GGplot is refusing to change the colors of my row annotation-CodePudding

There are some issues with my ggplot chart that I can't seem to fix.

# as you may geuss from the file name I have provided this matrix below
vis.matrix <- read.csv("csvfileprovidedbelow.csv")
    
# setting up annotation_row
cell_df <- data.frame ("Cells" = c(rep("Putative Engram Cell", 10), rep("Random Cell",10))
    )
rownames(cell_df) <- rownames(vis.matrix)
cell_df$Cells <- as.factor(cell_df$Cells)
    
#setting up colors
newCols <- colorRampPalette(grDevices::rainbow(length(unique(cell_df$Cells))))
annoCol <- c("2AFE00", "ACACAC") # green and grey
names(annoCol) <- levels(cell_df$Cells)
annoCol <- list(category = annoCol)
    
color=colorRampPalette(c("navy", "white", "red"))(50)
        
#plotting
pheatmap(vis.matrix,cluster_rows = F, cluster_cols=F, annotation_row = cell_df,
                 annotation_names_col = F, scale = "column", color = color, 
                 annotation_row_colors = annoCol,
                 show_rownames = F)

Result For some reason the Cells are not the colors I selected, you can search those colors here:

Variables as csv's for reproduction(copy and paste!)

vis.matrix is here:

"","LINGO1","ARC","INHBA","BDNF","MAPK4","ADGRL3","PTGS2","CHGB","BRINP1","KCNK1"
"P57_CATCGGGCATGTCGAT",-0.368245729284319,3.47987283505039,2.94634318740768,5.57309275653906,1.28904872906168,5.3650511213102,-0.368245729284319,2.25850383984707,4.60363764575367,-0.368245729284319
"P57_GAAGCAGGTAAAGGAG",-0.384074162377759,4.36118508997518,3.70326968156081,4.89874111968957,1.65959775959153,4.36118508997518,-0.384074162377759,-0.384074162377759,4.89874111968957,2.85506919772029
"P57_TGACTTTTCTTTACAC",-0.357194851773428,2.40812492004642,3.13225019258772,5.67855340720666,-0.357194851773428,3.13225019258772,-0.357194851773428,4.87697271476829,1.38752767040715,-0.357194851773428
"P57_CTAGAGTGTCCGACGT",1.50110424640379,3.34315724311024,2.57863617381809,6.67240079339861,3.34315724311024,3.93616585502151,-0.340948750302666,1.50110424640379,5.77821885172796,3.34315724311024
"P57_CCTTACGTCCAAGTAC",-0.381478022176755,4.73256922534426,2.17554560158375,6.70465771162764,1.23182426263886,3.36449387848259,-0.381478022176755,2.17554560158375,4.45842883227008,3.36449387848259
"P57_ATCCGAAGTGTGACCC",2.60172319423431,1.50562420175544,-0.36816940232616,5.57161579079479,1.50562420175544,3.37941780583703,-0.36816940232616,3.37941780583703,4.47551679831591,3.98264461101114
"P57_TCCACACAGCTCCTCT",-0.364903374339472,2.59101007342497,2.59101007342497,5.23001785519025,-0.364903374339472,3.36504411201368,-0.364903374339472,1.5000703688371,1.5000703688371,-0.364903374339472
"P57_CTGAAGTGTGCTTCTC",-0.384690873645543,3.35025193111807,2.83241374986762,4.71429931551947,3.35025193111807,3.35025193111807,-0.384690873645543,3.35025193111807,2.16480422093696,2.16480422093696
"P57_CTGATAGAGAATCTCC",1.6886646742164,2.87694996247181,-0.342722443403036,7.39148929746973,1.6886646742164,5.75143890945527,-0.342722443403036,5.75143890945527,4.37401237658979,-0.342722443403036
"P57_GGAGCAACATACAGCT",-0.351186802480077,1.4651606822983,1.4651606822983,5.40649850082577,-0.351186802480077,4.34400333395122,-0.351186802480077,1.4651606822983,5.09785565185506,1.4651606822983
"A57_CGTCTACCAGACGCAA",-0.229651158962319,-0.229651158962319,-0.229651158962319,-0.229651158962319,-0.229651158962319,3.72717582194343,-0.229651158962319,-0.229651158962319,-0.229651158962319,-0.229651158962319
"P57_GTTCGGGCAATGGACG",-0.269219507178484,-0.269219507178484,-0.269219507178484,-0.269219507178484,-0.269219507178484,4.26241026631276,-0.269219507178484,-0.269219507178484,-0.269219507178484,-0.269219507178484
"P56_GGTATTGTCATGTCTT",-0.294887130864939,-0.294887130864939,-0.294887130864939,-0.294887130864939,-0.294887130864939,5.06808977241301,-0.294887130864939,-0.294887130864939,-0.294887130864939,-0.294887130864939
"A67_AAATGCCAGATAGTCA",4.03836820795661,-0.211281061058977,-0.211281061058977,-0.211281061058977,-0.211281061058977,-0.211281061058977,-0.211281061058977,-0.211281061058977,-0.211281061058977,-0.211281061058977
"P76_CCCTGATAGAGGACTC",-0.507269585219581,-0.507269585219581,-0.507269585219581,1.90264065061749,-0.507269585219581,4.86614536666517,-0.507269585219581,1.40253909173334,-0.507269585219581,0.697685532698955
"P56_GATCGATTCCGTCAAA",2.00727896845415,-0.313514850319463,-0.313514850319463,2.00727896845415,-0.313514850319463,3.36485632434217,-0.313514850319463,-0.313514850319463,-0.313514850319463,-0.313514850319463
"P57_GCTGCAGCATAGGATA",2.32839123926114,-0.289105834618761,-0.289105834618761,-0.289105834618761,-0.289105834618761,2.32839123926114,-0.289105834618761,-0.289105834618761,-0.289105834618761,4.94588831314104
"P82_AGGATAACATAGGTTC",1.39699437520094,-0.501641808549684,0.696264250985952,1.39699437520094,-0.501641808549684,4.49353661848721,-0.501641808549684,-0.501641808549684,1.89417031052159,-0.501641808549684
"P82_CCAAGCGTCCGGCTTT",-0.328980171926236,-0.328980171926236,-0.328980171926236,4.08682708745919,-0.328980171926236,1.87892345776647,-0.328980171926236,-0.328980171926236,4.08682708745919,-0.328980171926236
"P57_CAGCGACCATGTCCTC",-0.316475979591103,-0.316475979591103,-0.316475979591103,2.18079240270816,-0.316475979591103,6.13886914288907,-0.316475979591103,2.18079240270816,-0.316475979591103,4.67806078500742

CodePudding user response：

pheatmap is not ggplot. It is drawn using grid graphics.

Anyway, you would pass the color specification as follows:

pheatmap(vis.matrix, cluster_rows = F, cluster_cols=F, annotation_row = cell_df,
         annotation_names_col = F, scale = "column", color = color, 
         annotation_colors = list(Cells = c("Putative Engram Cell" = "#2AFE00", 
                                            "Random Cell" = "#ACACAC")),
         show_rownames = F)