Show X axis ticks and labels in scatterplot-CodePudding

I was building a scatterplot to correlate the abundance of certain organisms with Temperature. While building the graph I realized that the x axis values do not appear.

This is an example of how my dataset looks like:


> dput(head(abundance))
structure(list(OGA_ID = c(20L, 22L, 66L, 75L, 91L), sample_ID = structure(c(5L, 
1L, 2L, 3L, 4L), .Label = c("TARA_N010000218", "TARA_N010000238", 
"TARA_N010000911", "TARA_N010000955", "TARA_N010000980"), class = "factor"), 
    vlookup = c(2.6820250147109e-06, 4.2504952889635e-07, 3.098736273373e-07, 
    4.7282955865616e-07, 6.4437058525603e-07), relative.abundance = c(2.6820250147109e-06, 
    4.2504952889635e-07, 3.098736273373e-07, 4.7282955865616e-07, 
    6.4437058525603e-07), log = c(-5.57153717588776, -6.37156046083652, 
    -6.50881538403584, -6.32529538161919, -6.19086429282228), 
    station = structure(c(3L, 2L, 2L, 1L, 3L), .Label = c("TARA_188", 
    "TARA_205", "TARA_210"), class = "factor"), depth = structure(c(2L, 
    3L, 2L, 1L, 2L), .Label = c("DCM", "MES", "SRF"), class = "factor"), 
    size.fraction = structure(c(2L, 2L, 2L, 2L, 1L), .Label = c("[>0.8µm]", 
    "[0.8-20µm]"), class = "factor"), temperature = c(61.5754, 
    72.4693, 72.4456, 78.3555, 61.5754)), row.names = c(NA, 5L
), class = "data.frame")

This is my code:

{r, fig.width=10, fig.height=5}
library(ggplot2)

abundance_environment <- read.table('/home/agalvez/data/environmental_data/vanellid/environmental_parameters.csv', sep="\t", header=TRUE)

lineplot <- ggplot(abundance_environment, aes( x = abundance_environment$temperature...C., y = abundance_environment$log, group = abundance_environment$Depth_Nominal , colour = abundance_environment$Depth_Nominal))  
  geom_point( size =2, shape =16)   
  xlab("Temperature(ºC)")   ylab("Relative abundance")   ggtitle("Abundance-Temperature")  
  theme_minimal()  
  labs(colour = "Depth") 

  
lineplot

I do not see why the axis are hidden. Could someone help me with that?

Thanks in advance!

CodePudding user response：

I see a few issues here.

When you call your variables to map them in ggplot(aes()), you should use just the unquoted variable name (e.g. ggplot(data = mtcars, aes(x = disp)) rather than ggplot(data = mtcars, aes(x = mtcars$disp))
The variable names in the data you shared don't match what's in your ggplot call. E.g. you are calling x = abundance_environment$temperature...C. but the variable in the data you shared is called temperature. This lead me to wonder if you're accidentally plotting another version of the data that's in your environment. Perhaps just try clearing your environment and re-loading the data and plot.
When I plot your data snippet after fixing the above issues, the plot looks as I would expect with x axis values. If you are also getting this result, please clarify what you want it to look like.

library(tidyverse)

d <- structure(list(temperature = c(61.5754, 72.4693, 72.4456, 78.3555, 61.5754), log = c(-5.57153717588776, -6.37156046083652, -6.50881538403584, -6.32529538161919, -6.19086429282228), depth = structure(c(2L, 3L, 2L, 1L, 2L), levels = c("DCM", "MES", "SRF"), class = "factor")), row.names = c(NA, 5L), class = "data.frame")

d %>% 
  ggplot(aes(x = temperature, y = log, colour = depth))  
  geom_point(size =2, shape =16)   
  xlab("Temperature(ºC)")   
  ylab("Relative abundance")   
  ggtitle("Abundance-Temperature")  
  theme_minimal()  
  labs(colour = "Depth")

^{Created on 2022-09-23 by the reprex package (v2.0.1)}

CodePudding user response：

the issue with my code was that I was specifying the dimensions of the plot and this was hiding the x axis.

So I solved it by changing {r, fig.width=10, fig.height=5} by simply {r}.

Thank you a lot for yuour help.