Closed allaway closed 4 years ago
Oh good catch! I thought I had done that already :)
On Fri, Dec 6, 2019 at 10:46 AM Jineta Banerjee notifications@github.com wrote:
@jaybee84 requested changes on this pull request. In figures/ridgeplot_cibersort.Rmd https://github.com/Sage-Bionetworks/NF_LandscapePaper_2019/pull/80#discussion_r354977683 : + + +{r} + +immune_df %>% filter(method == "cibersort") %>% filter(!is.na(tumorType)) %>% mutate(tumor_abbr = case_when(tumorType == "Malignant Peripheral Nerve Sheath Tumor" ~ "MPNST", tumorType == "Malignant peripheral nerve sheath tumor" ~ "MPNST" , tumorType == "Neurofibroma" ~ "NF", tumorType == "Plexiform Neurofibroma" ~ "pNF", tumorType == "Cutaneous Neurofibroma" ~ "cNF")) %>% ggplot() + geom_density_ridges(aes(x = score, y = cell_type, fill = cell_type)) + labs(x = 'CIBERSORT Enrichment', y = "Immune Cell Type") + theme_minimal() + update to theme_bw() — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Sage-Bionetworks/NF_LandscapePaper_2019/pull/80?email_source=notifications&email_token=AE3WNSD2WASLVT4FHLA2OPTQXKM2DA5CNFSM4JWLQ5CKYY3PNVWWK3TUL52HS4DFWFIHK3DMKJSXC5LFON2FEZLWNFSXPKTDN5WW2ZLOORPWSZGOCOJND5I#pullrequestreview-328389109, or unsubscribe https://github.com/notifications/unsubscribe-auth/AE3WNSBI5IS5GRBXBZZOMK3QXKM2DANCNFSM4JWLQ5CA .
In figures/ridgeplot_cibersort.Rmd https://github.com/Sage-Bionetworks/NF_LandscapePaper_2019/pull/80#discussion_r354977683 :
+ + +{r} + +immune_df %>% filter(method == "cibersort") %>% filter(!is.na(tumorType)) %>% mutate(tumor_abbr = case_when(tumorType == "Malignant Peripheral Nerve Sheath Tumor" ~ "MPNST", tumorType == "Malignant peripheral nerve sheath tumor" ~ "MPNST" , tumorType == "Neurofibroma" ~ "NF", tumorType == "Plexiform Neurofibroma" ~ "pNF", tumorType == "Cutaneous Neurofibroma" ~ "cNF")) %>% ggplot() + geom_density_ridges(aes(x = score, y = cell_type, fill = cell_type)) + labs(x = 'CIBERSORT Enrichment', y = "Immune Cell Type") + theme_minimal() +
+ + +{r} + +immune_df %>%
+ +
update to theme_bw()
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Sage-Bionetworks/NF_LandscapePaper_2019/pull/80?email_source=notifications&email_token=AE3WNSD2WASLVT4FHLA2OPTQXKM2DA5CNFSM4JWLQ5CKYY3PNVWWK3TUL52HS4DFWFIHK3DMKJSXC5LFON2FEZLWNFSXPKTDN5WW2ZLOORPWSZGOCOJND5I#pullrequestreview-328389109, or unsubscribe https://github.com/notifications/unsubscribe-auth/AE3WNSBI5IS5GRBXBZZOMK3QXKM2DANCNFSM4JWLQ5CA .
Oh good catch! I thought I had done that already :)
On Fri, Dec 6, 2019 at 10:46 AM Jineta Banerjee notifications@github.com wrote: