Add kidney alignment metric plot scripts

Manuscript_Code/NBISC100_project/kidney/alignment_metrics/Kidney_Genome_mapping_kaavya.R

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+# Built off of Charley's gastrocnemius genome alignment code
+
+#load library
+library(ggplot2)
+library(tidyverse)
+library(scales)
+library(RColorBrewer)
+
+#load data
+kidney.metrics.df <- read_csv("kidney_FLT_GC_qc_metrics_ORIGINAL.csv")
+
+#prepare data for genome mapping
+genome.alignment.kidney.metrics.df <- kidney.metrics.df %>% select(osd_num,sample,uniquely_mapped_percent,multimapped_percent,multimapped_toomany_percent,unmapped_tooshort_percent, unmapped_other_percent)
+
+#Add a new column for library_kit
+genome.alignment.kidney.metrics.df <-  genome.alignment.kidney.metrics.df %>%
+  mutate(library_kit= case_when(osd_num == "OSD-102" ~ "ribo-deplete kit",
+                                osd_num == "OSD-163" ~ "ribo-deplete kit",
+                                osd_num == "OSD-253" ~ "ribo-deplete kit",
+                                osd_num == "OSD-457" ~ "polyA-nonUPX kit",
+                                osd_num == "OSD-462" & str_detect(sample, "UPX") ~ "polyA-UPX kit",
+                                osd_num == "OSD-462" & str_detect(sample, "mRNA") ~ "polyA-nonUPX kit",
+                                osd_num == "OSD-462" & str_detect(sample, "totRNA") ~ "ribo-deplete kit",
+                                osd_num == "OSD-513" ~ "ribo-deplete kit",
+                                osd_num == "OSD-771" ~ "ribo-deplete kit")) %>% 
+  drop_na(library_kit)
+
+# Box_plot1: percentage of uniquely mapped data by library kit
+ggplot(genome.alignment.kidney.metrics.df, aes(x = osd_num, y= uniquely_mapped_percent, fill = osd_num)) +
+  geom_boxplot(linewidth = 0.1, varwidth = TRUE) +
+  stat_boxplot(geom = "errorbar", width = 0.2, size= 0.1)+
+  facet_wrap(~library_kit, scales = "free_x", drop = TRUE)+
+  scale_y_continuous(breaks = pretty_breaks(n = 8))+
+  scale_fill_brewer(palette = "Set2")+
+  labs(title = "Uniquely Mapped Percentage of Kidney Datasets by Library Kits", x = "OSD-number", y = "Uniquely mapped (%)") +
+  theme_classic() +
+  theme(legend.position = "none")+
+  theme(plot.title = element_text(hjust = 0.5))
+
+ggsave("genome_uniquely_mapped_kidney_LibraryKits.png", dpi = 300,
+       width = 14, height = 4, units = "in")
+
+
+# Box_plot2: percentage of total mapped data by library kit
+ggplot(genome.alignment.kidney.metrics.df, aes(x = osd_num, y= 100 - (unmapped_tooshort_percent + unmapped_other_percent), fill = osd_num)) +
+  geom_boxplot(linewidth = 0.1, varwidth = TRUE) +
+  stat_boxplot(geom = "errorbar", width = 0.2, size= 0.1)+
+  facet_wrap(~library_kit, scales = "free_x", drop = TRUE)+
+  scale_y_continuous(breaks = pretty_breaks(n = 10))+
+  scale_fill_brewer(palette = "Set2")+
+  labs(title = "Total Mapped Percentage of Kidney Datasets by Library Kits", x = "OSD-number", y = "Total mapped (%)") +
+  theme_classic() +
+  theme(legend.position = "none")+
+  theme(plot.title = element_text(hjust = 0.5))
+
+ggsave("genome_total_mapped_kidney_LibraryKits.png", dpi = 300,
+       width = 14, height = 4, units = "in")

Manuscript_Code/NBISC100_project/kidney/alignment_metrics/Kidney_Transcriptome_mapping_kaavya.R

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+# Built off of Charley's gastrocnemius transcriptome alignment code
+
+#load library
+library(ggplot2)
+library(tidyverse)
+library(scales)
+library(RColorBrewer)
+
+#load data
+kidney.metrics.df <- read_csv("kidney_FLT_GC_qc_metrics_ORIGINAL.csv")
+
+#prepare data for transcriptome mapping
+transcriptome.alignment.kidney.metrics.df <- kidney.metrics.df %>% select(osd_num,sample, pct_uniquely_aligned, pct_multi_aligned, pct_unalignable)
+
+#Add a new column for library_kit
+transcriptome.alignment.kidney.metrics.df <-  transcriptome.alignment.kidney.metrics.df %>%
+  mutate(library_kit= case_when(osd_num == "OSD-102" ~ "ribo-deplete kit",
+                                osd_num == "OSD-163" ~ "ribo-deplete kit",
+                                osd_num == "OSD-253" ~ "ribo-deplete kit",
+                                osd_num == "OSD-457" ~ "polyA-nonUPX kit",
+                                osd_num == "OSD-462" & str_detect(sample, "UPX") ~ "polyA-UPX kit",
+                                osd_num == "OSD-462" & str_detect(sample, "mRNA") ~ "polyA-nonUPX kit",
+                                osd_num == "OSD-462" & str_detect(sample, "totRNA") ~ "ribo-deplete kit",
+                                osd_num == "OSD-513" ~ "ribo-deplete kit",
+                                osd_num == "OSD-771" ~ "ribo-deplete kit")) %>% 
+  drop_na(library_kit)
+
+# Box_plot1: percentage of uniquely aligned data to transcriptome by library kit
+ggplot(transcriptome.alignment.kidney.metrics.df, aes(x = osd_num, y= pct_uniquely_aligned, fill = osd_num)) +
+  geom_boxplot(linewidth = 0.1, varwidth = TRUE) +
+  stat_boxplot(geom = "errorbar", width = 0.2, size= 0.1)+
+  facet_wrap(~library_kit, scales = "free_x", drop = TRUE)+
+  scale_y_continuous(breaks = pretty_breaks(n = 8))+
+  scale_fill_brewer(palette = "Set2")+
+  labs(title = "Uniquely Aligned Percentage of Kidney Datasets by Library Kits", x = "OSD-number", y = "Uniquely aligned (%)") +
+  theme_classic() +
+  theme(legend.position = "none")+
+  theme(plot.title = element_text(hjust = 0.5))
+
+ggsave("transcriptome_unique_alignment_kidney_libraryKits.png", dpi = 300,
+       width = 14, height = 4, units = "in")
+
+# Box_plot2: percentage of total aligned data to transcriptome by library kit
+ggplot(transcriptome.alignment.kidney.metrics.df, aes(x = osd_num, y= (pct_uniquely_aligned+pct_multi_aligned), fill = osd_num)) +
+  geom_boxplot(linewidth = 0.1, varwidth = TRUE) +
+  stat_boxplot(geom = "errorbar", width = 0.2, size= 0.1)+
+  facet_wrap(~library_kit, scales = "free_x", drop = TRUE)+
+  scale_y_continuous(breaks = pretty_breaks(n = 10))+
+  scale_fill_brewer(palette = "Set2")+
+  labs(title = "Total Aligned Percentage of Kidney Datasets by Library Kits", x = "OSD-number", y = "Total aligned (%)") +
+  theme_classic() +
+  theme(legend.position = "none")+
+  theme(plot.title = element_text(hjust = 0.5))
+
+ggsave("transcriptome_total_alignment_kidney_libraryKits.png", dpi = 300,
+       width = 14, height = 4, units = "in")