Skip to content

GitLab

You need to sign in or sign up before continuing.
Commit 4560b203 authored by Teresa Tavella's avatar Teresa Tavella
Browse files

add data and script

parent e777651b
Show whitespace changes
Inline Side-by-side
Paper_figures.Rmd
View file @ 4560b203
---
title: "geing GSEA reactome plot divided by category"
author: ""
pdf_document: default
author: ''
output:
html_document:
html_document: null
df_print: paged
pdf_document: default
word_document: default
pdf_document: default
title: "geing GSEA reactome plot divided by category"
---
......@@ -243,7 +244,7 @@ doHeatmap3 <- function(df, sinfo, num_row_clu = 2, high_genes = NULL, top_annot
width = 10, height = 10,
heatmap_legend_param = list(
title = "Z-score",
at = c(round(min(hm_matrix)),0,round(max(hm_matrix))),
#at = c(round(min(hm_matrix)),0,round(max(hm_matrix))),
legend_direction = "horizontal",
legend_width = unit(4, "cm")),
)
......@@ -286,9 +287,9 @@ mat_gg <- as.data.frame(dimicco$deseq$rlog)[unique(gg), ]
annocat_signif <- annotcat[rownames(mat_gg),]
mat_gg_scaled <- t(scale(t(mat_gg)))
dimicco_hm <- doHeatmap2(df = t(mat_gg_scaled), sinfo = sinfo, high_genes =unique(gg))
rorder <- row_order(dimicco_hm)
mat_gg_scaled_names <- mat_gg_scaled[rorder,]
#dimicco_hm <- doHeatmap2(df = t(mat_gg_scaled), sinfo = sinfo, high_genes =unique(gg))
#rorder <- row_order(dimicco_hm)
#mat_gg_scaled_names <- mat_gg_scaled[rorder,]
annocat_signif <- annocat_signif[,dt$Description]
annocat_signif <- annocat_signif[rownames(mat_gg_scaled ),] # order automatically
......@@ -304,13 +305,13 @@ for (i in dt$Description) {
cn <- dt[dt$Description == i, 'Category']
colors[i] <- my_cols[[cn]]
}
ht3 = Heatmap(as.matrix(annocat_signif), name = " ",show_column_names = TRUE,
show_row_names =FALSE,
border = TRUE,row_names_gp = gpar(fontsize = 4),
column_names_gp = gpar(fontsize = 6, rot = 90),
rect_gp = gpar(col = "black", lwd = 0.5),
col = colors ,na_col = "white",
heatmap_legend_param = list(labels = dt$Category ))#c(rep('', dim(annocat_signif)[2]))) )
# ht3 = Heatmap(as.matrix(annocat_signif), name = " ",show_column_names = TRUE,
# show_row_names =FALSE,
# border = TRUE,row_names_gp = gpar(fontsize = 4),
# column_names_gp = gpar(fontsize = 6, rot = 90),
# rect_gp = gpar(col = "black", lwd = 0.5),
# col = colors ,na_col = "white",
# heatmap_legend_param = list(labels = dt$Category ))#c(rep('', dim(annocat_signif)[2]))) )
## hm of gene in core enrichment and also signif all categories
# svg(filename=paste(plot.dir, paste0("HM_full_categories", "_ON_Old_vs_Young.svg"), sep = "/"),
......@@ -342,17 +343,18 @@ annocat_signif <- annotcat[rownames(mat_gg),]
#annocat_signif <- annocat_signif[,dt$Category]
#annocat_signif <- annocat_signif[rownames(mat_gg_scaled ),] # order automatically
table(rownames(annocat_signif ) == rownames(mat_gg_scaled))
my_cols <- c(hue_pal()(length(levels(dt$Category))))
names(my_cols) <- levels(dt$Category)
ht3 = Heatmap(as.matrix(annocat_signif), name = " ",show_column_names = TRUE,
show_row_names =FALSE,
border = TRUE,row_names_gp = gpar(fontsize = 12),
column_names_gp = gpar(fontsize = 12, rot = 90),
rect_gp = gpar(col = "black", lwd = 0.5),
col = my_cols ,na_col = "white",
heatmap_legend_param = list(labels = levels(dt$Category) ))#c(rep('', dim(annocat_signif)[2]))) )
# ht3 = Heatmap(as.matrix(annocat_signif), name = " ",show_column_names = TRUE,
# show_row_names =FALSE,
# border = TRUE,row_names_gp = gpar(fontsize = 12),
# column_names_gp = gpar(fontsize = 12, rot = 90),
# rect_gp = gpar(col = "black", lwd = 0.5),
# col = my_cols ,na_col = "white",
# heatmap_legend_param = list(labels = levels(dt$Category) ))#c(rep('', dim(annocat_signif)[2]))) )
# svg(filename=paste(plot.dir, paste0("HM_reduced_categories", "_ON_Old_vs_Young.svg"), sep = "/"),
# width=12,
......@@ -394,52 +396,52 @@ dev.off()
##### HM of genes in the core enrichment and also signif single HM
```{r echo=FALSE,echo=FALSE, warning=FALSE,message=FALSE}
#######################################################
for (y in unique(dt$Category)) { ## for each macro category
gg <- c()
for (n in names(real_sig)) {
if (n %in% dt[dt$Category == y,'Description']){
print(n)
#gg <- rownames(real_sig[[n]])
gg <- append(gg,rownames(real_sig[[n]]))
}
}
gx <- unique(gg)
mat_gg <- as.data.frame(dimicco$deseq$rlog)[gx, ]
mat_gg_scaled <- t(scale(t(mat_gg)))
dimicco_hm <- doHeatmap2(df = mat_gg_scaled, sinfo = sinfo)
str(sinfo)
n <- gsub(' ','_',gsub('/','_',n))
# svg(filename=paste(plot.dir, paste0("HM_", y, "_ON_Old_vs_Young.svg"), sep = "/"),
# width=6,
# height=6,
# pointsize=12)
# draw(dimicco_hm)
# dev.off()
#
if (length(gx) > 39) {
png(filename=paste(plot.dir, paste0("HM_", y, "_ON_Old_vs_Young.png"), sep = "/"),
units = "in", width = 8, height = 25, res = 300)
draw(dimicco_hm, merge_legend = TRUE,heatmap_legend_side = 'top',column_title =y)
dev.off()
} else if (length(gx) > 22) {
png(filename=paste(plot.dir, paste0("HM_", y, "_ON_Old_vs_Young.png"), sep = "/"),
units = "in", width = 5, height = 8, res = 300)
draw(dimicco_hm, merge_legend = TRUE,heatmap_legend_side = 'top',column_title =y)
dev.off()
} else if (length(gx) > 10) {
png(filename=paste(plot.dir, paste0("HM_", y, "_ON_Old_vs_Young.png"), sep = "/"),
units = "in", width = 5, height = 6, res = 300)
draw(dimicco_hm, merge_legend = TRUE,heatmap_legend_side = 'top',column_title =y)
dev.off()
} else {
png(filename=paste(plot.dir, paste0("HM_", y, "_ON_Old_vs_Young.png"), sep = "/"),
units = "in", width = 4, height = 4, res = 300)
draw(dimicco_hm, merge_legend = TRUE,heatmap_legend_side = 'top',column_title =y)
dev.off()
}
}
#
# for (y in unique(dt$Category)) { ## for each macro category
# gg <- c()
# for (n in names(real_sig)) {
# if (n %in% dt[dt$Category == y,'Description']){
# print(n)
# #gg <- rownames(real_sig[[n]])
# gg <- append(gg,rownames(real_sig[[n]]))
# }
# }
# gx <- unique(gg)
# mat_gg <- as.data.frame(dimicco$deseq$rlog)[gx, ]
# mat_gg_scaled <- t(scale(t(mat_gg)))
# dimicco_hm <- doHeatmap2(df = mat_gg_scaled, sinfo = sinfo)
#
# str(sinfo)
# n <- gsub(' ','_',gsub('/','_',n))
# # svg(filename=paste(plot.dir, paste0("HM_", y, "_ON_Old_vs_Young.svg"), sep = "/"),
# # width=6,
# # height=6,
# # pointsize=12)
# # draw(dimicco_hm)
# # dev.off()
# #
# if (length(gx) > 39) {
# png(filename=paste(plot.dir, paste0("HM_", y, "_ON_Old_vs_Young.png"), sep = "/"),
# units = "in", width = 8, height = 25, res = 300)
# draw(dimicco_hm, merge_legend = TRUE,heatmap_legend_side = 'top',column_title =y)
# dev.off()
# } else if (length(gx) > 22) {
# png(filename=paste(plot.dir, paste0("HM_", y, "_ON_Old_vs_Young.png"), sep = "/"),
# units = "in", width = 5, height = 8, res = 300)
# draw(dimicco_hm, merge_legend = TRUE,heatmap_legend_side = 'top',column_title =y)
# dev.off()
# } else if (length(gx) > 10) {
# png(filename=paste(plot.dir, paste0("HM_", y, "_ON_Old_vs_Young.png"), sep = "/"),
# units = "in", width = 5, height = 6, res = 300)
# draw(dimicco_hm, merge_legend = TRUE,heatmap_legend_side = 'top',column_title =y)
# dev.off()
# } else {
# png(filename=paste(plot.dir, paste0("HM_", y, "_ON_Old_vs_Young.png"), sep = "/"),
# units = "in", width = 4, height = 4, res = 300)
# draw(dimicco_hm, merge_legend = TRUE,heatmap_legend_side = 'top',column_title =y)
# dev.off()
# }
# }
```
data/HM_reduced_categories_reverse_ON_Old_vs_Young_v1.svg
View file @ 4560b203
This source diff could not be displayed because it is too large. You can view the blob instead.
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment