Bringing one line to front and change to dashed-CodePudding

I am trying to edit my current code to bring the "ECHO Fit" (see below) line to the front and make it "longdash". All colors and other line formats stay the same.

Extra: I'm actually also trying to get rid of the "size 0.5" from the graph and have x-axis ticks every 12 units (first tick at 12 and last tick at 72)...if anyone can help with that issue as well.

Here is what my dataframe looks like:

  gene_id       X12        X14        X16        X18        X20        X22          X24          X26        X28        X30
1     Rep2 0.7736722  0.4895358 -0.1152436 -0.5861007 -0.5185535 -0.4028582 -0.209116905  0.043706646 -0.0558864 -0.3015712
2     Rep3 0.2103065 -0.1527386 -0.4639241 -0.3344614  0.1491652  0.3355411  0.003713116 -0.466451880 -0.4138540  0.2252987
3 ECHO Fit 1.0061474  0.4496992 -0.1188764 -0.5488580 -0.7423424 -0.6742235 -0.390867010  0.009849424  0.4098608  0.7041348
         X32       X34       X36       X38         X40        X42        X44        X46         X48         X50         X52
1 0.06774353 0.5337989 0.7879655 0.9193020 -0.07623785 -0.8137335 -0.5964319 -0.7249979 -0.69457607 -0.32543356 -0.02661936
2 0.61276259 0.6278027 0.7112873 0.5867178 -0.03538973 -0.4893360 -0.5010887 -0.2860915  0.04822184 -0.08333534 -0.43714633
3 0.82685230 0.7644355 0.5534309 0.2654520 -0.01545444 -0.2162454 -0.2928780 -0.2387261 -0.08225048  0.12429807  0.32119703
         X54        X56        X58        X60       X62         X64         X66         X68          X70         X72
1  0.3506349  0.4740629  0.4997113 0.73874098 0.5660296 -0.08397613 -0.23776407  0.14677824 -0.019013891 -0.55853824
2 -0.4050637 -0.2733731 -0.1443974 0.05656335 0.4104595  0.45333028  0.01404726 -0.12725196 -0.000176578  0.07900585
3  0.4577582  0.5046638  0.4593446 0.34374438 0.1958867  0.05813341 -0.03441813 -0.06236729 -0.025399781  0.05970666

This is what my graph currently looks like:

Here is my code:

library(tidyverse)
Graph4_Clock <- read.csv("Graph4_Clock.csv")

Graph4_Clock |>
  pivot_longer(cols = contains("X"), names_to = "HPS", values_to = "Zscore")|>
  mutate(HPS = parse_number(HPS))|>
  ggplot(aes(x = HPS, y = Zscore, color = gene_id)) 
  geom_point() 
  geom_line(aes(group=gene_id,size=.5,)) 
  ggtitle("Clock") 
  scale_color_manual(values = c("black", "orange", "blue")) 
  theme_bw() 
  theme(legend.position = "bottom", axis.text = element_text(size = 20), axis.text.x = element_text(size = 20), axis.text.y = element_text(size = 20), axis.title = element_text(size = 20), plot.title = element_text(size = 20), legend.text = element_text(size = 20), legend.direction = "horizontal")

CodePudding user response：

Three things:

To guarantee the z-level (which is "on top" on the plot), one really needs to plot each group of lines separately, where the last plotted is "on top"; we can use data=~subset(., gene_id=...) for this, and using two geom_line layers.
I'm moving size=0.5 out of the aes(.) so that it does not create a singleton legend. This brings the lines to the actual width you expect (the literal 0.5, vice a categorical variable that is the same, "0.5", for all lines).
Setting "longdash" is easy enough by adding linetype=gene_id (to both geom_lines).
Controlling the x-axis is done with scale_x_continuous(breaks=.).
I took the liberty of: adding names to your scale_color_manual so that the color/linetype legends would combine; adding guides(.) to make the legend lines thicker, just a thought, not required.
FYI, geom_point() is completely masked ...

Graph4_Clock |>
  pivot_longer(cols = contains("X"), names_to = "HPS", values_to = "Zscore")|>
  mutate(HPS = readr::parse_number(HPS)) |>
  ggplot(aes(x = HPS, y = Zscore, color = gene_id))  
  # geom_point()   # doing nothing here, covered by the lines
  geom_line(aes(group=gene_id, linetype=gene_id), size = 0.5, data = ~ subset(., gene_id != "ECHO Fit"))  
  geom_line(aes(group=gene_id, linetype=gene_id), size = 0.5, data = ~ subset(., gene_id == "ECHO Fit"))  
  ggtitle("Clock")  
  scale_color_manual(values = c("Rep2" = "black", "Rep3" = "orange", "ECHO Fit" = "blue"))  
  scale_linetype_manual(values = c("Rep2" = "solid", "Rep3" = "solid", "ECHO Fit" = "longdash"))  
  scale_x_continuous(breaks = seq(12, 72, by = 5))  
  theme_bw()  
  guides(color = guide_legend(override.aes = list(size = 2)))  
  theme(
    legend.position = "bottom",
    axis.text = element_text(size = 20), axis.text.x = element_text(size = 20),
    axis.text.y = element_text(size = 20), axis.title = element_text(size = 20),
    plot.title = element_text(size = 20),
    legend.text = element_text(size = 20), legend.direction = "horizontal")

Data

Graph4_Clock <- structure(list(gene_id = c("Rep2", "Rep3", "ECHO Fit"), X12 = c(0.7736722, 0.2103065, 1.0061474), X14 = c(0.4895358, -0.1527386, 0.4496992), X16 = c(-0.1152436, -0.4639241, -0.1188764), X18 = c(-0.5861007, -0.3344614, -0.548858), X20 = c(-0.5185535, 0.1491652, -0.7423424), X22 = c(-0.4028582, 0.3355411, -0.6742235), X24 = c(-0.209116905, 0.003713116, -0.39086701), X26 = c(0.043706646, -0.46645188, 0.009849424), X28 = c(-0.0558864, -0.413854, 0.4098608), X30 = c(-0.3015712, 0.2252987, 0.7041348),      X32 = c(0.06774353, 0.61276259, 0.8268523), X34 = c(0.5337989, 0.6278027, 0.7644355), X36 = c(0.7879655, 0.7112873, 0.5534309), X38 = c(0.919302, 0.5867178, 0.265452), X40 = c(-0.07623785, -0.03538973, -0.01545444), X42 = c(-0.8137335, -0.489336, -0.2162454), X44 = c(-0.5964319, -0.5010887, -0.292878), X46 = c(-0.7249979, -0.2860915, -0.2387261), X48 = c(-0.69457607, 0.04822184, -0.08225048), X50 = c(-0.32543356, -0.08333534, 0.12429807), X52 = c(-0.02661936, -0.43714633, 0.32119703), X54 = c(0.3506349,      -0.4050637, 0.4577582), X56 = c(0.4740629, -0.2733731, 0.5046638), X58 = c(0.4997113, -0.1443974, 0.4593446), X60 = c(0.73874098, 0.05656335, 0.34374438), X62 = c(0.5660296, 0.4104595, 0.1958867), X64 = c(-0.08397613, 0.45333028, 0.05813341), X66 = c(-0.23776407, 0.01404726, -0.03441813), X68 = c(0.14677824, -0.12725196, -0.06236729), X70 = c(-0.019013891, -0.000176578, -0.025399781), X72 = c(-0.55853824, 0.07900585, 0.05970666)), row.names = c("1", "2", "3"), class = "data.frame")