.Rhistory

library(ggplot2)
ggplot(data = dat.select, aes(y=TF, x=Component)) +
geom_raster(aes(fill=`Z-score`), interpolate = T)
ggplot(data = dat.select, aes(y=TF, x=Component)) +
geom_raster(aes(fill=`Z-score`), interpolate = T) + theme_bw()
ggplot(data = dat.select, aes(y=TF, x=Component)) +
geom_raster(aes(fill=`Z-score`), interpolate = T) +
theme_classic()
ggplot(data = dat.select, aes(y=TF, x=Component)) +
geom_raster(aes(fill=`Z-score`), interpolate = T) +
theme_classic() + scale_fill_continuous(colors=c("purple","black","yellow"))
ggplot(data = dat.select, aes(y=TF, x=Component)) +
geom_raster(aes(fill=`Z-score`), interpolate = T) +
theme_classic() + scale_fill_continuous(col=c("purple","black","yellow"))
ggplot(data = dat.select, aes(y=TF, x=Component)) +
geom_raster(aes(fill=`Z-score`), interpolate = T) +
theme_classic() +  scale_fill_gradientn(colours = terrain.colors(10))
ggplot(data = dat.select, aes(y=TF, x=Component)) +
geom_raster(aes(fill=`Z-score`), interpolate = T) +
theme_classic() +
scale_fill_gradientn(colours = c("purple","black","yellow"))
ggplot(data = dat.select, aes(y=TF, x=Component)) +
# geom_raster(aes(fill=`Z-score`), interpolate = T) +
stat_density(aes(fill = stat(`Z-score`)), geom = "raster", position = "identity")
ggplot(data = dat.select, aes(y=TF, x=Component)) +
# geom_raster(aes(fill=`Z-score`), interpolate = T) +
stat_density(aes(fill = stat(count)), geom = "raster", position = "identity")
ggplot(data = dat.select, aes(y=TF, x=Component)) +
# geom_raster(aes(fill=`Z-score`), interpolate = T) +
stat_density(aes(fill = `Z-score`), geom = "raster", position = "identity")
ggplot(data = dat.select, aes(y=TF, x=Component)) +
geom_raster(aes(fill=`Z-score`), interpolate = T) +
# stat_density(aes(fill = `Z-score`), geom = "raster", position = "identity")
theme_classic() +
scale_fill_gradientn(colours = c("purple","black","yellow"))
dat.select[is.na(dat.select)] <-0
ggplot(data = dat.select, aes(y=TF, x=Component)) +
geom_raster(aes(fill=`Z-score`), interpolate = T) +
# stat_density(aes(fill = `Z-score`), geom = "raster", position = "identity")
theme_classic() +
scale_fill_gradientn(colours = c("purple","black","yellow")) +
theme(axis.text.x = element_text(angle = 90))
dat.select[abs(dat.select)==Inf] <=0
dat.select[abs(dat.select)==Inf] <-0
dat.select <- subset(dat, TF %in% c("IRF1","AP1","STAT1","NFKB1","NF-kappaB","USF1","SPI1","IRF2","CTCF","MEF2A","CEBPA") & isSig==1)
dat.select[is.na(dat.select)] <-0
dat.select[abs(dat.select)==Inf] <-0
dat.select
dat.select[abs(dat.select$Z-score)==Inf,"Z-score"] <-0
dat.select[abs(dat.select$`Z-score``)==Inf,"Z-score"] <-0
dat.select[abs(dat.select$`Z-score`)==Inf,"Z-score"] <-0
dat.select
dat.select[is.na(dat.select$`Z-score`),"Z-score"] <-0
dat.select <- subset(dat, TF %in% c("IRF1","AP1","STAT1","NFKB1","NF-kappaB","USF1","SPI1","IRF2","CTCF","MEF2A","CEBPA") & isSig==1)
dat.select[is.na(dat.select$`Z-score`),"Z-score"] <-0
dat.select[abs(dat.select$`Z-score`)==Inf,"Z-score"] <-0
ggplot(data = dat.select, aes(y=TF, x=Component)) +
geom_raster(aes(fill=`Z-score`), interpolate = T) +
# stat_density(aes(fill = `Z-score`), geom = "raster", position = "identity")
theme_classic() +
scale_fill_gradientn(colours = c("purple","black","yellow")) +
theme(axis.text.x = element_text(angle = 90))
colour = "black")
ggplot(data = dat.select, aes(y=TF, x=Component)) +
geom_raster(aes(fill=`Z-score`), interpolate = T) +
# stat_density(aes(fill = `Z-score`), geom = "raster", position = "identity")
theme_classic() +
scale_fill_gradientn(colours = c("purple","black","yellow")) +
theme(axis.text.x = element_text(angle = 90),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.background = element_rect(fill = "black", colour = "black"))
ggplot(data = dat.select, aes(y=TF, x=Component)) +
# geom_raster(aes(fill=`Z-score`), interpolate = T) +
geom_tile(aes(fill=`Z-score`)) +
# stat_density(aes(fill = `Z-score`), geom = "raster", position = "identity")
theme_classic() +
scale_fill_gradientn(colours = c("purple","black","yellow")) +
theme(axis.text.x = element_text(angle = 90),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.background = element_rect(fill = "black", colour = "black"))
ggplot(data = dat.select, aes(y=TF, x=Component, group=TF)) +
# geom_raster(aes(fill=`Z-score`), interpolate = T) +
geom_tile(aes(fill=`Z-score`)) +
# stat_density(aes(fill = `Z-score`), geom = "raster", position = "identity")
theme_classic() +
scale_fill_gradientn(colours = c("purple","black","yellow")) +
theme(axis.text.x = element_text(angle = 90),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.background = element_rect(fill = "black", colour = "black"))
ggplot(data = dat.select, aes(y=TF, x=Component, group=`Z-score`)) +
# geom_raster(aes(fill=`Z-score`), interpolate = T) +
geom_tile(aes(fill=`Z-score`)) +
# stat_density(aes(fill = `Z-score`), geom = "raster", position = "identity")
theme_classic() +
scale_fill_gradientn(colours = c("purple","black","yellow")) +
theme(axis.text.x = element_text(angle = 90),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.background = element_rect(fill = "black", colour = "black"))
ggplot(data = dat.select, aes(y=TF, x=Component, level=`Z-score`)) +
# geom_raster(aes(fill=`Z-score`), interpolate = T) +
geom_tile(aes(fill=`Z-score`)) +
# stat_density(aes(fill = `Z-score`), geom = "raster", position = "identity")
theme_classic() +
scale_fill_gradientn(colours = c("purple","black","yellow")) +
theme(axis.text.x = element_text(angle = 90),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.background = element_rect(fill = "black", colour = "black"))
dat.select %>% group_by(TF, Component) %>% tally()
dat.select %>% group_by(TF, Component) %>% tally() %>% max()
(dat.select %>% group_by(TF, Component) %>% tally()) %>% max()
(dat.select %>% group_by(TF, Component) %>% tally())$n %>% max()
hc.rows <- hclust(dist(dat.cast))
hc.cols <- hclust(dist(t(dat.cast)))
hc.cols
hc.cols$labels
hc.cols$merge
hc.cols$labels[hc.cols$order]
gsub("C_","",hc.cols$labels[hc.cols$order])
ordered.components <- gsub("C_","",hc.cols$labels[hc.cols$order])
dat.select$Component <-  factor(dat.select$Component, levels = ordered.components, labels = ordered.components, ordered = T)
ggplot(data = dat.select, aes(y=TF, x=Component, level=`Z-score`)) +
# geom_raster(aes(fill=`Z-score`), interpolate = T) +
geom_tile(aes(fill=`Z-score`)) +
# stat_density(aes(fill = `Z-score`), geom = "raster", position = "identity")
theme_classic() +
scale_fill_gradientn(colours = c("purple","black","yellow")) +
theme(axis.text.x = element_text(angle = 90),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.background = element_rect(fill = "black", colour = "black"))
ggplot(data = dat.select, aes(y=TF, x=Component, level=`Z-score`)) +
geom_raster(aes(fill=`Z-score`), interpolate = T) +
# geom_tile(aes(fill=`Z-score`)) +
# stat_density(aes(fill = `Z-score`), geom = "raster", position = "identity")
theme_classic() +
scale_fill_gradientn(colours = c("purple","black","yellow")) +
