CODEWITHSUNDEEP
rplot
Shaxi Liver
Shaxi Liver

Reputation: 1120

How to make the graph easier to read ? Editing plot

I would like to ask you for the suggestions how I can edit my plot function to make my graph more clear ?

Here I show you the code which I use for plotting:

# open the pdf file
pdf(file='LSF1_PWD_GWD.pdf')
a <- c('LSF1', 'PWD', 'GWD')
rowsToPlot<-c(1066,2269,109)
matplot(as.matrix(t(tbl_alles[rowsToPlot,])),type=rep("l", length(rowsToPlot)), col=rainbow(length(rowsToPlot)),xlab = 'Fraction Size', ylab = 'Intensity')
legend('topright',a,lty=1, bty='n', cex=.75, col = rainbow(length(rowsToPlot)))
# close the pdf file
dev.off()

and that's how the graph looks like:

Graph

It's just a basic plot because I have no idea how to edit it. The arrow indicates three lines on one position which you can't see because they overlap... and that's the most important part of this graph for me. Maybe I shouldn't use dotted line ? How to change it ?

Data:

tbl_alles <- 
  structure(list("10" = c(0, 0, 0, 0, 0, 0),
               "20" = c(0, 0, 0, 0, 0, 0),
               "52.5" = c(0, 0, 0, 0, 0, 0),
               "81" = c(0, 0, 1, 0, 0, 0),
               "110" = c(0, 0, 0, 0, 0, 0),
               "140.5" = c(0, 0, 0, 0, 0, 0),
               "189" = c(0, 0, 0, 0, 0, 0),
               "222.5" = c(0, 0, 0, 0, 0, 0 ),
               "278" = c(0, 0, 0, 0, 0, 0),
               "340" = c(0, 0, 0, 0, 0, 0),
               "397" = c(0, 1, 0, 0, 0, 0),
               "453.5" = c(0, 0.66069369, 0, 0, 0, 1),
               "529" = c(0, 0.521435654, 0, 0, 1, 0),
               "580" = c(0, 0.437291195, 0, 0, 1, 0),
               "630.5" = c(0, 0.52204783, 0, 0, 0, 0),
               "683.5" = c(0, 0.52429838, 0, 0, 0, 0),
               "735.5" = c(1, 0.3768651, 0, 1, 0, 0),
               "784" = c(0, 0, 0, 0, 0, 0),
               "832" = c(0, 0, 0, 0, 0, 0),
               "882.5" = c(0, 0, 0, 0, 0, 0),
               "926.5" = c(0, 0, 0, 0, 0, 0),
               "973" = c(0, 0, 0, 0, 0, 0),
               "1108" = c(0, 0, 0, 0, 0, 0),
               "1200" = c(0, 0, 0, 0, 0, 0)),
          .Names = c("10", "20", "52.5", "81",
                     "110", "140.5","189", "222.5",
                     "278", "340", "397", "453.5",
                     "529", "580", "630.5", "683.5",
                     "735.5", "784", "832", "882.5",
                     "926.5", "973", "1108", "1200"),
          row.names = c("at1g01050.1", "at1g01080.1",
                        "at1g01090.1","at1g01220.1",
                        "at1g01420.1", "at1g01470.1"),
          class = "data.frame")

RowsToPlot:

> dput(tbl_alles[rowsToPlot,])
structure(list(`10` = c(0, 0, 0), `20` = c(0, 0, 0), `52.5` = c(0, 
0, 0), `81` = c(0, 0, 0), `110` = c(0, 0, 0), `140.5` = c(0, 
0, 0), `189` = c(0, 0, 0), `222.5` = c(0, 0, 0), `278` = c(0, 
0, 0), `340` = c(0, 0, 0), `397` = c(0, 0, 0), `453.5` = c(0, 
0, 0), `529` = c(0, 0, 0), `580` = c(0, 0, 0), `630.5` = c(0, 
0, 0), `683.5` = c(0, 0, 0.57073483), `735.5` = c(0, 1, 0.85691826
), `784` = c(0, 0, 0.90706982), `832` = c(1, 1, 1), `882.5` = c(0, 
0, 0), `926.5` = c(0, 0, 0), `973` = c(0, 0, 0), `1108` = c(0, 
0, 0), `1200` = c(0, 0, 0)), .Names = c("10", "20", "52.5", "81", 
"110", "140.5", "189", "222.5", "278", "340", "397", "453.5", 
"529", "580", "630.5", "683.5", "735.5", "784", "832", "882.5", 
"926.5", "973", "1108", "1200"), row.names = c("at3g01510.1", 
"at5g26570.1", "at1g10760.1"), class = "data.frame")

Upvotes: 1

Views: 360

Answers (5)

Heather Turner
Heather Turner

Reputation: 3314

Since you have a discrete number of x values, I suggest using a barplot instead. This will make the categories easier to distinguish and highlight the aspect you are most interested in.

First put the data in long format

dat <- structure(list(`10` = c(0, 0, 0), `20` = c(0, 0, 0), `52.5` = c(0, 0, 0), 
                 `81` = c(0, 0, 0), `110` = c(0, 0, 0), `140.5` = c(0, 0, 0), 
                 `189` = c(0, 0, 0), `222.5` = c(0, 0, 0), `278` = c(0, 0, 0), 
                 `340` = c(0, 0, 0), `397` = c(0, 0, 0), `453.5` = c(0, 0, 0), 
                 `529` = c(0, 0, 0), `580` = c(0, 0, 0), `630.5` = c(0, 0, 0), 
                 `683.5` = c(0, 0, 0.57073483), `735.5` = c(0, 1, 0.85691826), 
                 `784` = c(0, 0, 0.90706982), `832` = c(1, 1, 1), 
                 `882.5` = c(0, 0, 0), `926.5` = c(0, 0, 0), `973` = c(0, 0, 0), 
                 `1108` = c(0, 0, 0), `1200` = c(0, 0, 0)), 
                 .Names = c("10", "20", "52.5", "81", "110", "140.5", "189", 
                            "222.5", "278", "340", "397", "453.5", "529", "580", 
                            "630.5", "683.5", "735.5", "784", "832", "882.5", 
                            "926.5", "973", "1108", "1200"), 
             row.names = c("at3g01510.1", "at5g26570.1", "at1g10760.1"), 
             class = "data.frame")

library(tidyr)
dat$rowname <- rownames(dat)
ggdat <- gather(dat, key = "colname", value = "Intensity", -rowname)

Then create the barplot using ggplot2

library(RColorBrewer)
library(ggplot2)
colors <- brewer.pal(nrow(dat), "Dark2")
ggplot(data = ggdat, aes(x = colname, y = Intensity, fill = rowname)) +
    geom_bar(aes(color = rowname), stat = "identity", 
             position = position_dodge(), width = 0.75) +
    scale_fill_manual(values = colors) + 
    scale_color_manual(values = colors) +
    theme(axis.title.x = element_blank(),
          axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5),
          legend.position = "bottom")

enter image description here

The code could be used for more than 3 rows, although the bars will get harder to distinguish with more categories. If this is a problem, you could consider dropping/binning x values, or perhaps splitting the plot into two:

ggdat$group <- factor(ggdat$colname %in% colnames(dat)[1:12],
                      levels = c(TRUE, FALSE), labels = c("Low x", "High x"))
ggplot(data = ggdat, aes(x = colname, y = Intensity, fill = rowname)) +
    geom_bar(aes(color = rowname), stat = "identity", 
             position = position_dodge(), width = 0.75) +
    scale_fill_manual(values = colors) + 
    scale_color_manual(values = colors) +
    theme(axis.title.x = element_blank(),
          axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5),
          legend.position = "bottom") + 
    facet_wrap(~ group, ncol = 1, scales = "free_x")

enter image description here

Upvotes: 1

arvi1000
arvi1000

Reputation: 9592

Okay, here's a way to distinguish the lines clearly, while keeping everything on one plot. I use non solid linetypes and different sizes to 'make room' for the overlayed lines.

library(reshape2)
library(ggplot2)

dat <- as.data.frame(as.matrix(t(tbl_alles)))
dat$x <- as.numeric(row.names(dat))

ggplot(melt(dat, id.vars='x'),  aes(x=x, y=value, group=variable)) +
  geom_line(aes(color=variable, linetype=variable, size=variable)) +

  scale_linetype_manual(values=c('solid', 'dotted', 'dashed')) +
  scale_size_manual(values=c(1,3,1)) +
  scale_color_manual(values=c('black', 'red', 'white')) +

  theme(axis.text = element_text(color='black'),
        panel.background = element_rect('grey'),
        legend.key = element_rect('grey'),
        panel.grid = element_blank()) +

  labs(title='This is not a pretty chart, but you can make out the lines')

enter image description here

I took as a starting point your data from the dput you pasted above:

tbl_alles <- structure(list(`10` = c(0, 0, 0), `20` = c(0, 0, 0), `52.5` = c(0, 0, 0), `81` = c(0, 0, 0), `110` = c(0, 0, 0), `140.5` = c(0, 0, 0), `189` = c(0, 0, 0), `222.5` = c(0, 0, 0), `278` = c(0, 0, 0), `340` = c(0, 0, 0), `397` = c(0, 0, 0), `453.5` = c(0, 0, 0), `529` = c(0, 0, 0), `580` = c(0, 0, 0), `630.5` = c(0, 0, 0), `683.5` = c(0, 0, 0.57073483), `735.5` = c(0, 1, 0.85691826), `784` = c(0, 0, 0.90706982), `832` = c(1, 1, 1), `882.5` = c(0, 0, 0), `926.5` = c(0, 0, 0), `973` = c(0, 0, 0), `1108` = c(0, 0, 0), `1200` = c(0, 0, 0)), .Names = c("10", "20", "52.5", "81", "110", "140.5", "189", "222.5", "278", "340", "397", "453.5", "529", "580", "630.5", "683.5", "735.5", "784", "832", "882.5", "926.5", "973", "1108", "1200"), row.names = c("at3g01510.1", "at5g26570.1", "at1g10760.1"), class = "data.frame")

Upvotes: 3

Cath
Cath

Reputation: 24074

You can try to play with the line types but this can become really difficult if you have too much lines to see : is 3 the maximum you'll have ? Else, you may consider another way to draw your data.

Here is an example with your data, when I plot it, I can see the 3 lines :

matplot(as.matrix(t(tbl_alles[rowsToPlot,])),type="l",lwd=2,lty=c("solid","48","36"), col=rainbow(length(rowsToPlot)),xlab = 'Fraction Size', ylab = 'Intensity')
legend('topright',c('LSF1', 'PWD', 'GWD'),lty=c("solid","48","36"),lwd=2, bty='n', cex=.75, col = rainbow(length(rowsToPlot)))

the 3 line types :

solid: this is the default type, as you already know...

48: first 4 units of line then a blank of 8 units

36: first 3 units of line then a blank of 6 units.

I also changed the width of the line with lwd=2.

There is another parameter to play with : transparency.

If (keeping the different lty) you change the colors to c("#FF000030","#0000FF50","#00FF0080") for example, it will be easier to see every lines (the two last characters of each hexadecimal code specify the transparency).

If you use transparency, then you can even specify a unique color and ovelapping lines will appear darker : for example, col=#00000044".

Upvotes: 0

Mitch
Mitch

Reputation: 702

How many records does the dataset have? It seems you are dealing with an overplotting issue. Follow @Nikos method to tidy the data.

Use size and alpha to change the size and transparency of the line.

ggplot(data = X.dt, aes(x = X, y = value, group = variable, color = variable)) +
geom_line(data = X.dt, aes(x = X, y = value, group = variable, color = variable), 
size = 3, alpha = .25)

The color of the line changes as they overlap. However this will only work for smaller datasets. My only other suggestion is to overlay geom_line() with geom_point() that will plot points over the lines. You can use position = position_jitter() to slightly augment the position of the points, that way if they overlap you can see where they overlap.

ggplot(data = X.dt, aes(x = X, y = value, group = variable, color = variable)) +
geom_point(position = position_jitter(w = 0.001, h = 0.02), size = 3, alpha = .5) +
geom_line(data = X.dt, aes(x = X, y = value, group = variable, color = variable), size = 1, alpha = .25)

Upvotes: 0

Nikos
Nikos

Reputation: 3297

This is most certainly not what you need, but perhaps it can give you another idea.

X=structure(list(`10` = c(0, 0, 0), `20` = c(0, 0, 0), `52.5` = c(0, 
0, 0), `81` = c(0, 0, 0), `110` = c(0, 0, 0), `140.5` = c(0, 
0, 0), `189` = c(0, 0, 0), `222.5` = c(0, 0, 0), `278` = c(0, 
0, 0), `340` = c(0, 0, 0), `397` = c(0, 0, 0), `453.5` = c(0, 
0, 0), `529` = c(0, 0, 0), `580` = c(0, 0, 0), `630.5` = c(0, 
0, 0), `683.5` = c(0, 0, 0.57073483), `735.5` = c(0, 1, 0.85691826
), `784` = c(0, 0, 0.90706982), `832` = c(1, 1, 1), `882.5` = c(0, 
0, 0), `926.5` = c(0, 0, 0), `973` = c(0, 0, 0), `1108` = c(0, 
0, 0), `1200` = c(0, 0, 0)), .Names = c("10", "20", "52.5", "81", 
"110", "140.5", "189", "222.5", "278", "340", "397", "453.5", 
"529", "580", "630.5", "683.5", "735.5", "784", "832", "882.5", 
"926.5", "973", "1108", "1200"), row.names = c("at3g01510.1", 
"at5g26570.1", "at1g10760.1"), class = "data.frame");

library(ggplot2)
library(reshape2)
library(data.table)

X.dt<-as.data.table(t(X))
X.dt[,X:=1:dim(X.dt)[1]]
X.dt<-melt(X.dt, id='X')
ggplot(X.dt,aes(X, value,group=variable,color=variable))+
 geom_line()+
 facet_wrap(~variable, nrow=3)+
 guides(color=FALSE)+labs(x="X",y="Intensity")

enter image description here

Upvotes: 1

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