182 lines
5.5 KiB
R
182 lines
5.5 KiB
R
colnames(str_df_short)
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table(str_df_short$effect_type)
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table(str_df_short$effect_sign)
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str(str_df_short)
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str_df_short$pe_outcome = ifelse(str_df_short$effect_sign<0, "DD", "SS")
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table(str_df_short$pe_outcome )
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table(str_df_short$effect_sign)
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affcols = c("affinity_scaled", "mmcsm_lig_scaled")
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ppi2_cols = c("mcsm_ppi2_scaled")
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#lig
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table(str_df_short$effect_type)
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str_df_short$effect_grouped = ifelse(str_df_short$effect_type%in%affcols
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, "affinity"
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, str_df_short$effect_type)
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table(str_df_short$effect_grouped)
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#ppi2
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str_df_short$effect_grouped = ifelse(str_df_short$effect_grouped%in%ppi2_cols
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, "ppi2"
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, str_df_short$effect_grouped)
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table(str_df_short$effect_grouped)
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#stability
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str_df_short$effect_grouped = ifelse(!str_df_short$effect_grouped%in%c("affinity", "ppi2")
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, "stability"
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, str_df_short$effect_grouped)
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table(str_df_short$effect_grouped)
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# create a sign as well
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str_df_short$effect_outcome = paste0(str_df_short$pe_outcome
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, str_df_short$effect_grouped)
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table(str_df_short$effect_outcome)
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pe_colour_map2 = c( "DDaffinity" = "#ffd700" # gold
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, "SSaffinity" = "#f0e68c" # khaki
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, "DDppi2" = "#ff1493" # deeppink
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, "SSppi2" = "#da70d6" # orchid
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, "DDstability " = "#ae301e"
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, "SSstability" = "#007d85"
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)
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str_df_short$effect_colours = str_df_short$effect_outcome
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str_df_short = dplyr::mutate(str_df_short
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, effect_colours = case_when(effect_colours == "DDaffinity" ~ "#ffd700"
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, effect_colours == "DDppi2" ~ '#ff1493'
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, effect_colours == "SSppi2" ~ '#da70d6'
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, effect_colours == "DDstability" ~ '#ae301e'
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, effect_colours =="SSstability" ~ '#007d85'
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, TRUE ~ 'ns'))
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"#F8766D" #red
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"#00BFC4" #blue
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table(str_df_short$effect_colours)
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###########################################
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ggplot(str_df_short
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, aes( x=effect_grouped
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, fill = effect_colours)) +
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geom_bar() +
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scale_fill_manual(values = str_df_short$effect_colours)
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first_col = c(38, 0)
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second_col = c(9, 22)
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third_col = c(681, 108)
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thing_df = data.frame(first_row, second_row, third_row)
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rownames(thing_df) = c("Destabilising","Stabilising")
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thing_df
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###############################################
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rect_colour_map = c("EMB" = "green"
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,"DSL" = "slategrey"
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, "CDL" = "navyblue"
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, "Ca" = "purple")
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rects <- data.frame(x = 1:6,
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colors = c("#ffd700" #gold
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, "#f0e68c" #khaki
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, "#da70d6"# orchid
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, "#ff1493"# deeppink
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, "#00BFC4" #, "#007d85" #blue
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, "#F8766D" )# red,
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)
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rects
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rects$text = c("-ve Lig affinty"
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, "+ve Lig affinity"
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, "+ve PPI2 affinity"
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, "-ve PPI2 affinity"
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, "+ve stability"
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, "-ve stability")
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rects$numbers = c(38, 0, 22, 9, 108, 681)
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rects$num_labels = paste0("n=", rects$numbers)
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rects
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outdir_images = paste0("~/git/Writing/thesis/images/results/", tolower(gene), "/")
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#https://stackoverflow.com/questions/47986055/create-a-rectangle-filled-with-text
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png(paste0(outdir_images, "test.png")
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, width = 0.5
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, height = 2.5
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, units = "in", res = 300)
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ggplot(rects, aes(x, y = 0, fill = colors, label = paste0(text,"\n", num_labels))) +
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geom_tile(width = 1, height = 1) + # make square tiles
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geom_text(color = "black", size = 1.5) + # add white text in the middle
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scale_fill_identity(guide = "none") + # color the tiles with the colors in the data frame
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coord_fixed() + # make sure tiles are square
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coord_flip()+ scale_x_reverse() +
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# theme_void() # remove any axis markings
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theme_nothing() # remove any axis markings
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dev.off()
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##########################################################
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tile_map=data.frame(tile=c("EMB","DSL","CDL","Ca")
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,tile_colour =c("green","darkslategrey","navyblue","purple"))
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# great
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tile_colour_map = c("EMB" = "green"
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,"DSL" = "darkslategrey"
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, "CDL" = "navyblue"
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, "Ca" = "purple")
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tile_legend=get_legend(
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ggplot(tile_map, aes(factor(tile),y=0
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, colour=tile_colour
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, fill=tile_colour))+
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geom_tile() +
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theme(legend.direction="horizontal") +
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scale_colour_manual(name=NULL
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#, values = tile_map$tile_colour
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, values=tile_colour_map) +
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scale_fill_manual(name=NULL
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#,values=tile_map$tile_colour
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, values = tile_colour_map)
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)
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#############################################################
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###############################################
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library(ggplot2)
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library(viridis)
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library(hrbrthemes)
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ggplot(str_df_short, aes(fill=effect_colours,x=effect_type)) +
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geom_bar() +
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scale_fill_viridis(discrete = T) +
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ggtitle("Studying 4 species..")
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####################################################
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