, height = plot_height, width = plot_width, dpi = plot_dpi, units = "cm")
255-
utils::write.csv(x = vv_plot_data$table, file = paste0(file.path(output_path, "D_validvalues", suffix), ".csv"), row.names = FALSE)
255+
utils::write.csv(x = vv_plot_data$table, file = file.path(output_path, paste0("D_validvalues", suffix, ".csv")), row.names = FALSE)
256256

257257

258258

@@ -265,7 +265,7 @@ workflow_QC <- function(data_path,
265265

266266
mess <- paste0(mess, boxplot_data[["message"]])
267267

268-
ggplot2::ggsave(paste0(file.path(output_path, "boxplot", suffix), ".", plot_device), plot = boxplot_data[["plot"]],
268+
ggplot2::ggsave(file.path(output_path, paste0("boxplot", suffix, ".", plot_device)), plot = boxplot_data[["plot"]],
269269
device = plot_device, height = plot_height, width = plot_width, dpi = plot_dpi, units = "cm")
270270

271271

@@ -310,10 +310,10 @@ workflow_QC <- function(data_path,
310310
mess <- paste0(mess, pca_data[["message"]])
311311

312312

313-
ggplot2::ggsave(paste0(file.path(output_path, "PCA_plot", suffix), ".", plot_device), plot = pca_data[["plot"]],
313+
ggplot2::ggsave(file.path(output_path, paste0("PCA_plot", suffix, ".", plot_device)), plot = pca_data[["plot"]],
314314
device = plot_device, height = plot_height, width = plot_width, dpi = plot_dpi, units = "cm")
315-
utils::write.csv(x = pca_data$D_PCA_plot, file = paste0(file.path(output_path, "D_PCA", suffix), ".csv"), row.names = FALSE)
316-
utils::write.csv(x = pca_data$filtered_D, file = paste0(file.path(output_path, "PCA_data_after_imputation", suffix), ".csv"), row.names = FALSE)
315+
utils::write.csv(x = pca_data$D_PCA_plot, file = file.path(output_path, paste0("D_PCA", suffix, ".csv")), row.names = FALSE)
316+
utils::write.csv(x = pca_data$filtered_D, file = file.path(output_path, paste0("PCA_data_after_imputation", suffix, ".csv")), row.names = FALSE)
317317

318318

319319
}

‎R/workflow_ttest.R‎

Lines changed: 7 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -125,7 +125,7 @@ workflow_ttest <- function(data_path,
125125
paired = paired, var.equal = var.equal,
126126
log_before_test = log_before_test, delog_for_FC = delog_for_FC, log_base = 2,
127127
min_obs_per_group = 3, min_obs_per_group_ratio = NULL,
128-
filename = paste0(file.path(output_path, "results_ttest", suffix), ".xlsx"))
128+
filename = file.path(output_path, paste0("results_ttest", suffix, ".xlsx")))
129129

130130
mess <- paste0(mess,
131131
ifelse(paired, "Paired", "Unaired"),
@@ -163,7 +163,7 @@ workflow_ttest <- function(data_path,
163163
columnname_p = "p", columnname_padj = "p.fdr",
164164
columnname_FC = fc_col_name, base_size = volcano_base_size)
165165

166-
ggplot2::ggsave(paste0(file.path(output_path, "volcano_plot", suffix), ".", plot_device), plot = volcano_plot,
166+
ggplot2::ggsave(file.path(output_path, paste0("volcano_plot", suffix, ".", plot_device)), plot = volcano_plot,
167167
device = plot_device, height = plot_height, width = plot_width, dpi = plot_dpi)
168168

169169
mess <- paste0(mess, "Volcano plot calculated. \n")
@@ -176,11 +176,11 @@ workflow_ttest <- function(data_path,
176176
columnname_p = "p", columnname_padj = "p.fdr",
177177
columnname_FC = fc_col_name)
178178

179-
ggplot2::ggsave(paste0(file.path(output_path, "histogram_p_value", suffix), ".", plot_device), plot = histograms[["histogram_p_value"]],
179+
ggplot2::ggsave(file.path(output_path, paste0("histogram_p_value", suffix, ".", plot_device)), plot = histograms[["histogram_p_value"]],
180180
device = plot_device, height = plot_height, width = plot_width, dpi = plot_dpi)
181-
ggplot2::ggsave(paste0(file.path(output_path, "histogram_adjusted_p_value", suffix), ".", plot_device), plot = histograms[["histogram_adjusted_p_value"]],
181+
ggplot2::ggsave(file.path(output_path, paste0("histogram_adjusted_p_value", suffix, ".", plot_device)), plot = histograms[["histogram_adjusted_p_value"]],
182182
device = plot_device, height = plot_height, width = plot_width, dpi = plot_dpi)
183-
ggplot2::ggsave(paste0(file.path(output_path, "histogram_fold_change", suffix), ".", plot_device), plot = histograms[["histogram_fold_change"]],
183+
ggplot2::ggsave(file.path(output_path, paste0("histogram_fold_change", suffix, ".", plot_device)), plot = histograms[["histogram_fold_change"]],
184184
device = plot_device, height = plot_height, width = plot_width, dpi = plot_dpi)
185185

186186
mess <- paste0(mess, "p-value, adjusted p-value and fold change histograms calculated. \n")
@@ -226,7 +226,7 @@ workflow_ttest <- function(data_path,
226226
id = data[["ID"]][candidates, ],
227227
groups = data[["group"]])
228228

229-
grDevices::pdf(paste0(file.path(output_path, "heatmap", suffix), ".pdf"), height = plot_height, width = plot_width)
229+
grDevices::pdf(file.path(output_path, paste0("heatmap", suffix, ".pdf")), height = plot_height, width = plot_width)
230230
graphics::plot(t_heatmap) # [["heatmap"]]
231231
grDevices::dev.off()
232232

@@ -259,7 +259,7 @@ workflow_ttest <- function(data_path,
259259

260260
#### Save message log ####
261261

262-
cat(mess, file = paste0(file.path(output_path, "message_log_ttest", suffix), ".txt"))
262+
cat(mess, file = file.path(output_path, paste0("message_log_ttest", suffix, ".txt")))
263263

264264
return(list("message" = mess))
265265
}

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