theme(axis.text.x = element_text(angle = 90),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.background = element_rect(fill = "black", colour = "black"))
ggplot(data = dat.select, aes(y=TF, x=Component, level=`Z-score`)) +
geom_raster(aes(fill=`Z-score`), interpolate = T) +
# geom_tile(aes(fill=`Z-score`)) +
# stat_density(aes(fill = `Z-score`), geom = "raster", position = "identity")
theme_classic() +
scale_fill_gradientn(colours = c("purple","black","yellow")) +
theme(axis.text.x = element_text(angle = 45),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.background = element_rect(fill = "black", colour = "black"))
ggplot(data = dat.select, aes(y=TF, x=Component, level=`Z-score`)) +
geom_raster(aes(fill=`Z-score`), interpolate = T) +
# geom_tile(aes(fill=`Z-score`)) +
# stat_density(aes(fill = `Z-score`), geom = "raster", position = "identity")
theme_classic() +
scale_fill_gradientn(colours = c("purple","black","yellow")) +
theme(axis.text.x = element_text(angle = 45, hjust = .5),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.background = element_rect(fill = "black", colour = "black"))
ggplot(data = dat.select, aes(y=TF, x=Component, level=`Z-score`)) +
geom_raster(aes(fill=`Z-score`), interpolate = T) +
# geom_tile(aes(fill=`Z-score`)) +
# stat_density(aes(fill = `Z-score`), geom = "raster", position = "identity")
theme_classic() +
scale_fill_gradientn(colours = c("purple","black","yellow")) +
theme(axis.text.x = element_text(angle = 45, hjust = -.5),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.background = element_rect(fill = "black", colour = "black"))
ggplot(data = dat.select, aes(y=TF, x=Component, level=`Z-score`)) +
geom_raster(aes(fill=`Z-score`), interpolate = T) +
# geom_tile(aes(fill=`Z-score`)) +
# stat_density(aes(fill = `Z-score`), geom = "raster", position = "identity")
theme_classic() +
scale_fill_gradientn(colours = c("purple","black","yellow")) +
theme(axis.text.x = element_text(angle = 45, vjust = -.5),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.background = element_rect(fill = "black", colour = "black"))
ggplot(data = dat.select, aes(y=TF, x=Component, level=`Z-score`)) +
geom_raster(aes(fill=`Z-score`), interpolate = T) +
# geom_tile(aes(fill=`Z-score`)) +
# stat_density(aes(fill = `Z-score`), geom = "raster", position = "identity")
theme_classic() +
scale_fill_gradientn(colours = c("purple","black","yellow")) +
theme(axis.text.x = element_text(angle = 45, vjust = .5),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.background = element_rect(fill = "black", colour = "black"))
ggplot(data = dat.select, aes(y=TF, x=Component, level=`Z-score`)) +
geom_raster(aes(fill=`Z-score`), interpolate = T) +
# geom_tile(aes(fill=`Z-score`)) +
# stat_density(aes(fill = `Z-score`), geom = "raster", position = "identity")
theme_classic() +
scale_fill_gradientn(colours = c("purple","black","yellow")) +
theme(axis.text.x = element_text(angle = 45, vjust = .5, hjust = 1),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.background = element_rect(fill = "black", colour = "black"))
ggplot(data = dat.select, aes(y=TF, x=Component, level=`Z-score`)) +
geom_raster(aes(fill=`Z-score`), interpolate = T) +
# geom_tile(aes(fill=`Z-score`)) +
# stat_density(aes(fill = `Z-score`), geom = "raster", position = "identity")
theme_classic() +
scale_fill_gradientn(colours = c("purple","black","yellow")) +
theme(axis.text.x = element_text(angle = 45, vjust = .1, hjust = 1),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.background = element_rect(fill = "black", colour = "black"))
ggplot(data = dat.select, aes(y=TF, x=Component, level=`Z-score`)) +
geom_raster(aes(fill=`Z-score`), interpolate = T) +
# geom_tile(aes(fill=`Z-score`)) +
# stat_density(aes(fill = `Z-score`), geom = "raster", position = "identity")
theme_classic() +
scale_fill_gradientn(colours = c("purple","black","yellow")) +
theme(axis.text.x = element_text(angle = 45, vjust = 0, hjust = 1),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.background = element_rect(fill = "black", colour = "black"))
ggplot(data = dat.select, aes(y=TF, x=Component, level=`Z-score`)) +
geom_raster(aes(fill=`Z-score`), interpolate = T) +
# geom_tile(aes(fill=`Z-score`)) +
# stat_density(aes(fill = `Z-score`), geom = "raster", position = "identity")
theme_classic() +
scale_fill_gradientn(colours = c("purple","black","yellow")) +
theme(axis.text.x = element_text(angle = 45, vjust = -.5, hjust = 1),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.background = element_rect(fill = "black", colour = "black"))
ggplot(data = dat.select, aes(y=TF, x=Component, level=`Z-score`)) +
geom_raster(aes(fill=`Z-score`), interpolate = T) +
# geom_tile(aes(fill=`Z-score`)) +
# stat_density(aes(fill = `Z-score`), geom = "raster", position = "identity")
theme_classic() +
scale_fill_gradientn(colours = c("purple","black","yellow")) +
theme(axis.text.x = element_text(angle = 45, vjust = .5, hjust = 1),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.background = element_rect(fill = "black", colour = "black"))
ggplot(data = dat.select, aes(y=TF, x=Component, level=`Z-score`)) +
geom_raster(aes(fill=`Z-score`), interpolate = T) +
# geom_tile(aes(fill=`Z-score`)) +
# stat_density(aes(fill = `Z-score`), geom = "raster", position = "identity")
theme_classic() +
scale_fill_gradientn(colours = c("purple","black","yellow")) +
theme(axis.text.x = element_text(angle = 45, vjust = .25, hjust = 1),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.background = element_rect(fill = "black", colour = "black"))
ggplot(data = dat.select, aes(y=TF, x=Component, level=`Z-score`)) +
geom_raster(aes(fill=`Z-score`), interpolate = T) +
# geom_tile(aes(fill=`Z-score`)) +
# stat_density(aes(fill = `Z-score`), geom = "raster", position = "identity")
theme_classic() +
scale_fill_gradientn(colours = c("purple","black","yellow")) +
theme(axis.text.x = element_text(angle = 45, vjust = .05, hjust = 1),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.background = element_rect(fill = "black", colour = "black"))
ggplot(data = dat.select, aes(y=TF, x=Component, level=`Z-score`)) +
geom_raster(aes(fill=`Z-score`), interpolate = T) +
# geom_tile(aes(fill=`Z-score`)) +
# stat_density(aes(fill = `Z-score`), geom = "raster", position = "identity")
theme_classic() +
scale_fill_gradientn(colours = c("purple","black","yellow")) +
theme(axis.text.x = element_text(angle = 45,, hjust = 1),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.background = element_rect(fill = "black", colour = "black"))
ggplot(data = dat.select, aes(y=TF, x=Component, level=`Z-score`)) +
geom_raster(aes(fill=`Z-score`), interpolate = T) +
# geom_tile(aes(fill=`Z-score`)) +
# stat_density(aes(fill = `Z-score`), geom = "raster", position = "identity")
theme_classic() +
scale_fill_gradientn(colours = c("purple","black","yellow")) +
theme(axis.text.x = element_text(angle = 50, hjust = 1),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.background = element_rect(fill = "black", colour = "black"))
selected.TFs <- c("IRF1","AP1","STAT1","NFKB1","NF-kappaB","USF1","SPI1","IRF2","CTCF","MEF2A","CEBPA")
dat.select <- subset(dat, TF %in%  & isSig==1)
dat.select <- subset(dat, TF %in% selected.TFs & isSig==1)
dat.select[is.na(dat.select$`Z-score`),"Z-score"] <-0
dat.select[abs(dat.select$`Z-score`)==Inf,"Z-score"] <-0
hc.rows <- hclust(dist(dat.cast))
# Order rows
dat.select$TF <- factor(dat.select$TF, levels = selected.TFs, labels = selected.TFs, ordered = T)
ggplot(data = dat.select, aes(y=TF, x=Component, level=`Z-score`)) +
geom_raster(aes(fill=`Z-score`), interpolate = T) +
# geom_tile(aes(fill=`Z-score`)) +
# stat_density(aes(fill = `Z-score`), geom = "raster", position = "identity")
theme_classic() +
scale_fill_gradientn(colours = c("purple","black","yellow")) +
theme(axis.text.x = element_text(angle = 50, hjust = 1),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.background = element_rect(fill = "black", colour = "black"))
rev(selected.TFs)
selected.TFs <- c("IRF1","AP1","STAT1","NFKB1","NF-kappaB","USF1","SPI1","IRF2","CTCF","MEF2A","CEBPA") %>% rev()
dat.select <- subset(dat, TF %in% selected.TFs & isSig==1)
dat.select[is.na(dat.select$`Z-score`),"Z-score"] <-0
dat.select[abs(dat.select$`Z-score`)==Inf,"Z-score"] <-0
hc.rows <- hclust(dist(dat.cast))
hc.cols <- hclust(dist(t(dat.cast)))
(dat.select %>% group_by(TF, Component) %>% tally())$n %>% max()
ordered.components <- gsub("C_","",hc.cols$labels[hc.cols$order])
# Order cols
dat.select$Component <- factor(dat.select$Component, levels = ordered.components, labels = ordered.components, ordered = T)
hc.rows <- hclust(dist(dat.cast))
# Order rows
hc.rows <- hclust(dist(dat.cast))
dat.select$TF <- factor(dat.select$TF, levels = selected.TFs, labels = selected.TFs, ordered = T)
# Order cols
# hc.cols <- hclust(dist(t(dat.cast)))
ordered.components <- gsub("C_","",hc.cols$labels[hc.cols$order])
dat.select$Component <- factor(dat.select$Component, levels = ordered.components, labels = ordered.components, ordered = T)
ggplot(data = dat.select, aes(y=TF, x=Component, level=`Z-score`)) +
geom_raster(aes(fill=`Z-score`), interpolate = T) +
# geom_tile(aes(fill=`Z-score`)) +
# stat_density(aes(fill = `Z-score`), geom = "raster", position = "identity")
theme_classic() +
scale_fill_gradientn(colours = c("purple","black","yellow")) +
theme(axis.text.x = element_text(angle = 50, hjust = 1),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.background = element_rect(fill = "black", colour = "black"))
ggplot(data = dat.select, aes(y=TF, x=Component, level=`Z-score`)) +
geom_raster(aes(fill=`Z-score`), interpolate = T) +
# geom_tile(aes(fill=`Z-score`)) +
# stat_density(aes(fill = `Z-score`), geom = "raster", position = "identity")
theme_classic() +
scale_fill_gradientn(colours = c("purple","black","yellow")) +
theme(axis.text.x = element_text(angle = 50, hjust = 1),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.background = element_rect(fill = "black", colour = "white"))
ggplot(data = dat.select, aes(y=TF, x=Component, level=`Z-score`)) +
geom_raster(aes(fill=`Z-score`), interpolate = T) +
# geom_tile(aes(fill=`Z-score`)) +
# stat_density(aes(fill = `Z-score`), geom = "raster", position = "identity")
theme_classic() +
scale_fill_gradientn(colours = c("purple","black","yellow")) +
theme(axis.text.x = element_text(angle = 50, hjust = 1),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.background = element_rect(fill = "white", colour = "black"))
ggplot(data = dat.select, aes(y=TF, x=Component, level=`Z-score`)) +
geom_raster(aes(fill=`Z-score`), interpolate = T) +
# geom_tile(aes(fill=`Z-score`)) +
# stat_density(aes(fill = `Z-score`), geom = "raster", position = "identity")
theme_classic() +
scale_fill_gradientn(colours = c("purple","black","yellow")) +
theme(axis.text.x = element_text(angle = 50, hjust = 1),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.background = element_rect(fill = "black", colour = "black"),
plot.margin=unit(c(0,0,0,0), "null"))
ggplot(data = dat.select, aes(y=TF, x=Component, level=`Z-score`)) +
geom_raster(aes(fill=`Z-score`), interpolate = T) +
# geom_tile(aes(fill=`Z-score`)) +
# stat_density(aes(fill = `Z-score`), geom = "raster", position = "identity")
theme_classic() +
scale_fill_gradientn(colours = c("purple","black","yellow")) +
theme(axis.text.x = element_text(angle = 50, hjust = 1),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.background = element_rect(fill = "black", colour = "black"),
plot.margin=unit(c(0,0,0,0), "null"),
panel.margin=unit(c(0,0,0,0), "null"))
ggplot(data = dat.select, aes(y=TF, x=Component, level=`Z-score`)) +
geom_raster(aes(fill=`Z-score`), interpolate = T) +
# geom_tile(aes(fill=`Z-score`)) +
# stat_density(aes(fill = `Z-score`), geom = "raster", position = "identity")
theme_classic() +
scale_fill_gradientn(colours = c("purple","black","yellow")) +
theme(axis.text.x = element_text(angle = 50, hjust = 1),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.background = element_rect(fill = "black", colour = "black"),
plot.margin=unit(c(0,0,0,0), "null"),
panel.spacing=unit(c(0,0,0,0), "null"))
ggplot(data = dat.select, aes(y=TF, x=Component, level=`Z-score`)) +
geom_raster(aes(fill=`Z-score`), interpolate = T) +
# geom_tile(aes(fill=`Z-score`)) +
# stat_density(aes(fill = `Z-score`), geom = "raster", position = "identity")
theme_classic() +
scale_fill_gradientn(colours = c("purple","black","yellow")) +
theme(axis.text.x = element_text(angle = 50, hjust = 1),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.background = element_rect(fill = "black", colour = "black"),
panel.background=element_rect(fill = "transparent",colour = NA))
ggplot(data = dat.select, aes(y=TF, x=Component, level=`Z-score`)) +
geom_raster(aes(fill=`Z-score`), interpolate = T) +
# geom_tile(aes(fill=`Z-score`)) +
# stat_density(aes(fill = `Z-score`), geom = "raster", position = "identity")
theme_classic() +
scale_fill_gradientn(colours = c("purple","black","yellow")) +
theme(axis.text.x = element_text(angle = 50, hjust = 1),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.background = element_rect(fill = "black", colour = NA),
panel.background=element_rect(fill = "transparent",colour = NA))
ggplot(data = dat.select, aes(y=TF, x=Component, level=`Z-score`)) +
geom_raster(aes(fill=`Z-score`), interpolate = T) +
# geom_tile(aes(fill=`Z-score`)) +
# stat_density(aes(fill = `Z-score`), geom = "raster", position = "identity")
theme_classic() +
scale_fill_gradientn(colours = c("purple","black","yellow")) +
theme(axis.text.x = element_text(angle = 50, hjust = 1),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.background = element_rect(fill = "black", colour = NA))
ggplot(data = dat.select, aes(y=TF, x=Component, level=`Z-score`)) +
geom_raster(aes(fill=`Z-score`), interpolate = T) +
# geom_tile(aes(fill=`Z-score`)) +
# stat_density(aes(fill = `Z-score`), geom = "raster", position = "identity")
theme_classic() +
scale_fill_gradientn(colours = c("purple","black","yellow")) +
theme(axis.text.x = element_text(angle = 50, hjust = 1),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
# panel.background = element_rect(fill = "black", colour = NA)
)
ggplot(data = dat.select, aes(y=TF, x=Component, level=`Z-score`)) +
geom_raster(aes(fill=`Z-score`), interpolate = T) +
# geom_tile(aes(fill=`Z-score`)) +
# stat_density(aes(fill = `Z-score`), geom = "raster", position = "identity")
theme_classic() +
scale_fill_gradientn(colours = c("purple","black","yellow")) +
theme(axis.text.x = element_text(angle = 50, hjust = 1),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.background = element_rect(fill = "black", colour = NA))
ggplot(data = dat.select, aes(y=TF, x=Component, level=`Z-score`)) +
geom_raster(aes(fill=`Z-score`), interpolate = T) +
# geom_tile(aes(fill=`Z-score`)) +
# stat_density(aes(fill = `Z-score`), geom = "raster", position = "identity")
theme_classic() +
scale_fill_gradientn(colours = c("purple","black","yellow")) +
theme(axis.text.x = element_text(angle = 50, hjust = 1),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.background = element_rect(fill = "black", colour = NA)) +
labs(title = "Transcription Factor Enrichment", y="Transciption Factor")
ggplot(data = dat.select, aes(y=TF, x=Component, level=`Z-score`)) +
geom_raster(aes(fill=`Z-score`), interpolate = T) +
# geom_tile(aes(fill=`Z-score`)) +
# stat_density(aes(fill = `Z-score`), geom = "raster", position = "identity")
theme_classic() +
scale_fill_gradientn(colours = c("purple","black","yellow")) +
theme(axis.text.x = element_text(angle = 50, hjust = 1),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.background = element_rect(fill = "black", colour = NA)) +
labs(title = "Transcription Factor Enrichment", y="Transcription Factor")
rp <- ggplot(data = dat.select, aes(y=TF, x=Component, level=`Z-score`)) +
geom_raster(aes(fill=`Z-score`), interpolate = T) +
# geom_tile(aes(fill=`Z-score`)) +
# stat_density(aes(fill = `Z-score`), geom = "raster", position = "identity")
theme_classic() +
scale_fill_gradientn(colours = c("purple","black","yellow")) +
theme(axis.text.x = element_text(angle = 50, hjust = 1),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.background = element_rect(fill = "black", colour = NA)) +
labs(title = "Transcription Factor Enrichment", y="Transcription Factor")
ggsave("./TF_raster_plot.png",rp,dpi = 400)
ggsave("./TF_raster_plot.png",rp,dpi = 400, width = 10)
library(shiny); runApp('Tensor_myeloid_ShinyApp.R')
library(shiny); runApp('Tensor_myeloid_ShinyApp.R')
remove(dat)
dat <- data.table::fread("./supp_tables/SUPPLEMENTARY_TABLE_2.txt")
dat <- data.table::fread("./supp_tables/SUPPLEMENTARY_TABLE_2.txt", sep="\t")
dat
dat <- data.table::fread("./supp_tables/SUPPLEMENTARY_TABLE_2.txt", sep="\t")
read.delim(paste("supp_tables/SUPPLEMENTARY_TABLE_",toString(tabNum),".txt", sep=""),
fill=NA, header=T, stringsAsFactors=F, na.strings = "NA")
tabNum <-2
read.delim(paste("supp_tables/SUPPLEMENTARY_TABLE_",toString(tabNum),".txt", sep=""),
fill=NA, header=T, stringsAsFactors=F, na.strings = "NA")
dat <- read.delim(paste("supp_tables/SUPPLEMENTARY_TABLE_",toString(tabNum),".txt", sep=""),
fill=NA, header=T, stringsAsFactors=F, na.strings = "NA")
translate <- function(tabNum){
newNumber <-switch(toString(tabNum), "0"=1, "1"=2, "XXX"=3, "2"=4,
"3"=5, "XX"=6, "4"=7, "5"=8, "6"=9, "7"=10)
return(toString(newNumber))
}
translate(2)
tabNum <- translate(0)
tabNum <- translate(0)
tabNum
file.numbers <- c(2,3,4,5,6,7,"XX","XXX")
library(xlsx)
library(xlsx)
library(xlsx)
for(n in file.numbers){
print("")
tabNum <- n
dat <- read.delim(paste("supp_tables/SUPPLEMENTARY_TABLE_",toString(tabNum),".txt", sep=""),
fill=NA, header=T, stringsAsFactors=F, na.strings = "NA")
library(xlsx)
}
library(xlsx)
clear()
clear