Ggplot2, Axis Not Showing After Using Theme(Axis.Line=Element_Line())

ggplot2 theme axis.line. axes do not connect at origin

The documentation of the element_line function lists some parameters. Of particular interest is the parameter lineend=. Default value is "butt". If you set this to "square" it fixes the issue:

ggplot(mpg, aes(displ, hwy, colour = class)) + 
    geom_point()+
    theme(axis.line = element_line(color = "black", size=3, lineend = 'square'))

ggplot2 theme_classic display x and y axes

Weirdly, I had no issue getting your first example to work exactly as you were hoping, which I can't explain. But perhaps you could try what I normally do:

ggplot(df, aes(x, y)) + 
  geom_point() + 
  theme(axis.line = element_line(colour = "black"),
        panel.grid.major = element_blank(),
        panel.grid.minor = element_blank(),
        panel.border = element_blank(),
        panel.background = element_blank()) 

Setting all theme elements blank does not affect the axis elemenets

You have put theme_bw() at the end, which over-writes your theme call. Put your custom themes at the end:

CCC %>%
  arrange(desc(CCC$GO))%>%
  ggplot(aes(x = FDR, y = GO, size = FE, color = FDR)) +
  geom_point(alpha = 0.5) +
  scale_size(range = c(5, 8), name = "Fold enrichment") + 
  scale_y_discrete(name = "GO biological process complete") +
  scale_x_continuous(name = "FDR") +
  scale_colour_gradient(low = "yellow", high = "red", name  = "FDR") +
  facet_grid(cols = vars(Facet), scales = "free") + 
  theme_bw() +
  theme(axis.title.x = element_blank(),
        axis.text.x = element_text(angle = 45, vjust = 0.5, hjust = 1))

I think it is good practice to lay out your calls to ggplot in a consistent way so that this kind of thing doesn't happen:

1. Call ggplot +
2. Geom (and stat) layers, ordered depending on which ones you want on top +
3. Scales +
4. Facets +
5. Labels and titles +
6. Global themes like theme_bw() +
7. Individual theme tweaks via theme

ggplot2 flipped y-axis bars not showing with correctly set limits

How about using geom_segement and shifting your data in the ggplot call? See this question for something similar ggplot2: Setting geom_bar baseline to 1 instead of zero:

ggplot(df) +
  geom_segment(aes(x=rownames, xend=rownames, y=-4700, yend=AIC.means), size = 10) + 
  scale_y_continuous(limits = c(-4700, -4500)) +
  coord_flip()

Data:

df <- structure(list(rownames = c("Sparse Dual Stream", "Heterogeneous Dual Stream A", 
"Heterogeneous Dual Stream B", "Dense Dual Stream", "Radical Storage", 
"Radical Sparse Comp.", "Radical Heterogeneous Comp. B", "Radical Dense Comp.", 
"Radical Heterogeneous Comp. A"), AIC.means = c(-4632.137, -4627.653, 
-4622.063, -4616.507, -4615.934, -4601.292, -4600.65, -4589.49, 
-4587.993), AIC.lci = c(-4655.353, -4650.866, -4645.194, -4639.633, 
-4639.052, -4624.428, -4623.785, -4612.632, -4611.141), AIC.uci = c(-4608.922, 
-4604.439, -4598.932, -4593.381, -4592.817, -4578.156, -4577.515, 
-4566.348, -4564.845)), .Names = c("rownames", "AIC.means", "AIC.lci", 
"AIC.uci"), row.names = c(NA, -9L), class = "data.frame")

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