How to write partial string of X labels in italics using ggplot2?-CodePudding

I have a data frame:

                        ID   Strain value Type      Gene
182 VFG007613(gi:27366370) Strain-1     0    X      motY
183 VFG007614(gi:37679367) Strain-1     1    X      motY
184 VFG007619(gi:27364700) Strain-1     0    X      motX
185 VFG007620(gi:37681249) Strain-1     1    X      motX
186 VFG007622(gi:27364235) Strain-1     0    X       wza
187 VFG007623(gi:37678521) Strain-1     1    X       wza
188 VFG007627(gi:37678523) Strain-1     1    X       wzb
189 VFG007629(gi:27364230) Strain-1     1    X       wzc
190 VFG007630(gi:37678524) Strain-1     0    X       wzc
191 VFG007640(gi:37678525) Strain-1     0    X wbjD/wecB
192 VFG007653(gi:27364224) Strain-1     1    X      wbfY
193 VFG007654(gi:37678548) Strain-1     0    X      wbfY
194 VFG007656(gi:27364223) Strain-1     0    X wbfV/wcvB
195 VFG007657(gi:37678549) Strain-1     0    X wbfV/wcvB
196 VFG007668(gi:27367928) Strain-1     1    X     GeneA
197 VFG007669(gi:37676055) Strain-1     0    X     GeneA

The name of the genes are like wbfY, always the last letter are in upper case, so I want to plot the axis.text.x using the column Gene in italic except the upper case, something like: wbfY, wbjD/wecB, motY, motX, geneG, anynameA. It possible to use some function to plot all the text in italic( genename) except the upper case notitalic(:upper:): genenameD.

Or any way to do it ?

ggplot(mydf, aes(x=Gene, y=Strain, fill = Type, alpha = value))   
    scale_fill_manual(values = c("#336666", "#006699"))  
    geom_tile(colour = "grey79")  
    scale_alpha_identity(guide = "none")  
    coord_fixed(ratio = 2.4)  
    theme_bw()  
    theme(text = element_text(family = "Times New Roman"), # corresponde a todo en Time New Romans 
          legend.position="bottom", 
          legend.title = element_text(size = 14), # legend size title, corresponde a Genotype
          legend.text  = element_text(size = 14), # corresponde a vcgC and vcgE
          panel.grid.major = element_blank(),
          panel.grid.minor = element_blank(),
          axis.text.x = element_text(angle = 90, size = 18, hjust =1, vjust = 0.5, face = "italic"),
          axis.title.x = element_text(size = 15, face = "bold"),
          axis.text.y = element_text(angle = 0, hjust = 1, size = 12, face = "bold"),
          axis.title.y = element_text(size = 15, face = "bold")
    )

in this case all axis.text.x are all in italic but I want to avoid the upper case !!!

How can I make that ?

Thanks so much

CodePudding user response：

What you can do is split the gene is parts and use glue to make the last letter italic using element_rmarkdown from ggtext like this:

library(tidyverse)
library(stringi)
library(glue)
library(ggtext)
mydf %>%
  mutate(Gene_last_letter = stri_sub(Gene, -1, -1),
         Gene_first_letters = str_sub(Gene, 1, str_length(Gene)-1)) %>%
  mutate(Gene = glue("<i>{Gene_first_letters}</i>{Gene_last_letter}")) %>%
  ggplot(aes(x=Gene, y=Strain, fill = Type, alpha = value))   
  scale_fill_manual(values = c("#336666", "#006699"))  
  geom_tile(colour = "grey79")  
  scale_alpha_identity(guide = "none")  
  coord_fixed(ratio = 2.4)  
  theme_bw()  
  theme(text = element_text(family = "Times New Roman"), # corresponde a todo en Time New Romans 
        legend.position="bottom", 
        legend.title = element_text(size = 14), # legend size title, corresponde a Genotype
        legend.text  = element_text(size = 14), # corresponde a vcgC and vcgE
        panel.grid.major = element_blank(),
        panel.grid.minor = element_blank(),
        axis.text.x =  element_markdown(angle = 90, size = 18, hjust =1, vjust = 0.5), 
        axis.title.x = element_text(size = 15, face = "bold"),
        axis.text.y = element_text(angle = 0, hjust = 1, size = 12, face = "bold"),
        axis.title.y = element_text(size = 15, face = "bold")
  )

Output: