I'm getting error when trying to save list of lists of plots in one pdf this way:
ggplot2::ggsave("plots.pdf",
gridExtra::marrangeGrob(grobs = unlist(plots,recursive = F), nrow=2, ncol=1),
device = "pdf",units = "in",width = 8,height = 13)
where "plots" is a list of lists of 2 plots. I hope to to plot each inner list of plots in one page. I'm using ggsave because I didn't find a solution where I can control the width and height of the plots.
> length(plots)
[1] 13
> length(plots[[1]])
[1] 2
This is the error:
Error: Can't add
themeto a theme object.
plotting code:
ggplot()+
ggplot2::geom_col(data = (merged_spec[[2]] %>%
dplyr::filter(is.na(ion))),
aes(x=mz,y=intensity_perc,color=col)) +
ggplot2::geom_pointrange(data = (merged_spec[[2]] %>%
dplyr::filter(!is.na(ion))),
aes(x=mz,y=intensity_perc,ymin=0,ymax=intensity_perc,color=col),
fatten = 3)+
ggrepel::geom_text_repel(data = merged_spec[[2]],
aes(x=mz,y=intensity_perc,color=col,label=ion),
show.legend = F,
size=3.5,nudge_y = -0.1,
#arrow = arrow(type = "closed",ends = "first",length = unit(2,"mm")),
segment.linetype = 3)+
ggplot2::geom_col(data = (merged_spec[[1]] %>%
dplyr::filter(is.na(ion))),
aes(x=mz,y=intensity_perc,color=col))+
ggplot2::geom_pointrange(data = (merged_spec[[1]] %>%
dplyr::filter(!is.na(ion))),
aes(x=mz,y=intensity_perc,ymin=0,ymax=intensity_perc,color=col), fatten = 3)+
ggrepel::geom_text_repel(data = (merged_spec[[1]] %>%
dplyr::filter(!is.na(ion))),
aes(x=mz,y=intensity_perc,color=col,label=ion),
show.legend = F,size=3.5,nudge_y = 0.1,
#arrow = arrow(angle = 45,type = "closed",ends = "first",length = unit(2,"mm")),
segment.linetype = 3)+
ggplot2::geom_hline(yintercept = 0)+
#xlim(min(rbind(syn_ions,endo_ions)$mz)-5,max(rbind(syn_ions,endo_ions)$mz)+5)+
ggplot2::scale_color_manual(values=c(colorb,colnoise,colory))+
#ggplot2::scale_x_continuous(breaks = seq(100,1200,50))+
ggplot2::scale_y_continuous(breaks = seq(-1,1,0.2), expand = expansion(mult = 0.09))+
ggplot2::scale_x_continuous(limits = c(min(rbind(syn_ions,endo_ions)$mz)-5,max(rbind(syn_ions,endo_ions)$mz)+5),breaks = seq(100,1200,100))+
ggplot2::labs(x= "m/z",y="Intensity (norm)",title = MS2Peptide,
subtitle = paste(method,"=",abs(round(corr,4))))+
ggplot2::theme_minimal(base_size = 18) +
ggplot2::theme(panel.grid = element_blank(),
panel.border = element_rect(fill=NA,size = 0.001),
axis.ticks=element_line(size = 0.001))+
ggplot2::guides(color=F,label=F,fill=F)+
# annotate(geom = "text",label="Endogenous", x = ((max.mz - min.mz)/2)-200,y=1.4,size=5)+
# annotate(geom = "text",label="Synthetic",x = ((max.mz - min.mz)/2)-200,y=-1.4,size=5)+
ggplot2::annotate(geom = "text",label="Endogenous", x = -Inf, y=Inf, hjust = -0.4, vjust = 4.7,size=5)+
ggplot2::annotate(geom = "text",label="Synthetic",x = -Inf, y=-Inf, hjust = -0.8, vjust = -3.9,size=5)+
ggplot2::annotate(geom = "text",label=pepAnno,x = seq(((max.mz - min.mz)/2)+100,((max.mz - min.mz)/2)+450,15)[1:length(pepAnno)],y=-1.4,size=5)+
ggplot2::annotate(geom = "text",label=pepAnno,x = seq(((max.mz - min.mz)/2)+100,((max.mz - min.mz)/2)+450,15)[1:length(pepAnno)],y=1.4,size=5)+
# Synthetic anno
ggplot2::geom_segment(data = annotations[[1]],
aes(x=startx,y=starty,
xend = endx, yend = endy,
color = col))+
ggplot2::annotate(geom = "text",label = annotations[[1]]$label,
x = annotations[[1]]$label_posx,y = annotations[[1]]$label_posy,
color = colory,size = 2.5)+
ggplot2::geom_segment(data = annotations[[2]],
aes(x=startx,y=starty,
xend = endx, yend = endy, color = col))+
ggplot2::geom_segment(data = annotations[[3]],
aes(x=startx,y=starty,
xend = endx, yend = endy, color = col))+
ggplot2::annotate(geom = "text",label = annotations[[3]]$label,
x = annotations[[3]]$label_posx,y = annotations[[3]]$label_posy,
color = colorb,size = 2.5)+
ggplot2::geom_segment(data = annotations[[4]],
aes(x=startx,y=starty,
xend = endx, yend = endy, color = col))+
# Endo anno
ggplot2::geom_segment(data = annotations[[5]],
aes(x=startx,y=starty,
xend = endx, yend = endy, color = col))+
ggplot2::annotate(geom = "text",label = annotations[[5]]$label,
x = annotations[[5]]$label_posx,y = annotations[[5]]$label_posy,
color = colory,size = 2.5)+
ggplot2::geom_segment(data = annotations[[6]],
aes(x=startx,y=starty,
xend = endx, yend = endy, color = col))+
ggplot2::geom_segment(data = annotations[[7]],
aes(x=startx,y=starty,
xend = endx, yend = endy, color = col))+
ggplot2::annotate(geom = "text",label = annotations[[7]]$label,
x = annotations[[7]]$label_posx,y = annotations[[7]]$label_posy,
color = colorb,size = 2.5)+
ggplot2::geom_segment(data = annotations[[8]],
aes(x=startx,y=starty,
xend = endx, yend = endy, color = col))
Any help will be greatly appreciated! Thanks!
