I used the answer in this question to remove the main plot to get the legend and then attach the legend to the main plot while keeping the original legend, but the plot shifted to the left (I can tell because I can see the second legend showing on the right corner), how can I bring it back? see photo here:
I added at the end of the code these lines:
legend <- cowplot::get_legend(legend1)
grid.newpage()
grid.draw(legend)
After assigning the second legend to merge with the plot.
library(dplyr, warn.conflicts = FALSE)
library(tidyverse, warn.conflicts = FALSE)
library(stringr, warn.conflicts = FALSE)
library(matrixStats, warn.conflicts = FALSE)
library(pheatmap, warn.conflicts = FALSE)
library(heatmaps, warn.conflicts = FALSE)
library(ggplot2, warn.conflicts = FALSE)
library(grid, warn.conflicts = FALSE)
library(gridExtra, warn.conflicts = FALSE)
dfc <- read.csv(url("https://github.com/learnseq/learning/raw/main/GSE133399_Fig2_FPKM.csv"))
values <- c('S100a10', 'Esm1', 'Itgb1', 'Anxa2', 'Hist1h1b',
'Il2rb', 'Lgals1', 'Mki67', 'Rora', 'S100a4',
'S100a6', 'Adam8', 'Areg', 'Bcl2l1', 'Calca',
'Capg', 'Ccr2', 'Cd44', 'Csda', 'Ehd1',
'Id2', 'Il10', 'Il1rl1', 'Il2ra', 'Lmna',
'Maf', 'Penk', 'Podnl1', 'Tiam1', 'Vim',
'Ern1', 'Furin', 'Ifng', 'Igfbp7', 'Il13',
'Il4', 'Il5', 'Nrp1', 'Ptprs', 'Rbpj',
'Spry1', 'Tnfsf11', 'Vdr', 'Xcl1', 'Bmpr2',
'Csf1', 'Dst', 'Foxp3', 'Itgav', 'Itgb8',
'Lamc1', 'Myo1e', 'Pmaip1', 'Prdm1', 'Ptpn5',
'Ramp1', 'Sdc4')
dfg <- dfc %>% slice(match(rev(values), tracking_id))
dfg$CD44low_rep <- rowMeans(dfg[,c('CD44low_rep1', 'CD44low_rep2')], na.rm=TRUE)
dfg$CD44hi_CD69low_rep <- rowMeans(dfg[,c('CD44hi_CD69low_rep1', 'CD44hi_CD69low_rep2')], na.rm=TRUE)
dfg$CD44hi_CD69hi_CD103low_rep <- rowMeans(dfg[,c('CD44hi_CD69hi_CD103low_rep1', 'CD44hi_CD69hi_CD103low_rep2')], na.rm=TRUE)
dfg$CD44hi_CD69hi_CD103hi_rep <- rowMeans(dfg[,c('CD44hi_CD69hi_CD103hi_rep1', 'CD44hi_CD69hi_CD103hi_rep2')], na.rm=TRUE)
rownameshm <-paste(dfg[,1])
colnameshm <- paste(dQuote(colnames(dfg[0, 10:13])), collapse = ", ")
dfg$Mean <- rowMeans(dfg[,10:13])
dfg$sd <- rowSds(as.matrix(dfg[,10:13]))
zScore <- function(p){
for(n in 10:13){
p[[n]]=(as.numeric(p[[n]])-as.numeric(p[[14]]))/as.numeric(p[[15]])
}
return(p)
}
Matrix_zScore <- t(apply(dfg,1,zScore))
Matrix_zScore_temp <- mapply(Matrix_zScore[,10:13], FUN=as.numeric)
Matrix_zScore_temp <- matrix(data=Matrix_zScore_temp, ncol=4, nrow=57)
Matrix_zScore_temp1<-as.data.frame(Matrix_zScore_temp)
rownames(Matrix_zScore_temp) <- dfg$tracking_id
plot_frame <- reshape2::melt(Matrix_zScore_temp)
library(repr, warn.conflicts = FALSE)
options(repr.plot.width=5, repr.plot.height=8.5)
zmapp023 <- ggplot(plot_frame, aes(Var2, Var1, fill = value)) +
geom_tile(color = "white", position = position_dodge(), show.legend = TRUE) +
geom_point(data = data.frame(Var2 = 1:4, Var1 = -1, value = 0), size = 5,
aes(color = factor(Var2))) +
geom_point(data = data.frame(Var2 = 1:4, Var1 = 0, value = 1), alpha = 0) +
scale_color_manual(values = c("black", "forestgreen", "#DE2D29", "#3C57A8"),
labels = c(expression(
CD44^{lo}~"T Cells",
CD44^{hi}~CD69^{lo}~"T Cells",
CD44^{hi}~CD69^{hi}~CD103^{lo}~"T Cells",
CD44^{hi}~CD69^{hi}~CD103^{hi}~"T Cells")),
guide = guide_legend(override.aes = list(fill = NA), label.hjust = 0, position="bottom", size = 5 )) +
scale_y_discrete(position = "right") +
labs(y = "", fill = "", color = " ", x = "") +
scale_fill_gradientn(colors = c("#3C57A8", "white", "#DE2D29"),
breaks = c(1.5, 0, -1.5),
labels = c("1.0", "0", "-1.0"),
limits = c(-1.5, 1.5),
space = "Lab",
guide = "colourbar",
aesthetics = "fill") +
theme_minimal() + guides(colour=FALSE) +
theme (panel.grid.major = element_blank(),
axis.text.y.right = element_text(margin = margin(l = unit(-5, "cm"))),
axis.text.y = element_text(face="italic", size=9,
color="black"),
legend.justification = c(-0.9, 0),
legend.direction = "vertical",
legend.key.size = unit(0.6, "cm"),
legend.key.width = unit(0.2,"cm"),
legend.title.align = 0.5,
axis.text.x = element_blank(),plot.margin = unit(c(1,1,5,1), "lines")) +
guides(
fill = guide_colourbar(
title = "Relative gene expression \n (z score)",
title.position = "right",
title.theme = element_text(angle = -90, size = 7.5),
direction = "vertical",
ticks = FALSE)) +
coord_cartesian( # This focuses the x-axis on the range of interest
clip = 'off')
legend1 <- ggplot(plot_frame, aes(Var2, Var1)) +
geom_point(data = data.frame(Var2 = 1:4, Var1 = 0, value = 0), size = 5,
aes(color = factor(Var2))) +
geom_point(data = data.frame(Var2 = 1:4, Var1 = 0, value = 1), alpha = 0) +
scale_color_manual(values = c("black", "forestgreen", "#DE2D29", "#3C57A8"),
labels = c(expression(
CD44^{lo}~"T Cells",
CD44^{hi}~CD69^{lo}~"T Cells",
CD44^{hi}~CD69^{hi}~CD103^{lo}~"T Cells",
CD44^{hi}~CD69^{hi}~CD103^{hi}~"T Cells")),
guide = guide_legend(override.aes = list(fill = NA), label.hjust = 0, size = 1 )) +
theme (panel.grid.major = element_blank(),
axis.text.y.right = element_text(margin = margin(l = unit(-5, "cm"))),
axis.text.y = element_text(face="italic", size=9,
color="black"),
legend.justification = c(-0.5, 0),
legend.direction = "vertical",
legend.key.size = unit(0.1, "cm"),
legend.key.width = unit(0.2,"cm"),
legend.title.align = 0.5,
axis.text.x = element_blank())
legend <- cowplot::get_legend(legend1)
grid.newpage()
grid.draw(legend)
This is what I get:
I was hoping to get something like this:
