Commit 1f7515ff authored by mirachirkova's avatar mirachirkova
Browse files

add new info to heatmaps

parent 9a15b77f
output/DESeq_heatmap.png

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output/DESeq_heatmap.png

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output/DESeq_heatmap.png
output/DESeq_heatmap.png
output/DESeq_heatmap.png
output/DESeq_heatmap.png
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output/EBSeq_heatmap.png

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output/EBSeq_heatmap.png

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output/EBSeq_heatmap.png
output/EBSeq_heatmap.png
output/EBSeq_heatmap.png
output/EBSeq_heatmap.png
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output/NOISeq_heatmap.png

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output/NOISeq_heatmap.png

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output/NOISeq_heatmap.png
output/NOISeq_heatmap.png
output/NOISeq_heatmap.png
output/NOISeq_heatmap.png
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......@@ -6,9 +6,9 @@ MUC6
PATE1
SERPINA5
RMRP
PAEP
PCA3
CYP4F8
PAEP
SLC26A3
PATE4
CLDN2
......@@ -19,12 +19,12 @@ COL2A1
AMACR
KRT13
SPINK2
SEMA5B
PDK4
SEMA5B
TFF3
STAC2
PTGS2
EMX2OS
RPPH1
OR51E2
RPPH1
EMX2OS
HPN
......@@ -65,8 +65,8 @@
"TFF3","-","-","-","+","-",1
"STAC2","-","-","-","+","-",1
"PTGS2","-","-","-","+","-",1
"RPPH1","-","-","-","+","-",1
"OR51E2","-","-","-","+","-",1
"RPPH1","-","-","-","+","-",1
"C2orf88","-","-","-","-","+",1
"APOBEC3C","-","-","-","-","+",1
"CA14","-","-","-","-","+",1
......
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output/edgeR_heatmap.png

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output/edgeR_heatmap.png

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output/edgeR_heatmap.png
output/edgeR_heatmap.png
output/edgeR_heatmap.png
output/edgeR_heatmap.png
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......@@ -2,4 +2,4 @@ DESeq 0.790475367665374
EBSeq 0.515586137502965
edgeR 0.522764214114926
voom 0.770472302946693
NOISeq 0.762135273715179
NOISeq 0.762927580399172
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output/voom_heatmap.png

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output/voom_heatmap.png

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output/voom_heatmap.png
output/voom_heatmap.png
output/voom_heatmap.png
output/voom_heatmap.png
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......@@ -129,19 +129,19 @@ condition <- coldata$condition
loginfo('Calculate heat maps for tools')
source("source/calculate_distmatrix_utils.R")
loginfo('Calculate DESeq heat map')
deseq_hm <- heatmap_v (count, "DESeq", condition, out)
deseq_hm <- heatmap_v (count, "DESeq", condition, ', |log2FC| < 0.25, sorted by p-value', out)
loginfo('DESeq heat map is done')
loginfo('Calculate EBSeq heat map')
ebseq_hm <- heatmap_v (count, "EBSeq", condition, out)
ebseq_hm <- heatmap_v (count, "EBSeq", condition, ', sorted by PostFC', out)
loginfo('EBSeq heat map is done')
loginfo('Calculate edgeR heat map')
edger_hm <- heatmap_v (count, "edgeR", condition, out)
edger_hm <- heatmap_v (count, "edgeR", condition, ', |log2FC| < 0.25, sorted by p-value', out)
loginfo('edgeR heat map is done')
loginfo('Calculate voom heat map')
voom_hm <- heatmap_v (count, "voom", condition, out)
voom_hm <- heatmap_v (count, "voom", condition, ', |log2FC| < 0.25, sorted by p-value', out)
loginfo('voom heat map is done')
loginfo('Calculate NOISeq heat map')
noiseq_hm <- heatmap_v (count, "NOISeq", condition, out)
noiseq_hm <- heatmap_v (count, "NOISeq", condition, ', q > 0.8, sorted by probability', out)
loginfo('NOISeq heat map is done')
loginfo('Heat maps for tools are made')
dev.off()
......
......@@ -18,7 +18,7 @@ calculate_distmatrix <- function(countMatrixFile, signatureFile) {
return(distMatrix)
}
heatmap_v <- function(countMatrixFile, tool_name, condition, out) {
heatmap_v <- function(countMatrixFile, tool_name, condition, sorting_condition, out) {
signatureFile <- file.path(out, paste0(tool_name, "_sig.txt"))
if (file.info(signatureFile)$size == 0) {
cat(paste0('There is no gene in ', tool_name, ' for that signature\n'))
......@@ -42,6 +42,6 @@ heatmap_v <- function(countMatrixFile, tool_name, condition, out) {
library('pheatmap')
pheatmap(data_subset_norm, annotation_col = my_sample_col, annotation_names_col = FALSE, annotation_legend = TRUE,
annotation_names_row = FALSE, main = paste0(tool_name, ' differential expression analysis'), drop_levels = FALSE, show_rownames = T, show_colnames = F,
annotation_names_row = FALSE, main = paste0(tool_name, ' DE analysis', sorting_condition), drop_levels = FALSE, show_rownames = T, show_colnames = F,
cluster_cols = F)
}
\ No newline at end of file
......@@ -62,8 +62,8 @@ edger_top <- function(results, n) {
suppressMessages(library("edgeR"))
suppressMessages(library("biomaRt"))
# Filter results by logFC > 1 or logFC < -1
filtered_results <- results[!is.na(results$logFC) > 0 && abs(results$logFC) > 1, ]
# Filter results by logFC > 0.25 or logFC < -0.25
filtered_results <- results[!is.na(results$logFC) > 0 && abs(results$logFC) > 0.25, ]
# Extract top-n differentially expressed genes ordered by p-value
top <- head(filtered_results[order(filtered_results$PValue), ], n)
......
......@@ -69,7 +69,7 @@ voom_top <- function(results, n) {
suppressMessages(library("biomaRt"))
# Filter results by logFC > 1 or logFC < -1
filtered_results <- results[!is.na(results$logFC) > 0 && abs(results$logFC) > 1, ]
filtered_results <- results[!is.na(results$logFC) > 0 && abs(results$logFC) > 0.25, ]
# Extract top-n differentially expressed genes ordered by p-value
top <- head(filtered_results[order(filtered_results$P.Value), ], n)
......
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