ggplot: Wie Heatmap plotten, unabhängig von der Anzahl der Variablen

Question

Mit dem data.frame unter

DATA

df <- read.table(text = c(" 
NA NA NA NA NA NA NA NA NA NA NA NA 
          0.4748 NA NA NA NA NA NA NA NA NA NA NA 
          0.905 0.5362 NA NA NA NA NA NA NA NA NA NA 
          0.0754 0.0118 0.0614 NA NA NA NA NA NA NA NA NA 
          0.8768 0.3958 0.7952 0.1034 NA NA NA NA NA NA NA NA 
          0.5708 0.2056 0.4984 0.2356 0.6736 NA NA NA NA NA NA NA 
          0.2248 0.6204 0.268 0.0014 0.183 0.0768 NA NA NA NA NA NA 
          0.483 0.9824 0.5314 0.0114 0.3906 0.1968 0.6308 NA NA NA NA NA 
          0.697 0.732 0.7604 0.0264 0.594 0.3334 0.416 0.7388 NA NA NA NA 
          0.2918 0.7286 0.3382 0.003 0.2386 0.1122 0.8712 0.7266 0.509 NA NA NA 
          0.5904 0.8352 0.6704 0.0188 0.4966 0.273 0.5192 0.8328 0.8736 0.5914 NA NA 
          0.3838 0.8768 0.4476 0.0042 0.3148 0.1498 0.7288 0.873 0.6178 0.8276 0.7432 NA 
          "), header = F) 

colnames(df) <- c("TK1", "TK2", "TK3", "TK4" , "TK5", "TK6", "TK7", "TK8", "TK9", "TK10", "TK11", "TK12") 
rownames(df) <- c("TK1", "TK2", "TK3", "TK4" , "TK5", "TK6", "TK7", "TK8", "TK9", "TK10", "TK11", "TK12") 

df 
#  TK1 TK2 TK3 TK4 TK5 TK6 TK7 TK8 TK9 TK10 TK11 TK12 
#TK1  NA  NA  NA  NA  NA  NA  NA  NA  NA  NA  NA NA 
#TK2 0.4748  NA  NA  NA  NA  NA  NA  NA  NA  NA  NA NA 
#TK3 0.9050 0.5362  NA  NA  NA  NA  NA  NA  NA  NA  NA NA 
#TK4 0.0754 0.0118 0.0614  NA  NA  NA  NA  NA  NA  NA  NA NA 
#TK5 0.8768 0.3958 0.7952 0.1034  NA  NA  NA  NA  NA  NA  NA NA 
#TK6 0.5708 0.2056 0.4984 0.2356 0.6736  NA  NA  NA  NA  NA  NA NA 
#TK7 0.2248 0.6204 0.2680 0.0014 0.1830 0.0768  NA  NA  NA  NA  NA NA 
#TK8 0.4830 0.9824 0.5314 0.0114 0.3906 0.1968 0.6308  NA  NA  NA  NA NA 
#TK9 0.6970 0.7320 0.7604 0.0264 0.5940 0.3334 0.4160 0.7388  NA  NA  NA NA 
#TK10 0.2918 0.7286 0.3382 0.0030 0.2386 0.1122 0.8712 0.7266 0.5090  NA  NA NA 
#TK11 0.5904 0.8352 0.6704 0.0188 0.4966 0.2730 0.5192 0.8328 0.8736 0.5914  NA NA 
#TK12 0.3838 0.8768 0.4476 0.0042 0.3148 0.1498 0.7288 0.8730 0.6178 0.8276 0.7432 NA 

Ich kann nicht die Eingabedaten ändern. Ich werde es in diesem Format mit verschiedenen Variablen jedes Mal basierend auf dem Benutzer erhalten.

verwendete ich den Code eine neue Variable erstellen Relationshipdf von breiten zu langen Format zu übertragen, dann die angeordneten Ebenen der Relation1 und Relationship Variablen dank akrun's answer to this question. Schließlich habe ich die Heatmap wie unten

gezeigt

trial <- df 
trial$Relationship <- rownames(df) 
trial1 <- subset(trial, select = c(13, 1, 2, 3,4,5,6,7,8,9,10,11,12)) 

df2 <- gather(trial1, "Relation1", "Strength", 2:13) 

df2 <- df2 %>% 
    dplyr::mutate(Strength1 = round(Strength, digits = 2))%>% 
    dplyr::select(Relationship,Relation1, Strength1) 

df3 <- df2 %>% 
    extract(Relationship, into = c("Relationship1", "Relationship2"), "(\\D+)(\\d+)", 
      remove = FALSE, convert=TRUE) %>% 
    mutate(Relationship = factor(Relationship, levels = paste0(Relationship1[1], 
                  min(Relationship2):max(Relationship2)))) %>% 
    select(-Relationship1, -Relationship2) %>% 
    extract(Relation1, into = c("Relation11", "Relation12"), "(\\D+)(\\d+)", 
      remove = FALSE, convert=TRUE) %>% 
    mutate(Relation1 = factor(Relation1, levels = paste0(Relation11[1], 
                 min(Relation12):max(Relation12)))) %>% 
    select(-Relation11, -Relation12) 


df3$Relation1 = with(df3, factor(Relation1, levels = rev(levels(Relation1)))) 


ggheatmap <- ggplot(df3, aes(Relationship, Relation1, fill = Strength1))+ 
    geom_tile(color = "white")+ 
    scale_fill_gradient2(low = "red", high = "green", mid = "lightgreen", 
         midpoint = 0.5, limit = c(0,1), space = "Lab", 
         name="Correlation") + theme_minimal() 

ggheatmap + 
    geom_text(aes(Relationship, Relation1, label = Strength1), color = "black", size = 4) + 
    labs(x = expression(""), 
     y=expression("")) 

RESULT

Frage

ich dynamisch den Plotten von Heatmap machen wollen. Unabhängig von der Anzahl der Variablen und Beobachtungen kann eine Heatmap gezeichnet werden, ohne dass der Code für eine andere Anzahl von Variablen geändert werden muss.

Gibt es das überhaupt zu tun?

Answer 1

library(ggplot2) 
library(tidyr) 
library(dplyr) 

Dieser Codeblock arbeitet unabhängig von der Anzahl der Spalten und Zeilen gibt

df <- 
    df %>% 
    mutate(Relationship = rownames(.)) %>% #Replaces trial$Relationship <- rownames(df) 
    select(Relationship, everything()) %>% #Replaces trial1 <- subset(trial, select = c(13, 1, 2, 3,4,5,6,7,8,9,10,11,12)) 
    gather('Relation1', 'Strength', -1) %>% #Replaces df2 <- gather(trial1, "Relation1", "Strength", 2:13) 
    mutate(Strength = round(Strength, digits = 2)) 

Der Codeblock unten sind, ist ein prägnanter Weise die Faktorstufen für die Spalten des Erhaltens

# Order Relatinoship variables by numeric suffix 
# Since its a square matrix you only have to do it once for both columns 

factorLevels <- 
    df %>% 
    select(Relationship) %>% 
    distinct() %>% 
    extract(Relationship, into = c("TK", "num"), "(\\D+)(\\d+)", 
      remove = FALSE, convert=TRUE) %>% 
    arrange(num) %>% 
    select(Relationship) 

df <- 
    df %>% 
    mutate(Relationship = factor(Relationship, levels = factorLevels$Relationship), 
     Relation1 = factor(Relation1, levels = rev(factorLevels$Relationship))) 

Modifizierter Zeichencode

ggheatmap <- ggplot(df, aes(Relationship, Relation1, fill = Strength))+ 
    geom_tile(color = "white")+ 
    scale_fill_gradient2(low = "red", high = "green", mid = "lightgreen", 
         midpoint = 0.5, limit = c(0,1), space = "Lab", 
         name="Correlation") + theme_minimal() 

ggheatmap + 
    geom_text(aes(Relationship, Relation1, label = Strength), color = "black", size = 4) + 
    labs(x = expression(""), 
     y=expression("")) 

Answer 2

In diesem Fall fühle ich Ihre Annäherung umständlich (ich bezog mich auf heatmap with values (ggplot2)). Dieser Code benötigt nur Spaltennamen (df) und rownames (df).

library(reshape2); library(ggplot2) 

df2 <- melt(as.matrix(df), id.var = names(df)[1]) # as.matrix() fixes colnames of long df. 
df2$Var2 <- with(df2, factor(Var2, levels=rev(levels(Var2)))) 

ggheatmap <- ggplot(df2, aes(Var1, Var2, fill=value)) + 
    geom_tile(color = "white")+ 
    scale_fill_gradient2(low = "red", high = "green", mid = "lightgreen", 
         midpoint = 0.5, limit = c(0,1), space = "Lab", 
         name="Correlation") + theme_minimal() 

ggheatmap + 
    geom_text(aes(label = round(value, 2)), color = "black", size = 4) + 
    labs(x = expression(""), y=expression(""))